Magnesium in PDB 7pva: 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc
Protein crystallography data
The structure of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc, PDB code: 7pva
was solved by
C.A.Schmitz,
M.Madej,
J.Potempa,
M.Sola,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
68.59 /
1.91
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.48,
77.29,
138.83,
82.42,
81.61,
76.51
|
|
R / Rfree (%)
|
15.9 /
19.2
|
Other elements in 7pva:
The structure of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Magnesium atom in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc
(pdb code 7pva). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the
1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc, PDB code: 7pva:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 11 in 7pva
Go back to
Magnesium Binding Sites List in 7pva
Magnesium binding site 1 out
of 11 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:43.1
occ:1.00
|
F1
|
A:BEF602
|
2.0
|
36.6
|
1.0
|
|
O
|
A:HOH872
|
2.0
|
40.6
|
1.0
|
|
OD2
|
A:ASP58
|
2.0
|
45.5
|
1.0
|
|
OD1
|
A:ASP15
|
2.1
|
55.1
|
1.0
|
|
O
|
A:HOH920
|
2.1
|
44.1
|
1.0
|
|
O
|
A:ASN60
|
2.2
|
46.0
|
1.0
|
|
CG
|
A:ASP58
|
3.0
|
42.8
|
1.0
|
|
BE
|
A:BEF602
|
3.0
|
34.5
|
1.0
|
|
CG
|
A:ASP15
|
3.1
|
56.5
|
1.0
|
|
OD1
|
A:ASP58
|
3.3
|
39.4
|
1.0
|
|
C
|
A:ASN60
|
3.3
|
37.5
|
1.0
|
|
OD2
|
A:ASP15
|
3.4
|
56.9
|
1.0
|
|
HB3
|
A:ASN60
|
3.4
|
50.8
|
1.0
|
|
H
|
A:ASP15
|
3.8
|
53.7
|
1.0
|
|
H
|
A:ASN60
|
3.8
|
43.6
|
1.0
|
|
HG3
|
A:MSE61
|
3.8
|
54.8
|
1.0
|
|
F2
|
A:BEF602
|
4.0
|
37.6
|
1.0
|
|
O
|
A:HOH980
|
4.0
|
56.3
|
1.0
|
|
HA
|
A:MSE61
|
4.0
|
52.7
|
1.0
|
|
OD1
|
A:ASP14
|
4.0
|
40.2
|
1.0
|
|
HG2
|
A:MSE61
|
4.1
|
54.8
|
1.0
|
|
HG3
|
A:GLU16
|
4.1
|
54.9
|
1.0
|
|
HZ2
|
A:LYS87
|
4.1
|
76.1
|
1.0
|
|
CA
|
A:ASN60
|
4.1
|
37.6
|
1.0
|
|
F3
|
A:BEF602
|
4.1
|
39.7
|
1.0
|
|
CB
|
A:ASN60
|
4.2
|
42.3
|
1.0
|
|
HZ2
|
A:LYS108
|
4.2
|
55.9
|
1.0
|
|
OE1
|
A:GLU16
|
4.2
|
46.7
|
1.0
|
|
N
|
A:ASN60
|
4.2
|
36.3
|
1.0
|
|
CB
|
A:ASP58
|
4.3
|
37.1
|
1.0
|
|
N
|
A:MSE61
|
4.4
|
43.6
|
1.0
|
|
HB3
|
A:ASP58
|
4.4
|
44.6
|
1.0
|
|
CG
|
A:MSE61
|
4.4
|
45.7
|
1.0
|
|
HE3
|
A:LYS87
|
4.5
|
72.1
|
1.0
|
|
HZ1
|
A:LYS108
|
4.5
|
55.9
|
1.0
|
|
CB
|
A:ASP15
|
4.5
|
52.1
|
1.0
|
|
N
|
A:ASP15
|
4.5
|
44.7
|
1.0
|
|
H
|
A:GLU16
|
4.5
|
56.2
|
1.0
|
|
HZ1
|
A:LYS87
|
4.5
|
76.1
|
1.0
|
|
HB2
|
A:ASP58
|
4.6
|
44.6
|
1.0
|
|
CG
|
A:ASP14
|
4.6
|
41.9
|
1.0
|
|
CA
|
A:MSE61
|
4.6
|
43.9
|
