Magnesium in PDB 7pv7: Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.
Protein crystallography data
The structure of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator., PDB code: 7pv7
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)
|
68.40 /
2.41
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.83,
77.08,
138.73,
82.26,
81.36,
76.41
|
|
R / Rfree (%)
|
18.6 /
21.6
|
Other elements in 7pv7:
The structure of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.
(pdb code 7pv7). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the
Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator., PDB code: 7pv7:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Magnesium binding site 1 out
of 9 in 7pv7
Go back to
Magnesium Binding Sites List in 7pv7
Magnesium binding site 1 out
of 9 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg602
b:28.9
occ:1.00
|
OD2
|
D:ASP58
|
1.8
|
55.8
|
1.0
|
|
O
|
D:ASN60
|
1.9
|
70.9
|
1.0
|
|
F3
|
D:BEF601
|
2.0
|
32.7
|
1.0
|
|
OD1
|
D:ASP15
|
2.1
|
58.5
|
1.0
|
|
O
|
D:HOH756
|
2.2
|
34.7
|
1.0
|
|
O
|
D:HOH784
|
2.2
|
40.3
|
1.0
|
|
CG
|
D:ASP58
|
2.9
|
50.8
|
1.0
|
|
CG
|
D:ASP15
|
3.0
|
53.0
|
1.0
|
|
BE
|
D:BEF601
|
3.1
|
33.5
|
1.0
|
|
C
|
D:ASN60
|
3.1
|
64.7
|
1.0
|
|
OD1
|
D:ASP58
|
3.3
|
56.4
|
1.0
|
|
HB3
|
D:ASN60
|
3.3
|
77.4
|
1.0
|
|
OD2
|
D:ASP15
|
3.4
|
53.9
|
1.0
|
|
HG3
|
D:MSE61
|
3.5
|
72.2
|
1.0
|
|
HG2
|
D:MSE61
|
3.6
|
72.2
|
1.0
|
|
HA
|
D:MSE61
|
3.7
|
74.3
|
1.0
|
|
H
|
D:ASP15
|
3.7
|
63.2
|
1.0
|
|
H
|
D:ASN60
|
3.8
|
66.2
|
1.0
|
|
OD1
|
D:ASP14
|
3.9
|
43.4
|
1.0
|
|
CA
|
D:ASN60
|
3.9
|
61.8
|
1.0
|
|
CG
|
D:MSE61
|
4.0
|
60.2
|
1.0
|
|
F1
|
D:BEF601
|
4.1
|
38.5
|
1.0
|
|
CB
|
D:ASN60
|
4.1
|
64.5
|
1.0
|
|
N
|
D:ASN60
|
4.1
|
55.2
|
1.0
|
|
HE3
|
D:LYS87
|
4.1
|
72.9
|
1.0
|
|
N
|
D:MSE61
|
4.1
|
62.4
|
1.0
|
|
F2
|
D:BEF601
|
4.2
|
37.5
|
1.0
|
|
CB
|
D:ASP58
|
4.2
|
45.3
|
1.0
|
|
HB3
|
D:ASP58
|
4.3
|
54.4
|
1.0
|
|
CA
|
D:MSE61
|
4.3
|
61.9
|
1.0
|
|
CB
|
D:ASP15
|
4.3
|
50.3
|
1.0
|
|
OE1
|
D:GLU16
|
4.4
|
51.4
|
1.0
|
|
HZ2
|
D:LYS87
|
4.4
|
77.5
|
1.0
|
|
HZ2
|
D:LYS108
|
4.4
|
54.7
|
1.0
