Magnesium in PDB 5ybh: Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens
Enzymatic activity of Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens
All present enzymatic activity of Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens:
3.6.3.14;
Protein crystallography data
The structure of Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens, PDB code: 5ybh
was solved by
Z.Mu,
X.Gao,
S.Cui,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
34.50 /
2.50
|
|
Space group
|
P 32 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.385,
105.385,
146.386,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
19.2 /
24.8
|
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Binding sites:
The binding sites of Magnesium atom in the Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens
(pdb code 5ybh). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 20 binding sites of Magnesium where determined in the
Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens, PDB code: 5ybh:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 20 in 5ybh
Go back to
Magnesium Binding Sites List in 5ybh
Magnesium binding site 1 out
of 20 in the Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg504
b:52.6
occ:1.00
|
HE
|
A:ARG256
|
2.6
|
50.1
|
1.0
|
|
HH21
|
A:ARG256
|
2.8
|
54.9
|
1.0
|
|
HH21
|
A:ARG272
|
2.9
|
0.6
|
1.0
|
|
HE
|
A:ARG272
|
3.3
|
0.4
|
1.0
|
|
NE
|
A:ARG256
|
3.3
|
41.8
|
1.0
|
|
HE1
|
A:TYR274
|
3.4
|
82.1
|
1.0
|
|
OH
|
A:TYR274
|
3.5
|
54.2
|
1.0
|
|
NH2
|
A:ARG256
|
3.5
|
45.7
|
1.0
|
|
NH2
|
A:ARG272
|
3.6
|
1.0
|
1.0
|
|
CZ
|
A:ARG256
|
3.9
|
41.0
|
1.0
|
|
HG2
|
A:ARG256
|
3.9
|
47.9
|
1.0
|
|
NE
|
A:ARG272
|
3.9
|
0.0
|
1.0
|
|
HH
|
A:TYR274
|
4.1
|
65.0
|
1.0
|
|
HH22
|
A:ARG272
|
4.1
|
0.6
|
1.0
|
|
CZ
|
A:ARG272
|
4.2
|
0.5
|
1.0
|
|
CE1
|
A:TYR274
|
4.2
|
68.4
|
1.0
|
|
HH22
|
A:ARG256
|
4.3
|
54.9
|
1.0
|
|
CZ
|
A:TYR274
|
4.3
|
60.8
|
1.0
|
|
CD
|
A:ARG256
|
4.4
|
44.8
|
1.0
|
|
CG
|
A:ARG256
|
4.4
|
39.9
|
1.0
|
|
HG3
|
A:ARG256
|
4.5
|
47.9
|
1.0
|
|
HG3
|
A:ARG272
|
4.5
|
0.1
|
1.0
|
|
HD3
|
A:ARG256
|
4.7
|
53.7
|
1.0
|
|
HE
|
A:ARG259
|
5.0
|
63.2
|
1.0
|
|
Magnesium binding site 2 out