1.0
|
|
NZ
|
A:LYS87
|
4.7
|
63.4
|
1.0
|
|
NZ
|
A:LYS108
|
4.7
|
46.5
|
1.0
|
|
HB2
|
A:GLU16
|
4.7
|
57.5
|
1.0
|
|
OD2
|
A:ASP14
|
4.7
|
39.6
|
1.0
|
|
HB3
|
A:ASP15
|
4.7
|
62.5
|
1.0
|
|
O
|
A:HOH933
|
4.8
|
66.0
|
1.0
|
|
CD
|
A:GLU16
|
4.8
|
45.7
|
1.0
|
|
CG
|
A:GLU16
|
4.8
|
45.7
|
1.0
|
|
HZ3
|
A:LYS108
|
4.9
|
55.9
|
1.0
|
|
HA
|
A:ASP14
|
4.9
|
50.4
|
1.0
|
|
CG
|
A:ASN60
|
4.9
|
47.3
|
1.0
|
|
HB2
|
A:ASN60
|
4.9
|
50.8
|
1.0
|
|
H
|
A:GLU59
|
5.0
|
47.9
|
1.0
|
|
Magnesium binding site 2 out
of 11 in 7pva
Go back to
Magnesium Binding Sites List in 7pva
Magnesium binding site 2 out
of 11 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg612
b:101.1
occ:1.00
|
O
|
A:MSE61
|
2.3
|
53.0
|
1.0
|
|
O
|
A:HOH883
|
2.4
|
102.9
|
1.0
|
|
O
|
A:GLY63
|
2.8
|
62.6
|
1.0
|
|
O
|
A:HOH1075
|
2.9
|
54.9
|
1.0
|
|
H
|
A:GLY63
|
3.2
|
70.8
|
1.0
|
|
O
|
A:HOH1047
|
3.3
|
80.5
|
1.0
|
|
C
|
A:MSE61
|
3.4
|
50.6
|
1.0
|
|
HA
|
A:PRO62
|
3.4
|
69.5
|
1.0
|
|
N
|
A:GLY63
|
3.5
|
59.0
|
1.0
|
|
H
|
A:MSE61
|
3.6
|
52.4
|
1.0
|
|
C
|
A:GLY63
|
3.7
|
61.0
|
1.0
|
|
HA2
|
A:GLY65
|
3.9
|
62.5
|
1.0
|
|
CA
|
A:PRO62
|
3.9
|
57.9
|
1.0
|
|
C
|
A:PRO62
|
4.0
|
57.9
|
1.0
|
|
N
|
A:PRO62
|
4.1
|
52.6
|
1.0
|
|
CA
|
A:GLY63
|
4.3
|
58.4
|
1.0
|
|
N
|
A:MSE61
|
4.3
|
43.6
|
1.0
|
|
N
|
A:GLY65
|
4.3
|
58.0
|
1.0
|
|
C
|
A:ILE64
|
4.3
|
57.9
|
1.0
|
|
O
|
A:ILE64
|
4.4
|
55.1
|
1.0
|
|
CA
|
A:GLY65
|
4.5
|
52.0
|
1.0
|
|
CA
|
A:MSE61
|
4.5
|
43.9
|
1.0
|
|
HA3
|
A:GLY65
|
4.5
|
62.5
|
1.0
|
|
H
|
A:GLY65
|
4.5
|
69.6
|
1.0
|
|
N
|
A:ILE64
|
4.7
|
60.7
|
1.0
|
|
OD1
|
A:ASN60
|
4.7
|
51.4
|
1.0
|
|
HA
|
A:ILE64
|
4.7
|
74.0
|
1.0
|
|
HA2
|
A:GLY63
|
4.8
|
70.1
|
1.0
|
|
HA
|
A:ASN60
|
4.8
|
45.1
|
1.0
|
|
O
|
A:PRO62
|
4.8
|
55.5
|
1.0
|
|
CA
|
A:ILE64
|
4.9
|
61.6
|
1.0
|
|
O
|
A:HOH758
|
4.9
|
60.9
|
1.0
|
|
HB2
|
A:MSE61
|
5.0
|
50.8
|
1.0
|
|
HA3
|
A:GLY63
|
5.0
|
70.1
|
1.0
|
|
Magnesium binding site 3 out
of 11 in 7pva
Go back to
Magnesium Binding Sites List in 7pva
Magnesium binding site 3 out
of 11 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:40.5
occ:1.00
|
F1
|
B:BEF602
|
1.7
|
30.5
|
1.0
|
|
O
|
B:HOH828
|
2.0
|
34.1
|
1.0
|
|
O
|
B:HOH852
|
2.0
|
33.1
|
1.0
|
|
OD1
|
B:ASP15
|
2.0
|
38.0
|
1.0
|
|
OD2
|
B:ASP58
|
2.1
|
34.4
|
1.0
|
|
O
|
B:ASN60
|
2.1
|
33.5
|
1.0
|
|
BE
|
B:BEF602
|
2.9
|
28.9
|
1.0
|
|
CG
|
B:ASP58
|
3.0
|
30.4
|
1.0
|
|
CG
|
B:ASP15
|
3.1
|
39.0
|
1.0
|
|
C
|
B:ASN60
|
3.3
|
33.4
|
1.0
|
|
OD1
|
B:ASP58
|
3.3
|
32.8
|
1.0