|
|
HB3
|
D:ASP15
|
4.4
|
60.3
|
1.0
|
|
N
|
D:ASP15
|
4.4
|
52.6
|
1.0
|
|
H
|
D:GLU16
|
4.4
|
61.5
|
1.0
|
|
HG3
|
D:GLU16
|
4.5
|
61.4
|
1.0
|
|
HB2
|
D:ASP58
|
4.6
|
54.4
|
1.0
|
|
HZ1
|
D:LYS108
|
4.6
|
54.7
|
1.0
|
|
HZ3
|
D:LYS108
|
4.6
|
54.7
|
1.0
|
|
CG
|
D:ASP14
|
4.6
|
42.6
|
1.0
|
|
HZ1
|
D:LYS87
|
4.7
|
77.5
|
1.0
|
|
CB
|
D:MSE61
|
4.8
|
62.7
|
1.0
|
|
NZ
|
D:LYS108
|
4.8
|
45.6
|
1.0
|
|
HB2
|
D:ASN60
|
4.8
|
77.4
|
1.0
|
|
HA
|
D:ASP14
|
4.8
|
56.8
|
1.0
|
|
OD1
|
D:ASN60
|
4.8
|
69.2
|
1.0
|
|
HA
|
D:ASN60
|
4.8
|
74.2
|
1.0
|
|
NZ
|
D:LYS87
|
4.8
|
64.5
|
1.0
|
|
H
|
D:GLU59
|
4.9
|
45.0
|
1.0
|
|
HD3
|
D:PRO62
|
4.9
|
66.1
|
1.0
|
|
CE
|
D:LYS87
|
4.9
|
60.8
|
1.0
|
|
OD2
|
D:ASP14
|
4.9
|
39.1
|
1.0
|
|
H
|
D:MSE61
|
4.9
|
74.8
|
1.0
|
|
CA
|
D:ASP15
|
4.9
|
51.5
|
1.0
|
|
O
|
D:HOH740
|
4.9
|
70.9
|
1.0
|
|
CG
|
D:ASN60
|
4.9
|
69.4
|
1.0
|
|
HB2
|
D:GLU16
|
5.0
|
62.8
|
1.0
|
|
Magnesium binding site 2 out
of 9 in 7pv7
Go back to
Magnesium Binding Sites List in 7pv7
Magnesium binding site 2 out
of 9 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg606
b:83.8
occ:1.00
|
O
|
D:HOH880
|
2.0
|
83.4
|
1.0
|
|
O
|
D:HOH902
|
2.4
|
57.3
|
1.0
|
|
O
|
D:HOH894
|
2.5
|
84.8
|
1.0
|
|
O
|
D:MSE61
|
2.6
|
62.9
|
1.0
|
|
O
|
D:HOH727
|
2.8
|
75.1
|
1.0
|
|
O
|
D:GLY63
|
3.1
|
59.1
|
1.0
|
|
H
|
D:MSE61
|
3.6
|
74.8
|
1.0
|
|
C
|
D:MSE61
|
3.7
|
60.7
|
1.0
|
|
HA2
|
D:GLY65
|
3.9
|
63.8
|
1.0
|
|
HA
|
D:PRO62
|
4.0
|
68.6
|
1.0
|
|
O
|
D:HOH735
|
4.0
|
65.8
|
1.0
|
|
O
|
D:HOH832
|
4.1
|
58.1
|
1.0
|
|
H
|
D:GLY63
|
4.2
|
70.7
|
1.0
|
|
C
|
D:GLY63
|
4.2
|
58.6
|
1.0
|
|
N
|
D:MSE61
|
4.2
|
62.4
|
1.0
|
|
O
|
D:HOH778
|
4.2
|
71.7
|
1.0
|
|
N
|
D:GLY65
|
4.3
|
54.8
|
1.0
|
|
N
|
D:GLY63
|
4.4
|
58.9
|
1.0
|
|
C
|
D:ILE64
|
4.4
|
55.9
|
1.0
|
|
CA
|
D:GLY65
|
4.5
|
53.1
|
1.0
|
|
HA3
|
D:GLY65
|
4.5
|
63.8
|
1.0
|
|
H
|
D:GLY65
|
4.5
|
65.8
|
1.0
|
|
N
|
D:PRO62
|
4.5
|
57.9
|
1.0
|
|
CA
|
D:PRO62
|
4.6
|
57.1
|
1.0
|
|
O
|
D:ILE64
|
4.6
|
55.2
|
1.0
|
|
CA
|
D:MSE61
|
4.6
|
61.9
|
1.0
|
|
HA
|
D:ASN60
|
4.6
|
74.2
|
1.0
|
|
HA
|
D:ILE64
|
4.7
|
69.2
|
1.0
|
|
C
|
D:PRO62