of 20 in 5ybh
Go back to
Magnesium Binding Sites List in 5ybh
Magnesium binding site 2 out
of 20 in the Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg505
b:47.4
occ:1.00
|
HA
|
A:TYR218
|
3.5
|
36.8
|
1.0
|
|
O
|
A:ASP217
|
3.6
|
39.9
|
1.0
|
|
CD2
|
A:TYR218
|
3.9
|
26.8
|
1.0
|
|
CE2
|
A:TYR218
|
3.9
|
27.5
|
1.0
|
|
HB2
|
A:ASP217
|
4.0
|
36.7
|
1.0
|
|
CG
|
A:TYR218
|
4.1
|
32.9
|
1.0
|
|
C
|
A:ASP217
|
4.1
|
36.4
|
1.0
|
|
HD2
|
A:TYR218
|
4.1
|
32.2
|
1.0
|
|
OD2
|
A:ASP217
|
4.2
|
38.1
|
1.0
|
|
CZ
|
A:TYR218
|
4.2
|
26.9
|
1.0
|
|
HE2
|
A:TYR218
|
4.2
|
33.0
|
1.0
|
|
CA
|
A:TYR218
|
4.3
|
30.7
|
1.0
|
|
CD1
|
A:TYR218
|
4.4
|
33.9
|
1.0
|
|
CE1
|
A:TYR218
|
4.4
|
29.6
|
1.0
|
|
N
|
A:TYR218
|
4.5
|
33.4
|
1.0
|
|
CG
|
A:ASP217
|
4.5
|
39.4
|
1.0
|
|
CB
|
A:ASP217
|
4.7
|
30.6
|
1.0
|
|
CB
|
A:TYR218
|
4.8
|
38.3
|
1.0
|
|
OH
|
A:TYR218
|
4.8
|
27.1
|
1.0
|
|
HD1
|
A:TYR218
|
4.9
|
40.6
|
1.0
|
|
HE1
|
A:TYR218
|
4.9
|
35.5
|
1.0
|
|
Magnesium binding site 3 out
of 20 in 5ybh
Go back to
Magnesium Binding Sites List in 5ybh
Magnesium binding site 3 out
of 20 in the Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg506
b:59.7
occ:1.00
|
HG1
|
A:THR421
|
2.5
|
54.9
|
1.0
|
|
OG1
|
A:THR421
|
2.5
|
45.7
|
1.0
|
|
OD2
|
A:ASP144
|
2.7
|
39.3
|
1.0
|
|
O
|
A:PHE416
|
2.7
|
57.8
|
1.0
|
|
HB2
|
A:ASP144
|
2.9
|
46.1
|
1.0
|
|
HB3
|
A:ASP144
|
3.1
|
46.1
|
1.0
|
|
HA2
|
A:GLY139
|
3.1
|
50.4
|
1.0
|
|
CB
|
A:ASP144
|
3.2
|
38.4
|
1.0
|
|
HA
|
A:TYR418
|
3.3
|
69.3
|
1.0
|
|
CG
|
A:ASP144
|
3.4
|
44.1
|
1.0
|
|
O
|
A:THR417
|
3.6
|
39.2
|
1.0
|
|
HB
|
A:THR421
|
3.6
|
55.1
|
1.0
|
|
CB
|
A:THR421
|
3.6
|
45.9
|
1.0
|
|
HA
|
A:LYS141
|
3.7
|
51.4
|
1.0
|
|
HB2
|
A:PHE416
|
3.7
|
53.9
|
1.0
|
|
C
|
A:PHE416
|
3.7
|
53.4
|
1.0
|
|
C
|
A:THR417
|
3.8
|
53.5
|
1.0
|
|
CA
|
A:GLY139
|
3.8
|
42.0
|
1.0
|
|
H
|
A:GLY139
|
3.8
|
60.4
|
1.0
|
|
HG21
|
A:THR421
|
3.9
|
51.3
|
1.0
|
|
C
|
A:GLY139
|
3.9
|
40.1
|
1.0
|
|
N
|
A:TYR418
|
4.0
|
53.2
|
1.0
|
|
HB3
|
A:PHE416
|
4.0
|
53.9
|
1.0
|
|
N
|
A:ILE140
|
4.0
|
35.5
|
1.0
|
|
CA
|
A:TYR418
|
4.0
|
57.7
|
1.0
|
|
H
|
A:ILE140
|
4.0
|
42.6
|
1.0
|
|
CB