|
|
OD2
|
B:ASP15
|
3.4
|
37.2
|
1.0
|
|
HB3
|
B:ASN60
|
3.5
|
42.5
|
1.0
|
|
HE3
|
B:LYS87
|
3.6
|
61.8
|
1.0
|
|
HG2
|
B:MSE61
|
3.6
|
51.2
|
1.0
|
|
H
|
B:ASN60
|
3.8
|
46.3
|
1.0
|
|
H
|
B:ASP15
|
3.8
|
43.3
|
1.0
|
|
HA
|
B:MSE61
|
3.9
|
40.2
|
1.0
|
|
HG3
|
B:GLU16
|
3.9
|
55.2
|
1.0
|
|
OD1
|
B:ASP14
|
4.0
|
36.0
|
1.0
|
|
F2
|
B:BEF602
|
4.0
|
32.5
|
1.0
|
|
OE2
|
B:GLU16
|
4.1
|
49.5
|
1.0
|
|
F3
|
B:BEF602
|
4.1
|
32.6
|
1.0
|
|
CA
|
B:ASN60
|
4.1
|
34.2
|
1.0
|
|
HZ2
|
B:LYS108
|
4.1
|
49.8
|
1.0
|
|
CB
|
B:ASN60
|
4.2
|
35.4
|
1.0
|
|
HZ1
|
B:LYS87
|
4.2
|
73.6
|
1.0
|
|
N
|
B:ASN60
|
4.2
|
38.5
|
1.0
|
|
HG3
|
B:MSE61
|
4.3
|
51.2
|
1.0
|
|
N
|
B:MSE61
|
4.3
|
41.0
|
1.0
|
|
CB
|
B:ASP58
|
4.3
|
31.0
|
1.0
|
|
CG
|
B:MSE61
|
4.4
|
42.7
|
1.0
|
|
HB3
|
B:ASP58
|
4.4
|
37.2
|
1.0
|
|
H
|
B:GLU16
|
4.4
|
46.7
|
1.0
|
|
CE
|
B:LYS87
|
4.4
|
51.5
|
1.0
|
|
N
|
B:ASP15
|
4.5
|
36.1
|
1.0
|
|
HZ1
|
B:LYS108
|
4.5
|
49.8
|
1.0
|
|
CB
|
B:ASP15
|
4.5
|
38.9
|
1.0
|
|
CA
|
B:MSE61
|
4.5
|
33.5
|
1.0
|
|
CG
|
B:ASP14
|
4.6
|
39.2
|
1.0
|
|
HZ2
|
B:LYS87
|
4.6
|
73.6
|
1.0
|
|
HB2
|
B:ASP58
|
4.6
|
37.2
|
1.0
|
|
NZ
|
B:LYS87
|
4.6
|
61.3
|
1.0
|
|
OD2
|
B:ASP14
|
4.6
|
32.1
|
1.0
|
|
NZ
|
B:LYS108
|
4.7
|
41.5
|
1.0
|
|
CG
|
B:GLU16
|
4.7
|
46.0
|
1.0
|
|
O
|
B:HOH939
|
4.7
|
61.1
|
1.0
|
|
CD
|
B:GLU16
|
4.7
|
49.5
|
1.0
|
|
HB3
|
B:ASP15
|
4.8
|
46.7
|
1.0
|
|
HZ3
|
B:LYS108
|
4.8
|
49.8
|
1.0
|
|
HE2
|
B:LYS87
|
4.8
|
61.8
|
1.0
|
|
HA
|
B:ASP14
|
4.9
|
37.8
|
1.0
|
|
CG
|
B:ASN60
|
4.9
|
47.7
|
1.0
|
|
O
|
B:HOH841
|
4.9
|
77.7
|
1.0
|
|
N
|
B:GLU16
|
5.0
|
38.9
|
1.0
|
|
HB2
|
B:GLU16
|
5.0
|
50.9
|
1.0
|
|
HB2
|
B:ASN60
|
5.0
|
42.5
|
1.0
|
|
H
|
B:GLU59
|
5.0
|
40.0
|
1.0
|
|
HD22
|
B:ASN60
|
5.0
|
63.9
|
1.0
|
|
Magnesium binding site 4 out
of 11 in 7pva
Go back to
Magnesium Binding Sites List in 7pva
Magnesium binding site 4 out
of 11 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg616
b:66.6
occ:1.00
|
O
|
B:HOH1093
|
2.1
|
65.4
|
1.0
|
|
O
|
B:GLY63
|
2.3
|
43.6
|
1.0
|
|
O
|
B:MSE61
|
2.4
|
42.7
|
1.0
|
|
O
|
B:HOH1058
|
2.4
|
44.8
|
1.0
|
|
O
|
B:HOH1108
|
2.6
|
65.9
|
1.0
|
|
C
|
B:GLY63
|
3.4
|
42.0
|
1.0
|
|
H
|
B:MSE61
|
3.5
|
49.2
|
1.0
|
|
C
|
B:ILE64
|
3.6
|
40.4
|
1.0
|
|
C
|
B:MSE61
|
3.6
|
37.3
|
1.0
|
|
HA2
|
B:GLY65
|
3.6
|
49.0
|
1.0
|
|
O
|
B:ILE64
|
3.6
|
44.4
|
1.0
|
|
H
|
B:GLY63
|
3.7
|
50.4
|
1.0
|
|
N
|
B:GLY65
|
3.8
|
40.6
|
1.0
|
|
N
|
B:GLY63
|
3.8
|
42.0
|
1.0
|
|
HA
|
B:PRO62
|
4.0
|
51.1
|
1.0
|
|