|
4.7
|
58.2
|
1.0
|
|
OD1
|
D:ASN60
|
4.9
|
69.2
|
1.0
|
|
CA
|
D:GLY63
|
5.0
|
59.6
|
1.0
|
|
CA
|
D:ILE64
|
5.0
|
57.7
|
1.0
|
|
Magnesium binding site 3 out
of 9 in 7pv7
Go back to
Magnesium Binding Sites List in 7pv7
Magnesium binding site 3 out
of 9 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg602
b:38.2
occ:1.00
|
OD1
|
C:ASP15
|
1.8
|
70.6
|
1.0
|
|
F1
|
C:BEF601
|
2.0
|
41.3
|
1.0
|
|
O
|
C:HOH723
|
2.1
|
40.3
|
1.0
|
|
OD2
|
C:ASP58
|
2.2
|
70.5
|
1.0
|
|
O
|
C:HOH781
|
2.3
|
84.5
|
1.0
|
|
O
|
C:ASN60
|
2.4
|
53.8
|
1.0
|
|
CG
|
C:ASP15
|
2.6
|
66.2
|
1.0
|
|
OD2
|
C:ASP15
|
2.8
|
67.5
|
1.0
|
|
CG
|
C:ASP58
|
3.2
|
63.9
|
1.0
|
|
BE
|
C:BEF601
|
3.2
|
39.1
|
1.0
|
|
HG3
|
C:GLU16
|
3.3
|
73.1
|
1.0
|
|
OD1
|
C:ASP14
|
3.5
|
58.6
|
1.0
|
|
H
|
C:ASP15
|
3.5
|
70.5
|
1.0
|
|
OD1
|
C:ASP58
|
3.6
|
68.7
|
1.0
|
|
HB3
|
C:ASN60
|
3.6
|
76.4
|
1.0
|
|
HZ2
|
C:LYS87
|
3.6
|
75.4
|
1.0
|
|
C
|
C:ASN60
|
3.6
|
58.9
|
1.0
|
|
OE2
|
C:GLU16
|
3.7
|
65.0
|
1.0
|
|
HG2
|
C:MSE61
|
3.9
|
73.9
|
1.0
|
|
CB
|
C:ASP15
|
4.0
|
62.4
|
1.0
|
|
F2
|
C:BEF601
|
4.1
|
42.8
|
1.0
|
|
HG3
|
C:MSE61
|
4.1
|
73.9
|
1.0
|
|
HA
|
C:MSE61
|
4.1
|
77.1
|
1.0
|
|
H
|
C:GLU16
|
4.1
|
72.5
|
1.0
|
|
CG
|
C:GLU16
|
4.2
|
60.9
|
1.0
|
|
H
|
C:ASN60
|
4.2
|
74.3
|
1.0
|
|
N
|
C:ASP15
|
4.2
|
58.8
|
1.0
|
|
HZ2
|
C:LYS108
|
4.3
|
63.6
|
1.0
|
|
HZ3
|
C:LYS108
|
4.3
|
63.6
|
1.0
|
|
CD
|
C:GLU16
|
4.3
|
63.7
|
1.0
|
|
F3
|
C:BEF601
|
4.3
|
40.0
|
1.0
|
|
NZ
|
C:LYS87
|
4.4
|
62.9
|
1.0
|
|
HB3
|
C:ASP15
|
4.4
|
74.8
|
1.0
|
|
HZ1
|
C:LYS87
|
4.4
|
75.4
|
1.0
|
|
CG
|
C:ASP14
|
4.4
|
56.2
|
1.0
|
|
CB
|
C:ASP58
|
4.4
|
56.7
|
1.0
|
|
CB
|
C:ASN60
|
4.4
|
63.6
|
1.0
|
|
HZ1
|
C:LYS108
|
4.4
|
63.6
|
1.0
|
|
CA
|
C:ASN60
|
4.4
|
61.5
|
1.0
|
|
HB3
|
C:ASP58
|
4.5
|
68.0
|
1.0
|
|
CG
|
C:MSE61
|
4.5
|
61.6
|
1.0
|
|
HE3
|
C:LYS87
|
4.5
|
75.1
|
1.0
|
|
NZ
|
C:LYS108
|
4.6
|
53.0
|
1.0
|
|
N
|
C:ASN60
|
4.6
|
61.9
|
1.0
|
|
CA
|
C:ASP15
|
4.6
|
60.4
|
1.0
|
|
HB2
|
C:ASP15
|
4.6
|
74.8
|
1.0
|
|
N
|
C:MSE61
|
4.6
|
62.0
|
1.0
|
|
HB2
|
C:ASP58
|
4.6
|
68.0
|
1.0
|
|
N
|
C:GLU16
|
4.7
|
60.5
|
1.0
|
|
HG2