|
A:PHE416
|
4.2
|
44.9
|
1.0
|
|
N
|
A:GLY139
|
4.2
|
50.3
|
1.0
|
|
CG2
|
A:THR421
|
4.3
|
42.8
|
1.0
|
|
C
|
A:ILE140
|
4.3
|
40.3
|
1.0
|
|
O
|
A:ILE140
|
4.3
|
43.5
|
1.0
|
|
HG3
|
A:LYS141
|
4.3
|
54.7
|
1.0
|
|
H
|
A:THR421
|
4.4
|
58.8
|
1.0
|
|
O
|
A:GLY139
|
4.4
|
46.9
|
1.0
|
|
H
|
A:TYR418
|
4.4
|
63.8
|
1.0
|
|
HA
|
A:THR417
|
4.4
|
63.6
|
1.0
|
|
CA
|
A:LYS141
|
4.5
|
42.8
|
1.0
|
|
N
|
A:LYS141
|
4.5
|
45.0
|
1.0
|
|
N
|
A:THR417
|
4.5
|
53.6
|
1.0
|
|
CA
|
A:PHE416
|
4.5
|
46.8
|
1.0
|
|
CA
|
A:THR417
|
4.5
|
53.0
|
1.0
|
|
OD1
|
A:ASP144
|
4.6
|
39.0
|
1.0
|
|
HG23
|
A:THR421
|
4.6
|
51.3
|
1.0
|
|
H
|
A:PHE416
|
4.6
|
64.1
|
1.0
|
|
HD1
|
A:TYR418
|
4.6
|
58.9
|
1.0
|
|
HA3
|
A:GLY139
|
4.6
|
50.4
|
1.0
|
|
CA
|
A:ASP144
|
4.7
|
36.9
|
1.0
|
|
HB2
|
A:TYR418
|
4.7
|
68.0
|
1.0
|
|
HD22
|
A:LEU137
|
4.7
|
43.2
|
1.0
|
|
CA
|
A:ILE140
|
4.8
|
34.2
|
1.0
|
|
CA
|
A:THR421
|
4.9
|
48.5
|
1.0
|
|
H
|
A:ASP144
|
4.9
|
42.9
|
1.0
|
|
H
|
A:LYS141
|
5.0
|
54.0
|
1.0
|
|
N
|
A:THR421
|
5.0
|
49.0
|
1.0
|
|
C
|
A:TYR418
|
5.0
|
50.9
|
1.0
|
|
Magnesium binding site 4 out
of 20 in 5ybh
Go back to
Magnesium Binding Sites List in 5ybh
Magnesium binding site 4 out
of 20 in the Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg507
b:48.9
occ:1.00
|
HG23
|
A:THR166
|
2.5
|
34.2
|
1.0
|
|
OG1
|
A:THR166
|
2.8
|
39.1
|
1.0
|
|
O
|
A:HOH629
|
3.0
|
31.2
|
1.0
|
|
HG1
|
A:THR166
|
3.0
|
47.0
|
1.0
|
|
OD2
|
A:ASP249
|
3.2
|
32.2
|
1.0
|
|
CG2
|
A:THR166
|
3.2
|
28.5
|
1.0
|
|
HA
|
A:THR166
|
3.4
|
41.5
|
1.0
|
|
HG21
|
A:THR166
|
3.4
|
34.2
|
1.0
|
|
CB
|
A:THR166
|
3.5
|
42.0
|
1.0
|
|
O
|
A:HOH610
|
3.6
|
38.0
|
1.0
|
|
O
|
A:HOH608
|
3.8
|
36.3
|
1.0
|
|
HD22
|
A:LEU185
|
3.8
|
30.6
|
1.0
|
|
OG1
|
A:THR196
|
3.9
|
34.0
|
1.0
|
|
CA
|
A:THR166
|
3.9
|
34.6
|
1.0
|
|
HD21
|
A:LEU185
|
4.0
|
30.6
|
1.0
|
|
HG1
|
A:THR196
|
4.0
|
40.8
|
1.0
|
|
OE2
|
A:GLU188
|
4.0
|
34.0
|
1.0
|
|
HG22
|
A:THR166
|
4.1
|
34.2
|
1.0
|
|
HZ1
|
A:LYS165
|
4.1
|
47.5
|
1.0
|
|
HZ2
|
A:LYS165
|
4.1
|
47.5
|
1.0
|
|
CG
|
A:ASP249
|
4.3
|
33.0
|
1.0
|
|
CD2
|
A:LEU185
|
4.4
|
25.5
|
1.0
|
|
HB
|
A:THR166
|
4.4
|
50.4
|
1.0
|
|
NZ
|