HA
|
B:ILE64
|
4.0
|
53.4
|
1.0
|
|
O
|
B:HOH898
|
4.1
|
51.4
|
1.0
|
|
H
|
B:GLY65
|
4.2
|
48.8
|
1.0
|
|
CA
|
B:GLY65
|
4.2
|
40.8
|
1.0
|
|
CA
|
B:ILE64
|
4.2
|
44.5
|
1.0
|
|
N
|
B:ILE64
|
4.2
|
43.0
|
1.0
|
|
C
|
B:PRO62
|
4.2
|
40.6
|
1.0
|
|
CA
|
B:GLY63
|
4.2
|
44.2
|
1.0
|
|
N
|
B:MSE61
|
4.2
|
41.0
|
1.0
|
|
CA
|
B:PRO62
|
4.4
|
42.5
|
1.0
|
|
N
|
B:PRO62
|
4.4
|
40.2
|
1.0
|
|
HA3
|
B:GLY65
|
4.5
|
49.0
|
1.0
|
|
O
|
B:HOH882
|
4.5
|
51.1
|
1.0
|
|
CA
|
B:MSE61
|
4.5
|
33.5
|
1.0
|
|
HB2
|
B:MSE61
|
4.7
|
38.4
|
1.0
|
|
HA
|
B:ASN60
|
4.8
|
41.0
|
1.0
|
|
HA2
|
B:GLY63
|
4.8
|
53.1
|
1.0
|
|
O
|
B:PRO62
|
4.9
|
37.3
|
1.0
|
|
HA3
|
B:GLY63
|
4.9
|
53.1
|
1.0
|
|
OD1
|
B:ASN60
|
4.9
|
48.3
|
1.0
|
|
H
|
B:ILE64
|
5.0
|
51.6
|
1.0
|
|
O
|
B:HOH824
|
5.0
|
36.3
|
1.0
|
|
Magnesium binding site 5 out
of 11 in 7pva
Go back to
Magnesium Binding Sites List in 7pva
Magnesium binding site 5 out
of 11 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg617
b:63.3
occ:1.00
|
O
|
B:LYS456
|
2.4
|
50.0
|
1.0
|
|
O
|
B:LEU468
|
2.4
|
75.5
|
1.0
|
|
O
|
B:ASP470
|
2.5
|
64.4
|
1.0
|
|
O
|
B:HOH994
|
2.8
|
67.2
|
1.0
|
|
HA
|
B:SER469
|
3.2
|
81.7
|
1.0
|
|
HG2
|
B:LYS471
|
3.4
|
81.0
|
1.0
|
|
HA
|
B:ASP457
|
3.5
|
51.2
|
1.0
|
|
C
|
B:ASP470
|
3.5
|
65.0
|
1.0
|
|
C
|
B:LEU468
|
3.5
|
76.2
|
1.0
|
|
C
|
B:SER469
|
3.5
|
66.5
|
1.0
|
|
HD3
|
B:PRO458
|
3.5
|
53.7
|
1.0
|
|
C
|
B:LYS456
|
3.7
|
43.6
|
1.0
|
|
CA
|
B:SER469
|
3.7
|
68.0
|
1.0
|
|
N
|
B:ASP470
|
3.7
|
66.4
|
1.0
|
|
HD2
|
B:PRO458
|
3.8
|
53.7
|
1.0
|
|
O
|
B:SER469
|
3.8
|
66.3
|
1.0
|
|
H
|
B:ASP470
|
4.0
|
79.6
|
1.0
|
|
N
|
B:SER469
|
4.0
|
70.0
|
1.0
|
|
CD
|
B:PRO458
|
4.1
|
44.7
|
1.0
|
|
HA
|
B:LYS471
|
4.1
|
60.3
|
1.0
|
|
CA
|
B:ASP470
|
4.2
|
65.9
|
1.0
|
|
CG
|
B:LYS471
|
4.3
|
67.5
|
1.0
|
|
CA
|
B:ASP457
|
4.3
|
42.7
|
1.0
|
|
N
|
B:LYS471
|
4.4
|
48.6
|
1.0
|
|
HD2
|
B:HIS465
|
4.4
|
92.3
|
1.0
|
|
N
|
B:ASP457
|
4.4
|
45.4
|
1.0
|
|
HA
|
B:LYS456
|
4.5
|
54.0
|
1.0
|
|
HG3
|
B:LYS471
|
4.5
|
81.0
|
1.0
|
|
HB3
|
B:LYS456
|
4.6
|
59.0
|
1.0
|
|
HG
|
B:LEU468
|
4.6
|
88.1
|
1.0
|
|
HA
|
B:LEU468
|
4.6
|
93.4
|
1.0
|
|
CA
|
B:LYS456
|
4.7
|
45.0
|
1.0
|
|
CA
|
B:LYS471
|
4.7
|
50.3
|
1.0
|
|
O
|
B:ASN467
|
4.7
|
87.8
|
1.0
|
|
CA
|
B:LEU468
|
4.7
|
77.8
|
1.0
|
|
HB2
|
B:ASP470
|
4.8
|
79.0
|
1.0
|
|
HB2
|
B:ASP457
|
4.8
|
50.1
|
1.0
|
|
H
|
B:SER469
|
4.8
|
84.0
|
1.0
|
|
HE3
|
B:LYS471
|
4.9
|
99.5
|
1.0
|
|
HA
|
B:ASP470
|
4.9
|
79.0
|
1.0
|
|
HD12
|
B:LEU468
|
5.0
|