|
C:GLU16
|
4.7
|
73.1
|
1.0
|
|
HA
|
C:ASP14
|
4.8
|
65.4
|
1.0
|
|
OD2
|
C:ASP14
|
4.8
|
56.5
|
1.0
|
|
CA
|
C:MSE61
|
4.8
|
64.3
|
1.0
|
|
O
|
C:HOH905
|
4.8
|
67.1
|
1.0
|
|
HB2
|
C:GLU16
|
4.9
|
72.2
|
1.0
|
|
CE
|
C:LYS87
|
5.0
|
62.6
|
1.0
|
|
C
|
C:ASP15
|
5.0
|
60.6
|
1.0
|
|
Magnesium binding site 4 out
of 9 in 7pv7
Go back to
Magnesium Binding Sites List in 7pv7
Magnesium binding site 4 out
of 9 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg611
b:93.2
occ:1.00
|
O
|
C:HOH853
|
2.3
|
73.5
|
1.0
|
|
O
|
C:GLY63
|
2.8
|
67.7
|
1.0
|
|
O
|
C:MSE61
|
3.0
|
68.0
|
1.0
|
|
H
|
C:MSE61
|
3.7
|
74.3
|
1.0
|
|
HA2
|
C:GLY65
|
3.8
|
84.0
|
1.0
|
|
C
|
C:GLY63
|
4.0
|
69.7
|
1.0
|
|
N
|
C:GLY65
|
4.1
|
74.7
|
1.0
|
|
H
|
C:GLY63
|
4.2
|
78.7
|
1.0
|
|
C
|
C:MSE61
|
4.2
|
65.7
|
1.0
|
|
HA3
|
C:GLY65
|
4.2
|
84.0
|
1.0
|
|
C
|
C:ILE64
|
4.2
|
77.8
|
1.0
|
|
CA
|
C:GLY65
|
4.3
|
70.0
|
1.0
|
|
H
|
C:GLY65
|
4.3
|
89.6
|
1.0
|
|
HA
|
C:ILE64
|
4.5
|
94.3
|
1.0
|
|
O
|
C:ILE64
|
4.5
|
78.7
|
1.0
|
|
N
|
C:GLY63
|
4.5
|
65.6
|
1.0
|
|
N
|
C:MSE61
|
4.5
|
62.0
|
1.0
|
|
HA
|
C:ASN60
|
4.6
|
73.8
|
1.0
|
|
HA
|
C:PRO62
|
4.6
|
75.8
|
1.0
|
|
CA
|
C:ILE64
|
4.8
|
78.6
|
1.0
|
|
N
|
C:ILE64
|
4.8
|
75.2
|
1.0
|
|
OD1
|
C:ASN60
|
4.9
|
72.5
|
1.0
|
|
CA
|
C:GLY63
|
4.9
|
67.6
|
1.0
|
|
Magnesium binding site 5 out
of 9 in 7pv7
Go back to
Magnesium Binding Sites List in 7pv7
Magnesium binding site 5 out
of 9 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:26.4
occ:1.00
|
O
|
B:ASN60
|
2.0
|
52.5
|
1.0
|
|
F2
|
B:BEF601
|
2.0
|
26.9
|
1.0
|
|
OD1
|
B:ASP15
|
2.0
|
47.8
|
1.0
|
|
O
|
B:HOH753
|
2.1
|
27.7
|
1.0
|
|
OD2
|
B:ASP58
|
2.1
|
44.8
|
1.0
|
|
O
|
B:HOH844
|
2.2
|
32.3
|
1.0
|
|
CG
|
B:ASP15
|
2.9
|
45.6
|
1.0
|
|
OD2
|
B:ASP15
|
3.1
|
47.8
|
1.0
|
|
C
|
B:ASN60
|
3.2
|
46.9
|
1.0
|
|
CG
|
B:ASP58
|
3.2
|
41.3
|
1.0
|
|
BE
|
B:BEF601
|
3.3
|
28.1
|
1.0
|
|
HB3
|
B:ASN60
|
3.5
|
53.4
|
1.0
|
|
OD1
|
B:ASP58
|
3.6
|
45.2
|
1.0
|
|
HG2
|
B:MSE61
|
3.6
|
58.5
|
1.0
|
|
HA
|
B:MSE61
|
3.7
|
56.1
|
1.0
|
|
H
|
B:ASP15
|
3.7
|
48.0
|
1.0
|
|
HG3
|
B:MSE61
|
3.8
|
58.5
|
1.0
|
|
H
|