A:LYS165
|
4.4
|
39.6
|
1.0
|
|
HZ3
|
A:LYS165
|
4.4
|
47.5
|
1.0
|
|
HB3
|
A:ASP249
|
4.5
|
33.1
|
1.0
|
|
OE1
|
A:GLU188
|
4.6
|
33.6
|
1.0
|
|
CG
|
A:MET169
|
4.7
|
42.3
|
1.0
|
|
CD
|
A:GLU188
|
4.8
|
33.8
|
1.0
|
|
HB2
|
A:ASP249
|
4.8
|
33.1
|
1.0
|
|
HD23
|
A:LEU185
|
4.8
|
30.6
|
1.0
|
|
CB
|
A:MET169
|
4.8
|
33.9
|
1.0
|
|
CB
|
A:ASP249
|
4.8
|
27.6
|
1.0
|
|
O
|
A:THR166
|
4.8
|
43.4
|
1.0
|
|
C
|
A:THR166
|
4.9
|
39.0
|
1.0
|
|
N
|
A:THR166
|
5.0
|
37.8
|
1.0
|
|
Magnesium binding site 5 out
of 20 in 5ybh
Go back to
Magnesium Binding Sites List in 5ybh
Magnesium binding site 5 out
of 20 in the Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg508
b:55.3
occ:1.00
|
HH12
|
A:ARG320
|
1.8
|
76.4
|
1.0
|
|
HH11
|
A:ARG320
|
2.2
|
76.4
|
1.0
|
|
NH1
|
A:ARG320
|
2.3
|
63.7
|
1.0
|
|
HH21
|
A:ARG350
|
2.9
|
74.0
|
1.0
|
|
O
|
A:HOH654
|
2.9
|
60.3
|
1.0
|
|
HH22
|
A:ARG350
|
3.2
|
74.0
|
1.0
|
|
NH2
|
A:ARG350
|
3.3
|
61.7
|
1.0
|
|
CZ
|
A:ARG320
|
3.6
|
67.2
|
1.0
|
|
O
|
A:HOH615
|
3.6
|
53.9
|
1.0
|
|
HH22
|
A:ARG320
|
4.0
|
81.6
|
1.0
|
|
HD3
|
A:ARG320
|
4.2
|
73.3
|
1.0
|
|
NH2
|
A:ARG320
|
4.3
|
68.0
|
1.0
|
|
HG2
|
A:ARG320
|
4.3
|
61.1
|
1.0
|
|
HE2
|
A:HIS326
|
4.5
|
56.5
|
1.0
|
|
CZ
|
A:ARG350
|
4.5
|
62.6
|
1.0
|
|
O
|
A:HOH675
|
4.6
|
49.8
|
1.0
|
|
NE
|
A:ARG320
|
4.6
|
64.2
|
1.0
|
|
CD
|
A:ARG320
|
4.7
|
61.0
|
1.0
|
|
HE
|
A:ARG350
|
4.8
|
64.8
|
1.0
|
|
Magnesium binding site 6 out
of 20 in 5ybh
Go back to
Magnesium Binding Sites List in 5ybh
Magnesium binding site 6 out
of 20 in the Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg509
b:59.3
occ:1.00
|
O
|
A:HOH659
|
2.3
|
48.1
|
1.0
|
|
HB2
|
A:ASN121
|
2.7
|
46.7
|
1.0
|
|
O
|
A:PRO118
|
2.9
|
35.7
|
1.0
|
|
OE1
|
A:GLU235
|
3.0
|
33.6
|
1.0
|
|
HH21
|
A:ARG117
|
3.1
|
48.5
|
0.3
|
|
NH2
|
A:ARG117
|
3.2
|
40.4
|
0.3
|
|
CG
|
A:ASN121
|
3.2
|
47.2
|
1.0
|
|
ND2
|
A:ASN121
|
3.3
|
49.0
|
1.0
|
|
HD21
|
A:ASN121
|
3.3
|
58.8
|
1.0
|
|
HG2
|
A:PRO118
|
3.3
|
54.3
|
1.0
|
|
CB
|
A:ASN121
|
3.4
|
38.9
|
1.0
|
|
HH22
|
A:ARG117
|
3.4
|
48.5
|
0.3
|
|
CZ
|
A:ARG117
|
3.5
|
42.3
|
0.3
|
|
HD22
|
A:ASN121
|
3.7
|
58.8
|
1.0
|
|
HA
|
A:ALA232