84.7
|
1.0
|
|
Magnesium binding site 6 out
of 11 in 7pva
Go back to
Magnesium Binding Sites List in 7pva
Magnesium binding site 6 out
of 11 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg601
b:52.2
occ:1.00
|
O
|
C:ASN60
|
1.9
|
84.9
|
1.0
|
|
OD1
|
C:ASP15
|
2.0
|
66.5
|
1.0
|
|
F2
|
C:BEF602
|
2.1
|
51.3
|
1.0
|
|
O
|
C:HOH824
|
2.1
|
57.3
|
1.0
|
|
O
|
C:HOH731
|
2.1
|
49.9
|
1.0
|
|
OD2
|
C:ASP58
|
2.3
|
62.4
|
1.0
|
|
CG
|
C:ASP15
|
2.8
|
69.3
|
1.0
|
|
OD2
|
C:ASP15
|
3.0
|
67.4
|
1.0
|
|
C
|
C:ASN60
|
3.1
|
82.2
|
1.0
|
|
CG
|
C:ASP58
|
3.2
|
61.8
|
1.0
|
|
BE
|
C:BEF602
|
3.2
|
48.6
|
1.0
|
|
HB3
|
C:ASN60
|
3.3
|
93.8
|
1.0
|
|
OD1
|
C:ASP58
|
3.5
|
60.3
|
1.0
|
|
HG3
|
C:MSE61
|
3.7
|
72.2
|
1.0
|
|
HG2
|
C:MSE61
|
3.7
|
72.2
|
1.0
|
|
HA
|
C:MSE61
|
3.7
|
95.4
|
1.0
|
|
H
|
C:ASP15
|
3.8
|
71.1
|
1.0
|
|
H
|
C:ASN60
|
3.8
|
89.6
|
1.0
|
|
CA
|
C:ASN60
|
3.9
|
81.1
|
1.0
|
|
CB
|
C:ASN60
|
4.1
|
78.1
|
1.0
|
|
N
|
C:MSE61
|
4.1
|
86.4
|
1.0
|
|
CG
|
C:MSE61
|
4.1
|
60.2
|
1.0
|
|
OD1
|
C:ASP14
|
4.1
|
53.7
|
1.0
|
|
N
|
C:ASN60
|
4.1
|
74.7
|
1.0
|
|
F3
|
C:BEF602
|
4.1
|
51.5
|
1.0
|
|
CB
|
C:ASP15
|
4.2
|
69.5
|
1.0
|
|
HG3
|
C:GLU16
|
4.2
|
81.7
|
1.0
|
|
HZ2
|
C:LYS87
|
4.2
|
80.7
|
1.0
|
|
HD22
|
C:ASN60
|
4.2
|
82.8
|
1.0
|
|
CA
|
C:MSE61
|
4.3
|
79.5
|
1.0
|
|
OE1
|
C:GLU16
|
4.3
|
61.7
|
1.0
|
|
F1
|
C:BEF602
|
4.3
|
50.2
|
1.0
|
|
HZ2
|
C:LYS108
|
4.4
|
65.5
|
1.0
|
|
H
|
C:GLU16
|
4.4
|
79.8
|
1.0
|
|
N
|
C:ASP15
|
4.4
|
59.2
|
1.0
|
|
HB3
|
C:ASP15
|
4.5
|
83.4
|
1.0
|
|
HB3
|
C:ASP58
|
4.5
|
71.5
|
1.0
|
|
CB
|
C:ASP58
|
4.5
|
59.5
|
1.0
|
|
HZ1
|
C:LYS108
|
4.6
|
65.5
|
1.0
|
|
HB2
|
C:GLU16
|
4.7
|
81.5
|
1.0
|
|
ND2
|
C:ASN60
|
4.8
|
68.9
|
1.0
|
|
HE3
|
C:LYS87
|
4.8
|
75.7
|
1.0
|
|
HB2
|
C:ASN60
|
4.8
|
93.8
|
1.0
|
|
CG
|
C:ASP14
|
4.8
|
54.8
|
1.0
|
|
CB
|
C:MSE61
|
4.8
|
68.9
|
1.0
|
|
HZ1
|
C:LYS87
|
4.8
|
80.7
|
1.0
|
|
HB2
|
C:ASP15
|
4.8
|
83.4
|
1.0
|
|
CG
|
C:ASN60
|
4.8
|
70.5
|
1.0
|
|
HA
|
C:ASN60
|
4.8
|
97.4
|
1.0
|
|
CA
|
C:ASP15
|
4.8
|
64.5
|
1.0
|
|
NZ
|
C:LYS108
|
4.9
|
54.6
|
1.0
|
|
H
|
C:MSE61
|
4.9
|
103.7
|
1.0
|
|
HZ3
|
C:LYS108
|
4.9
|
65.5
|
1.0
|
|
CD
|
C:GLU16
|
4.9
|
66.2
|
1.0
|
|
NZ
|
C:LYS87
|
4.9
|
67.2
|
1.0
|
|
HA
|
C:ASP14
|
4.9
|
74.4
|
1.0
|
|
CG
|
C:GLU16
|
4.9
|
68.1
|
1.0
|
|
HB2
|
C:ASP58
|
4.9
|
71.5
|
1.0
|
|
HD3
|
C:PRO62
|
4.9
|
86.3
|
1.0
|
|
N
|
C:GLU16
|
4.9
|
66.5
|
1.0
|
|
H
|
C:GLU59
|
4.9
|
60.3
|
1.0
|
|
Magnesium binding site 7 out
of 11 in 7pva
Go back to