B:ASN60
|
3.8
|
54.1
|
1.0
|
|
OE2
|
B:GLU16
|
4.0
|
49.9
|
1.0
|
|
HZ2
|
B:LYS87
|
4.0
|
68.7
|
1.0
|
|
CA
|
B:ASN60
|
4.0
|
42.6
|
1.0
|
|
CB
|
B:ASN60
|
4.1
|
44.5
|
1.0
|
|
CG
|
B:MSE61
|
4.1
|
48.7
|
1.0
|
|
F1
|
B:BEF601
|
4.2
|
32.5
|
1.0
|
|
N
|
B:MSE61
|
4.2
|
47.9
|
1.0
|
|
OD1
|
B:ASP14
|
4.2
|
48.6
|
1.0
|
|
N
|
B:ASN60
|
4.2
|
45.1
|
1.0
|
|
CB
|
B:ASP15
|
4.2
|
42.0
|
1.0
|
|
F3
|
B:BEF601
|
4.3
|
30.6
|
1.0
|
|
CA
|
B:MSE61
|
4.3
|
46.8
|
1.0
|
|
HB3
|
B:ASP15
|
4.4
|
50.4
|
1.0
|
|
HE3
|
B:LYS87
|
4.4
|
66.8
|
1.0
|
|
H
|
B:GLU16
|
4.4
|
50.0
|
1.0
|
|
HG3
|
B:GLU16
|
4.5
|
57.6
|
1.0
|
|
HZ1
|
B:LYS87
|
4.5
|
68.7
|
1.0
|
|
N
|
B:ASP15
|
4.5
|
40.0
|
1.0
|
|
CB
|
B:ASP58
|
4.5
|
39.0
|
1.0
|
|
HB3
|
B:ASP58
|
4.5
|
46.9
|
1.0
|
|
HD22
|
B:ASN60
|
4.6
|
62.6
|
1.0
|
|
NZ
|
B:LYS87
|
4.6
|
57.2
|
1.0
|
|
HZ2
|
B:LYS108
|
4.7
|
47.8
|
1.0
|
|
HZ3
|
B:LYS108
|
4.7
|
47.8
|
1.0
|
|
CG
|
B:ASN60
|
4.7
|
47.1
|
1.0
|
|
CG
|
B:ASP14
|
4.7
|
47.7
|
1.0
|
|
O
|
B:HOH804
|
4.7
|
49.0
|
1.0
|
|
HD3
|
B:PRO62
|
4.8
|
57.3
|
1.0
|
|
ND2
|
B:ASN60
|
4.8
|
52.1
|
1.0
|
|
OD2
|
B:ASP14
|
4.8
|
46.6
|
1.0
|
|
CB
|
B:MSE61
|
4.8
|
45.1
|
1.0
|
|
HB2
|
B:ASP58
|
4.9
|
46.9
|
1.0
|
|
HB2
|
B:ASP15
|
4.9
|
50.4
|
1.0
|
|
HB2
|
B:GLU16
|
4.9
|
55.2
|
1.0
|
|
HZ1
|
B:LYS108
|
4.9
|
47.8
|
1.0
|
|
CD
|
B:GLU16
|
4.9
|
50.6
|
1.0
|
|
CA
|
B:ASP15
|
4.9
|
41.1
|
1.0
|
|
HA
|
B:ASN60
|
4.9
|
51.2
|
1.0
|
|
HB2
|
B:ASN60
|
5.0
|
53.4
|
1.0
|
|
NZ
|
B:LYS108
|
5.0
|
39.8
|
1.0
|
|
H
|
B:MSE61
|
5.0
|
57.4
|
1.0
|
|
N
|
B:GLU16
|
5.0
|
41.7
|
1.0
|
|
Magnesium binding site 6 out
of 9 in 7pv7
Go back to
Magnesium Binding Sites List in 7pv7
Magnesium binding site 6 out
of 9 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg609
b:110.1
occ:1.00
|
O
|
B:HOH818
|
2.3
|
66.6
|
1.0
|
|
O
|
B:LEU468
|
2.4
|
96.7
|
1.0
|
|
O
|
B:LYS456
|
2.6
|
48.0
|
1.0
|
|
O
|
B:ASP470
|
2.7
|
64.1
|
1.0
|
|
HA
|
B:ASP457
|
3.2
|
59.8
|
1.0
|
|
HD3
|
B:PRO458
|
3.3
|
59.5
|
1.0
|
|
HA
|
B:SER469
|
3.3
|
87.6
|
1.0
|
|
C
|
B:LEU468
|
3.4
|
92.2
|
1.0
|
|
HD2
|
B:PRO458
|
3.4
|
59.5
|
1.0
|
|
C
|
B:SER469
|
3.6
|
68.7
|
1.0