|
3.7
|
36.0
|
1.0
|
|
HB3
|
A:ASN121
|
3.7
|
46.7
|
1.0
|
|
OD1
|
A:ASN121
|
3.8
|
59.8
|
1.0
|
|
HE
|
A:ARG117
|
3.8
|
49.3
|
0.3
|
|
HB1
|
A:ALA232
|
3.8
|
41.4
|
1.0
|
|
HH21
|
A:ARG288
|
3.8
|
31.9
|
1.0
|
|
HB3
|
A:ARG117
|
3.8
|
50.8
|
0.3
|
|
NE
|
A:ARG117
|
3.8
|
41.1
|
0.3
|
|
HB3
|
A:ARG117
|
3.9
|
50.6
|
0.7
|
|
HD2
|
A:PRO118
|
3.9
|
50.4
|
1.0
|
|
HB2
|
A:GLU235
|
4.0
|
40.8
|
1.0
|
|
C
|
A:PRO118
|
4.0
|
41.2
|
1.0
|
|
CD
|
A:GLU235
|
4.0
|
32.9
|
1.0
|
|
HB3
|
A:GLU235
|
4.1
|
40.8
|
1.0
|
|
NH1
|
A:ARG117
|
4.2
|
35.5
|
0.3
|
|
CG
|
A:PRO118
|
4.2
|
45.3
|
1.0
|
|
HB2
|
A:ALA232
|
4.2
|
41.4
|
1.0
|
|
HH12
|
A:ARG117
|
4.3
|
42.6
|
0.3
|
|
CB
|
A:ALA232
|
4.3
|
34.5
|
1.0
|
|
NH2
|
A:ARG288
|
4.4
|
26.6
|
1.0
|
|
HH22
|
A:ARG288
|
4.4
|
31.9
|
1.0
|
|
CA
|
A:ALA232
|
4.4
|
30.0
|
1.0
|
|
CD
|
A:PRO118
|
4.4
|
42.0
|
1.0
|
|
CB
|
A:GLU235
|
4.4
|
34.0
|
1.0
|
|
N
|
A:PRO118
|
4.6
|
44.2
|
1.0
|
|
HD3
|
A:ARG117
|
4.6
|
51.9
|
0.3
|
|
HH11
|
A:ARG117
|
4.7
|
42.6
|
0.3
|
|
O
|
A:ALA232
|
4.7
|
35.4
|
1.0
|
|
CA
|
A:ASN121
|
4.7
|
38.2
|
1.0
|
|
HB2
|
A:PRO118
|
4.7
|
50.7
|
1.0
|
|
HA
|
A:VAL119
|
4.7
|
55.5
|
1.0
|
|
CA
|
A:PRO118
|
4.7
|
43.7
|
1.0
|
|
HD2
|
A:ARG117
|
4.8
|
53.2
|
0.7
|
|
OE2
|
A:GLU235
|
4.8
|
29.1
|
1.0
|
|
CB
|
A:ARG117
|
4.8
|
42.3
|
0.3
|
|
CB
|
A:ARG117
|
4.8
|
42.2
|
0.7
|
|
CD
|
A:ARG117
|
4.8
|
43.3
|
0.3
|
|
CB
|
A:PRO118
|
4.8
|
42.3
|
1.0
|
|
O
|
A:ASP120
|
4.8
|
51.2
|
1.0
|
|
CG
|
A:GLU235
|
4.9
|
33.2
|
1.0
|
|
HG3
|
A:PRO118
|
4.9
|
54.3
|
1.0
|
|
HA
|
A:ASN121
|
4.9
|
45.9
|
1.0
|
|
HB2
|
A:ARG117
|
5.0
|
50.6
|
0.7
|
|
Magnesium binding site 7 out
of 20 in 5ybh
Go back to
Magnesium Binding Sites List in 5ybh
Magnesium binding site 7 out
of 20 in the Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg510
b:44.3
occ:1.00
|
HG21
|
A:THR252
|
2.3
|
30.1
|
1.0
|
|
HG22
|
A:THR252
|
2.3
|
30.1
|
1.0
|
|
HB
|
A:THR252
|
2.6
|
41.5
|
1.0
|
|
CG2
|
A:THR252
|
2.6
|
25.1
|
1.0
|
|
HD21
|
A:LEU315
|
2.8
|
53.8
|
1.0
|
|
HG13
|
A:VAL304
|
3.0
|
43.3
|
1.0
|
|
CB
|
A:THR252
|
3.1
|
34.6
|
1.0
|
|
O
|
A:LEU305
|
3.2
|
45.2
|
1.0
|
|
HB3
|
A:LEU315
|
3.3
|
50.8
|
1.0
|
|