Magnesium Binding Sites List in 7pva
Magnesium binding site 7 out
of 11 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg611
b:89.5
occ:1.00
|
O
|
C:HOH927
|
1.9
|
62.2
|
1.0
|
|
O
|
C:HOH833
|
2.5
|
62.0
|
1.0
|
|
HE
|
C:ARG384
|
2.5
|
57.5
|
1.0
|
|
OE2
|
C:GLU172
|
2.6
|
70.4
|
0.5
|
|
OE2
|
C:GLU172
|
2.7
|
70.5
|
0.5
|
|
HG23
|
C:ILE169
|
3.0
|
73.6
|
1.0
|
|
O
|
C:HOH1020
|
3.1
|
68.0
|
1.0
|
|
CD
|
C:GLU172
|
3.2
|
71.4
|
0.5
|
|
CD
|
C:GLU172
|
3.3
|
71.2
|
0.5
|
|
NE
|
C:ARG384
|
3.3
|
47.9
|
1.0
|
|
HG12
|
C:ILE169
|
3.3
|
65.7
|
1.0
|
|
HD2
|
C:ARG384
|
3.3
|
59.8
|
1.0
|
|
OE1
|
C:GLU172
|
3.4
|
71.3
|
0.5
|
|
HB3
|
C:ARG384
|
3.4
|
50.0
|
1.0
|
|
OE1
|
C:GLU172
|
3.5
|
71.4
|
0.5
|
|
HB2
|
C:ARG384
|
3.6
|
50.0
|
1.0
|
|
CG2
|
C:ILE169
|
3.8
|
61.3
|
1.0
|
|
HG21
|
C:ILE169
|
3.8
|
73.6
|
1.0
|
|
CD
|
C:ARG384
|
3.8
|
49.8
|
1.0
|
|
CB
|
C:ARG384
|
3.9
|
41.6
|
1.0
|
|
HH21
|
C:ARG384
|
4.0
|
62.4
|
1.0
|
|
HG3
|
C:GLU172
|
4.1
|
87.7
|
0.5
|
|
CG1
|
C:ILE169
|
4.2
|
54.8
|
1.0
|
|
HA
|
C:ILE169
|
4.2
|
69.0
|
1.0
|
|
CG
|
C:GLU172
|
4.2
|
73.0
|
0.5
|
|
OG
|
C:SER248
|
4.2
|
45.5
|
1.0
|
|
HD13
|
C:ILE169
|
4.3
|
62.7
|
1.0
|
|
HA
|
C:ALA381
|
4.4
|
58.0
|
1.0
|
|
CZ
|
C:ARG384
|
4.4
|
53.0
|
1.0
|
|
HD2
|
C:LYS388
|
4.5
|
81.3
|
1.0
|
|
CB
|
C:ILE169
|
4.5
|
58.4
|
1.0
|
|
CG
|
C:ARG384
|
4.5
|
48.3
|
1.0
|
|
HG22
|
C:ILE169
|
4.6
|
73.6
|
1.0
|
|
NH2
|
C:ARG384
|
4.6
|
52.0
|
1.0
|
|
HG2
|
C:GLU172
|
4.6
|
87.7
|
0.5
|
|
CG
|
C:GLU172
|
4.6
|
73.0
|
0.5
|
|
HG
|
C:SER248
|
4.6
|
54.6
|
1.0
|
|
HD3
|
C:ARG384
|
4.7
|
59.8
|
1.0
|
|
HG3
|
C:GLU172
|
4.7
|
87.7
|
0.5
|
|
CD1
|
C:ILE169
|
4.8
|
52.3
|
1.0
|
|
CA
|
C:ILE169
|
4.9
|
57.5
|
1.0
|
|
HB1
|
C:ALA381
|
4.9
|
62.6
|
1.0
|
|
HZ2
|
C:LYS388
|
4.9
|
90.8
|
1.0
|
|
HG13
|
C:ILE169
|
4.9
|
65.7
|
1.0
|
|
O
|
C:ALA381
|
4.9
|
41.9
|
1.0
|
|
Magnesium binding site 8 out
of 11 in 7pva
Go back to
Magnesium Binding Sites List in 7pva
Magnesium binding site 8 out
of 11 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg612
b:117.6
occ:1.00
|
O
|
C:GLY63
|
2.7
|
88.9
|
1.0
|
|
O
|
C:HOH761
|
2.7
|
67.8
|
1.0
|
|
O
|
C:HOH1031
|
3.1
|
108.2
|
1.0
|
|
O
|
C:MSE61
|
3.2
|
79.2
|
1.0
|
|
O
|
C:HOH978
|
3.4
|
73.5
|
1.0
|
|
H
|
C:GLY63
|
3.7
|
97.8
|
1.0
|
|
C
|
C:GLY63
|
3.9
|
85.2
|
1.0
|
|
N
|
C:GLY63
|
4.1
|
81.5
|
1.0
|
|
H
|
C:MSE61
|
4.2
|
103.7
|
1.0
|
|
HA2
|
C:GLY65
|
4.3
|
87.6
|
1.0
|
|
HA
|
C:PRO62
|
4.3
|
91.5
|
1.0
|
|
C
|
C:MSE61
|
4.3
|
79.4
|
1.0
|
|
O
|
C:HOH898
|
4.4