|
|
C
|
B:ASP470
|
3.6
|
69.2
|
1.0
|
|
N
|
B:ASP470
|
3.8
|
68.9
|
1.0
|
|
CA
|
B:SER469
|
3.8
|
73.0
|
1.0
|
|
C
|
B:LYS456
|
3.8
|
48.4
|
1.0
|
|
CD
|
B:PRO458
|
3.8
|
49.6
|
1.0
|
|
HG2
|
B:LYS471
|
3.9
|
99.5
|
1.0
|
|
O
|
B:SER469
|
3.9
|
67.8
|
1.0
|
|
N
|
B:SER469
|
4.0
|
81.7
|
1.0
|
|
H
|
B:ASP470
|
4.0
|
82.7
|
1.0
|
|
HD1
|
B:HIS465
|
4.1
|
135.4
|
1.0
|
|
CA
|
B:ASP457
|
4.1
|
49.8
|
1.0
|
|
HA
|
B:LYS471
|
4.2
|
71.1
|
1.0
|
|
CA
|
B:ASP470
|
4.3
|
70.0
|
1.0
|
|
HA
|
B:LEU468
|
4.3
|
118.4
|
1.0
|
|
N
|
B:ASP457
|
4.4
|
48.7
|
1.0
|
|
HE1
|
B:HIS465
|
4.4
|
134.4
|
1.0
|
|
CA
|
B:LEU468
|
4.5
|
98.7
|
1.0
|
|
HG
|
B:LEU468
|
4.5
|
118.7
|
1.0
|
|
N
|
B:LYS471
|
4.5
|
52.8
|
1.0
|
|
HD23
|
B:LEU468
|
4.5
|
120.0
|
1.0
|
|
O
|
B:ASN467
|
4.6
|
102.7
|
1.0
|
|
ND1
|
B:HIS465
|
4.6
|
112.8
|
1.0
|
|
CG
|
B:LYS471
|
4.7
|
82.9
|
1.0
|
|
HG3
|
B:LYS471
|
4.7
|
99.5
|
1.0
|
|
HB2
|
B:ASP457
|
4.7
|
61.9
|
1.0
|
|
CE1
|
B:HIS465
|
4.8
|
112.0
|
1.0
|
|
CA
|
B:LYS471
|
4.8
|
59.2
|
1.0
|
|
H
|
B:SER469
|
4.8
|
98.0
|
1.0
|
|
HG2
|
B:PRO458
|
4.8
|
58.1
|
1.0
|
|
OD1
|
B:ASP457
|
4.8
|
53.4
|
1.0
|
|
HA
|
B:LYS456
|
4.8
|
60.9
|
1.0
|
|
N
|
B:PRO458
|
4.8
|
51.9
|
1.0
|
|
HB2
|
B:ASP470
|
4.8
|
84.6
|
1.0
|
|
CG
|
B:PRO458
|
4.9
|
48.4
|
1.0
|
|
CB
|
B:ASP457
|
4.9
|
51.5
|
1.0
|
|
CA
|
B:LYS456
|
4.9
|
50.8
|
1.0
|
|
Magnesium binding site 7 out
of 9 in 7pv7
Go back to
Magnesium Binding Sites List in 7pv7
Magnesium binding site 7 out
of 9 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg610
b:59.0
occ:1.00
|
O
|
B:MSE61
|
2.3
|
49.1
|
1.0
|
|
O
|
B:HOH903
|
2.4
|
47.2
|
1.0
|
|
O
|
B:GLY63
|
2.4
|
44.9
|
1.0
|
|
O
|
B:HOH867
|
2.8
|
53.2
|
1.0
|
|
H
|
B:MSE61
|
3.3
|
57.4
|
1.0
|
|
C
|
B:MSE61
|
3.5
|
48.0
|
1.0
|
|
C
|
B:GLY63
|
3.5
|
47.4
|
1.0
|
|
O
|
B:HOH1044
|
3.6
|
58.1
|
1.0
|
|
HA2
|
B:GLY65
|
3.6
|
56.4
|
1.0
|
|
O
|
B:ILE64
|
3.6
|
50.7
|
1.0
|
|
C
|
B:ILE64
|
3.7
|
50.1
|
1.0
|
|
H
|
B:GLY63
|
3.8
|
56.5
|
1.0
|
|
N
|
B:GLY63
|
3.9
|
47.1
|
1.0
|
|
O
|
B:HOH895
|
3.9
|
59.1
|
1.0
|
|
N
|
B:GLY65
|
4.0
|
49.6
|
1.0
|
|
HA
|
B:PRO62
|
4.0
|
57.5
|
1.0
|
|
N
|