|
85.2
|
1.0
|
|
N
|
C:GLY65
|
4.5
|
80.9
|
1.0
|
|
C
|
C:ILE64
|
4.5
|
84.0
|
1.0
|
|
HA
|
C:ILE64
|
4.5
|
99.7
|
1.0
|
|
H
|
C:GLY65
|
4.6
|
97.1
|
1.0
|
|
CA
|
C:GLY63
|
4.6
|
83.2
|
1.0
|
|
CA
|
C:GLY65
|
4.7
|
73.0
|
1.0
|
|
HA3
|
C:GLY65
|
4.8
|
87.6
|
1.0
|
|
C
|
C:PRO62
|
4.8
|
78.3
|
1.0
|
|
OD1
|
C:ASN60
|
4.8
|
68.0
|
1.0
|
|
O
|
C:ILE64
|
4.8
|
85.3
|
1.0
|
|
CA
|
C:PRO62
|
4.8
|
76.2
|
1.0
|
|
N
|
C:ILE64
|
4.9
|
80.2
|
1.0
|
|
CA
|
C:ILE64
|
4.9
|
83.0
|
1.0
|
|
N
|
C:MSE61
|
5.0
|
86.4
|
1.0
|
|
Magnesium binding site 9 out
of 11 in 7pva
Go back to
Magnesium Binding Sites List in 7pva
Magnesium binding site 9 out
of 11 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg601
b:44.9
occ:1.00
|
F3
|
D:BEF602
|
1.9
|
33.3
|
1.0
|
|
OD2
|
D:ASP58
|
2.0
|
50.3
|
1.0
|
|
O
|
D:ASN60
|
2.0
|
49.4
|
1.0
|
|
O
|
D:HOH765
|
2.0
|
38.2
|
1.0
|
|
O
|
D:HOH808
|
2.1
|
43.8
|
1.0
|
|
OD1
|
D:ASP15
|
2.1
|
44.9
|
1.0
|
|
CG
|
D:ASP58
|
3.0
|
50.5
|
1.0
|
|
BE
|
D:BEF602
|
3.1
|
38.3
|
1.0
|
|
CG
|
D:ASP15
|
3.1
|
44.6
|
1.0
|
|
C
|
D:ASN60
|
3.3
|
49.1
|
1.0
|
|
OD1
|
D:ASP58
|
3.4
|
42.0
|
1.0
|
|
OD2
|
D:ASP15
|
3.4
|
42.2
|
1.0
|
|
HG2
|
D:MSE61
|
3.5
|
56.9
|
1.0
|
|
HB3
|
D:ASN60
|
3.5
|
54.1
|
1.0
|
|
H
|
D:ASP15
|
3.8
|
43.2
|
1.0
|
|
HA
|
D:MSE61
|
3.8
|
63.2
|
1.0
|
|
H
|
D:ASN60
|
3.8
|
50.9
|
1.0
|
|
HE3
|
D:LYS87
|
3.9
|
79.2
|
1.0
|
|
OD1
|
D:ASP14
|
4.0
|
40.8
|
1.0
|
|
F1
|
D:BEF602
|
4.0
|
37.1
|
1.0
|
|
HG3
|
D:MSE61
|
4.0
|
56.9
|
1.0
|
|
CA
|
D:ASN60
|
4.1
|
47.6
|
1.0
|
|
OE1
|
D:GLU16
|
4.1
|
51.4
|
1.0
|
|
F2
|
D:BEF602
|
4.2
|
41.0
|
1.0
|
|
CG
|
D:MSE61
|
4.2
|
47.4
|
1.0
|
|
CB
|
D:ASN60
|
4.2
|
45.1
|
1.0
|
|
N
|
D:ASN60
|
4.2
|
42.5
|
1.0
|
|
N
|
D:MSE61
|
4.2
|
55.4
|
1.0
|
|
HD22
|
D:ASN60
|
4.3
|
62.7
|
1.0
|
|
HZ2
|
D:LYS108
|
4.3
|
45.2
|
1.0
|
|
HG3
|
D:GLU16
|
4.3
|
62.3
|
1.0
|
|
CB
|
D:ASP58
|
4.3
|
47.3
|
1.0
|
|
HB3
|
D:ASP58
|
4.4
|
56.7
|
1.0
|
|
CB
|
D:ASP15
|
4.4
|
37.5
|
1.0
|
|
HZ1
|
D:LYS87
|
4.4
|
88.7
|
1.0
|
|
HZ1
|
D:LYS108
|
4.4
|
45.2
|
1.0
|
|
H
|
D:GLU16
|
4.4
|
50.1
|
1.0
|
|
N
|
D:ASP15
|
4.4
|
36.0
|
1.0
|
|
CA
|
D:MSE61
|
4.4
|
52.7
|
1.0
|
|
HZ2
|
D:LYS87
|
4.5
|
88.7
|
1.0
|
|
CG
|
D:ASP14
|
4.6
|
42.8
|
1.0
|
|
HB3
|
D:ASP15
|
4.6
|
45.0
|
1.0
|
|
HB2
|
D:ASP58
|
4.6
|
56.7
|
1.0
|
|
ND2
|
D:ASN60
|
4.7
|
52.3
|
1.0
|
|
NZ
|
D:LYS108
|
4.7
|
37.6
|
1.0
|
|
HZ3
|
D:LYS108
|
4.7
|
45.2
|
1.0
|
|
NZ
|
D:LYS87
|
4.7
|
73.9
|
1.0
|
|
CG
|
D:ASN60
|
4.8
|
47.8
|
1.0
|
|
CE
|
D:LYS87
|
4.8
|
66.0
|
1.0
|
|
HA
|
D:ASP14
|
4.8
|
48.8
|
1.0
|
|
HB2
|
D:GLU16
|
4.8
|
62.7
|
1.0
|
|
OD2
|
D:ASP14
|
4.8
|
41.7
|
1.0
|
|
CD
|
D:GLU16
|
4.8
|
53.9
|
1.0
|
|
CB
|
D:MSE61
|
4.9
|
50.1
|
1.0
|
|
CA
|
D:ASP15
|
5.0
|
39.1
|
1.0
|
|
CG
|
D:GLU16
|
5.0
|
51.9
|
1.0
|
|
N
|
D:GLU16
|
5.0
|
41.8
|
1.0
|
|
HA
|
D:ASN60
|
5.0
|
57.1
|
1.0
|
|
Magnesium binding site 10 out
of 11 in 7pva
Go back to
Magnesium Binding Sites List in 7pva
Magnesium binding site 10 out
of 11 in the 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of 1.9 Angstrom Crystal Structure of Dimeric Porx, Co-Crystallized in the Presence of Zinc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg611
b:64.6
occ:1.00
|
O
|
D:HOH1001
|
2.2
|
52.4
|
1.0
|
|
O
|
D:HOH988
|
2.3
|
75.6
|
1.0
|
|
O
|
D:MSE61
|
2.4
|
51.2
|
1.0
|
|
O
|
D:HOH976
|
2.6
|
59.3
|
1.0
|
|
O
|
D:GLY63
|
2.6
|
50.3
|
1.0
|
|
HA2
|
D:GLY65
|
3.5
|
55.9
|
1.0
|
|
H
|
D:MSE61
|
3.5
|
66.5
|
1.0
|
|
C
|
D:MSE61
|
3.5
|
53.7
|
1.0
|
|
C
|
D:GLY63
|
3.6
|
50.5
|
1.0
|
|
C
|
D:ILE64
|
3.6
|
44.6
|
1.0
|
|
O
|
D:HOH1008
|
3.7
|
80.1
|
1.0
|
|
O
|
D:ILE64
|
3.7
|
44.4
|
1.0
|
|
N
|
D:GLY65
|
3.7
|
49.5
|
1.0
|
|
H
|
D:GLY63
|
3.8
|
64.0
|
1.0
|
|
N
|
D:GLY63
|
4.0
|
53.3
|
1.0
|
|
HA
|
D:PRO62
|
4.0
|
62.6
|
1.0
|
|
CA
|
D:GLY65
|
4.0
|
46.6
|
1.0
|
|
H
|
D:GLY65
|
4.1
|
59.5
|
1.0
|
|
HA
|
D:ILE64
|
4.1
|
57.9
|
1.0
|
|
O
|
D:HOH893
|
4.2
|
57.4
|
1.0
|
|
N
|
D:MSE61
|
4.2
|
55.4
|
1.0
|
|
CA
|
D:ILE64
|
4.3
|
48.2
|
1.0
|
|
C
|
D:PRO62
|
4.3
|
50.7
|
1.0
|
|
HA3
|
D:GLY65
|
4.3
|
55.9
|
1.0
|
|
N
|
D:ILE64
|
4.3
|
48.6
|
1.0
|
|
CA
|
D:PRO62
|
4.4
|
52.1
|
1.0
|
|
N
|
D:PRO62
|
4.4
|
49.4
|
1.0
|
|
CA
|
D:GLY63
|
4.4
|
55.1
|
1.0
|
|
CA
|
D:MSE61
|
4.5
|
52.7
|
1.0
|
|
O
|
D:HOH923
|
4.6
|
78.9
|
1.0
|
|
O
|
D:HOH1065
|
4.6
|
97.0
|
1.0
|
|
HB2
|
D:MSE61
|
4.7
|
60.1
|
1.0
|
|
O
|
D:HOH973
|
4.8
|
58.2
|
1.0
|
|
HA
|
D:ASN60
|
4.8
|
57.1
|
1.0
|
|
OD1
|
D:ASN60
|
4.9
|
55.5
|
1.0
|
|
O
|
D:HOH725
|
5.0
|
43.0
|
1.0
|
|
O
|
D:HOH708
|
5.0
|
60.1
|
1.0
|
|
Reference:
C.Schmitz,
M.Madej,
Z.Nowakowska,
A.Cuppari,
A.Jacula,
M.Ksiazek,
K.Mikruta,
J.Wisniewski,
N.Pudelko-Malik,
A.Saran,
N.Zeytuni,
P.Mlynarz,
R.J.Lamont,
I.Uson,
V.Siksnys,
J.Potempa,
M.Sola.
Response Regulator Porx Coordinates Oligonucleotide Signalling and Gene Expression to Control the Secretion of Virulence Factors. Nucleic Acids Res. V. 50 12558 2022.
ISSN: ESSN 1362-4962
PubMed: 36464236
DOI: 10.1093/NAR/GKAC1103
Page generated: Thu Apr 6 19:17:31 2023
|