B:MSE61
|
4.0
|
47.9
|
1.0
|
|
HA
|
B:ILE64
|
4.1
|
58.6
|
1.0
|
|
CA
|
B:GLY65
|
4.2
|
47.0
|
1.0
|
|
N
|
B:ILE64
|
4.3
|
47.7
|
1.0
|
|
C
|
B:PRO62
|
4.3
|
47.1
|
1.0
|
|
CA
|
B:ILE64
|
4.3
|
48.9
|
1.0
|
|
CA
|
B:GLY63
|
4.3
|
46.5
|
1.0
|
|
CA
|
B:MSE61
|
4.4
|
46.8
|
1.0
|
|
N
|
B:PRO62
|
4.4
|
47.0
|
1.0
|
|
H
|
B:GLY65
|
4.4
|
59.5
|
1.0
|
|
CA
|
B:PRO62
|
4.4
|
47.9
|
1.0
|
|
HA3
|
B:GLY65
|
4.5
|
56.4
|
1.0
|
|
HB2
|
B:MSE61
|
4.6
|
54.1
|
1.0
|
|
OD1
|
B:ASN60
|
4.6
|
45.8
|
1.0
|
|
HA
|
B:ASN60
|
4.6
|
51.2
|
1.0
|
|
HA2
|
B:GLY63
|
4.9
|
55.8
|
1.0
|
|
HA3
|
B:GLY63
|
5.0
|
55.8
|
1.0
|
|
O
|
B:HOH772
|
5.0
|
35.9
|
1.0
|
|
Magnesium binding site 8 out
of 9 in 7pv7
Go back to
Magnesium Binding Sites List in 7pv7
Magnesium binding site 8 out
of 9 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg602
b:33.7
occ:1.00
|
OD2
|
A:ASP58
|
2.0
|
56.7
|
1.0
|
|
F2
|
A:BEF601
|
2.0
|
34.1
|
1.0
|
|
OD1
|
A:ASP15
|
2.0
|
60.3
|
1.0
|
|
O
|
A:HOH802
|
2.1
|
49.8
|
1.0
|
|
O
|
A:ASN60
|
2.2
|
68.1
|
1.0
|
|
O
|
A:HOH731
|
2.2
|
37.7
|
1.0
|
|
CG
|
A:ASP15
|
2.9
|
54.9
|
1.0
|
|
OD2
|
A:ASP15
|
3.0
|
56.5
|
1.0
|
|
CG
|
A:ASP58
|
3.1
|
53.9
|
1.0
|
|
BE
|
A:BEF601
|
3.2
|
36.1
|
1.0
|
|
C
|
A:ASN60
|
3.4
|
58.0
|
1.0
|
|
HB3
|
A:ASN60
|
3.4
|
67.3
|
1.0
|
|
OD1
|
A:ASP58
|
3.7
|
56.0
|
1.0
|
|
H
|
A:ASP15
|
3.7
|
59.8
|
1.0
|
|
HG3
|
A:MSE61
|
3.8
|
72.4
|
1.0
|
|
HG3
|
A:GLU16
|
3.8
|
64.8
|
1.0
|
|
HZ2
|
A:LYS87
|
3.9
|
65.6
|
1.0
|
|
HA
|
A:MSE61
|
3.9
|
67.9
|
1.0
|
|
H
|
A:ASN60
|
4.0
|
64.4
|
1.0
|
|
F1
|
A:BEF601
|
4.1
|
40.1
|
1.0
|
|
OD1
|
A:ASP14
|
4.1
|
36.6
|
1.0
|
|
CB
|
A:ASN60
|
4.1
|
56.1
|
1.0
|
|
CA
|
A:ASN60
|
4.2
|
54.1
|
1.0
|
|
HZ1
|
A:LYS87
|
4.2
|
65.6
|
1.0
|
|
H
|
A:GLU16
|
4.2
|
58.4
|
1.0
|
|
HE3
|
A:LYS87
|
4.2
|
62.8
|
1.0
|
|
OE1
|
A:GLU16
|
4.3
|
58.3
|
1.0
|
|
HG2
|
A:MSE61
|
4.3
|
72.4
|
1.0
|
|
CB
|
A:ASP15
|
4.3
|
50.5
|
1.0
|
|
F3
|
A:BEF601
|
4.3
|
38.7
|
1.0
|
|
N
|
A:ASN60
|
4.3
|
53.7
|
1.0
|
|
HZ2
|
A:LYS108
|
4.3
|
40.5
|
1.0
|
|
HB3
|
A:ASP58
|
4.4
|
59.5
|
1.0
|
|
CB
|
A:ASP58
|
4.4
|
49.6
|
1.0
|
|
N
|
A:MSE61
|
4.4
|
55.9
|
1.0
|
|
N
|
A:ASP15
|
4.4
|
49.9
|
1.0
|
|
NZ
|
A:LYS87
|
4.4
|
54.7
|
1.0
|
|
CG
|
A:MSE61
|
4.5
|
60.3
|
1.0
|
|
HB3
|
A:ASP15
|
4.6
|
60.6
|
1.0
|
|
CA
|
A:MSE61
|
4.6
|
56.6
|
1.0
|
|
CG
|
A:GLU16
|
4.6
|
54.0
|
1.0
|
|
CD
|
A:GLU16
|
4.6
|
57.2
|
1.0
|
|
HB2
|
A:ASP58
|
4.7
|
59.5
|
1.0
|
|
CG
|
A:ASP14
|
4.7
|
37.5
|
1.0
|
|
CG
|
A:ASN60
|
4.7
|
59.2
|
1.0
|
|
OD1
|
A:ASN60
|
4.7
|
59.2
|
1.0
|
|
HZ1
|
A:LYS108
|
4.8
|
40.5
|
1.0
|
|
N
|
A:GLU16
|
4.8
|
48.7
|
1.0
|
|
OD2
|
A:ASP14
|
4.8
|
35.3
|
1.0
|
|
HB2
|
A:GLU16
|
4.8
|
61.2
|
1.0
|
|
HD3
|
A:PRO62
|
4.9
|
72.9
|
1.0
|
|
CA
|
A:ASP15
|
4.9
|
48.6
|
1.0
|
|
HZ3
|
A:LYS108
|
4.9
|
40.5
|
1.0
|
|
CE
|
A:LYS87
|
4.9
|
52.3
|
1.0
|
|
NZ
|
A:LYS108
|
4.9
|
33.8
|
1.0
|
|
HA
|
A:ASP14
|
4.9
|
54.7
|
1.0
|
|
HB2
|
A:ASP15
|
4.9
|
60.6
|
1.0
|
|
HB2
|
A:ASN60
|
4.9
|
67.3
|
1.0
|
|
Magnesium binding site 9 out
of 9 in 7pv7
Go back to
Magnesium Binding Sites List in 7pv7
Magnesium binding site 9 out
of 9 in the Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator.
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of Dimeric Porphyromonas Gingivalis Porx, A Type 9 Secretion System Response Regulator. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg611
b:78.6
occ:1.00
|
O
|
A:GLY63
|
2.5
|
59.2
|
1.0
|
|
O
|
A:HOH927
|
2.8
|
60.5
|
1.0
|
|
O
|
A:MSE61
|
3.1
|
56.7
|
1.0
|
|
HA2
|
A:GLY65
|
3.6
|
65.8
|
1.0
|
|
N
|
A:GLY65
|
3.7
|
57.2
|
1.0
|
|
H
|
A:GLY65
|
3.7
|
68.7
|
1.0
|
|
C
|
A:GLY63
|
3.7
|
59.9
|
1.0
|
|
HA3
|
A:GLY65
|
3.9
|
65.8
|
1.0
|
|
CA
|
A:GLY65
|
3.9
|
54.9
|
1.0
|
|
C
|
A:ILE64
|
4.0
|
59.3
|
1.0
|
|
H
|
A:GLY63
|
4.1
|
72.9
|
1.0
|
|
H
|
A:MSE61
|
4.1
|
67.1
|
1.0
|
|
HA
|
A:ILE64
|
4.3
|
72.8
|
1.0
|
|
O
|
A:HOH911
|
4.3
|
60.1
|
1.0
|
|
N
|
A:GLY63
|
4.3
|
60.8
|
1.0
|
|
C
|
A:MSE61
|
4.3
|
56.3
|
1.0
|
|
O
|
A:ILE64
|
4.4
|
59.8
|
1.0
|
|
CA
|
A:ILE64
|
4.5
|
60.7
|
1.0
|
|
HA
|
A:PRO62
|
4.5
|
72.5
|
1.0
|
|
N
|
A:ILE64
|
4.6
|
60.0
|
1.0
|
|
CA
|
A:GLY63
|
4.6
|
59.4
|
1.0
|
|
N
|
A:MSE61
|
4.8
|
55.9
|
1.0
|
|
C
|
A:PRO62
|
4.9
|
58.5
|
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 Aug 14 13:19:13 2025
|