OD2
|
A:ASP313
|
3.4
|
65.3
|
1.0
|
|
HG12
|
A:VAL304
|
3.5
|
43.3
|
1.0
|
|
HG23
|
A:THR252
|
3.5
|
30.1
|
1.0
|
|
CG1
|
A:VAL304
|
3.6
|
36.1
|
1.0
|
|
OD1
|
A:ASP313
|
3.6
|
56.9
|
1.0
|
|
CD2
|
A:LEU315
|
3.7
|
44.8
|
1.0
|
|
H
|
A:LEU305
|
3.8
|
50.5
|
1.0
|
|
HD23
|
A:LEU315
|
3.9
|
53.8
|
1.0
|
|
CG
|
A:ASP313
|
3.9
|
60.8
|
1.0
|
|
OG1
|
A:THR252
|
4.0
|
49.1
|
1.0
|
|
HA
|
A:THR252
|
4.0
|
45.3
|
1.0
|
|
HG11
|
A:VAL304
|
4.0
|
43.3
|
1.0
|
|
C
|
A:LEU305
|
4.1
|
36.9
|
1.0
|
|
CA
|
A:THR252
|
4.2
|
37.8
|
1.0
|
|
CB
|
A:LEU315
|
4.2
|
42.4
|
1.0
|
|
N
|
A:LEU305
|
4.2
|
42.1
|
1.0
|
|
HD22
|
A:LEU315
|
4.3
|
53.8
|
1.0
|
|
CG
|
A:LEU315
|
4.5
|
45.9
|
1.0
|
|
H
|
A:ALA316
|
4.5
|
52.6
|
1.0
|
|
HA
|
A:VAL304
|
4.5
|
39.5
|
1.0
|
|
HB2
|
A:LEU305
|
4.5
|
39.8
|
1.0
|
|
HB2
|
A:LEU315
|
4.5
|
50.8
|
1.0
|
|
HG1
|
A:THR252
|
4.6
|
59.0
|
1.0
|
|
HD23
|
A:LEU306
|
4.6
|
42.9
|
1.0
|
|
HG
|
A:LEU315
|
4.6
|
55.1
|
1.0
|
|
HA
|
A:LEU306
|
4.6
|
50.5
|
1.0
|
|
HB2
|
A:ALA316
|
4.7
|
57.6
|
1.0
|
|
CA
|
A:LEU305
|
4.7
|
32.5
|
1.0
|
|
C
|
A:VAL304
|
4.8
|
32.2
|
1.0
|
|
CB
|
A:VAL304
|
4.9
|
40.4
|
1.0
|
|
N
|
A:ALA316
|
4.9
|
43.9
|
1.0
|
|
CA
|
A:VAL304
|
4.9
|
32.9
|
1.0
|
|
H
|
A:THR252
|
5.0
|
34.2
|
1.0
|
|
N
|
A:THR252
|
5.0
|
28.5
|
1.0
|
|
Magnesium binding site 8 out
of 20 in 5ybh
Go back to
Magnesium Binding Sites List in 5ybh
Magnesium binding site 8 out
of 20 in the Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg511
b:69.1
occ:1.00
|
OE1
|
A:GLU358
|
2.0
|
59.0
|
1.0
|
|
OE2
|
A:GLU358
|
2.2
|
47.2
|
1.0
|
|
O
|
A:HOH676
|
2.2
|
63.9
|
1.0
|
|
CD
|
A:GLU358
|
2.4
|
60.1
|
1.0
|
|
O
|
A:HOH681
|
2.5
|
59.6
|
1.0
|
|
H
|
A:GLU358
|
3.6
|
61.3
|
1.0
|
|
HA
|
A:ASP357
|
3.7
|
58.9
|
1.0
|
|
HH22
|
A:ARG361
|
3.7
|
70.4
|
1.0
|
|
CG
|
A:GLU358
|
4.0
|
75.6
|
1.0
|
|
HH21
|
A:ARG361
|
4.0
|
70.4
|
1.0
|
|
NH2
|
A:ARG361
|
4.2
|
58.7
|
1.0
|
|
N
|
A:GLU358
|
4.2
|
51.1
|
1.0
|
|
HG2
|
A:GLU358
|
4.3
|
90.8
|
1.0
|
|
HG3
|
A:GLU358
|
4.4
|
90.8
|
1.0
|
|
OD1
|
A:ASP357
|
4.5
|
58.9
|
1.0
|
|
CA
|
A:ASP357
|
4.6
|
49.1
|
1.0
|
|
HB2
|
A:GLU358
|
4.7
|
74.3
|
1.0
|
|
C
|
A:ASP357
|
4.8
|
45.4
|
1.0
|
|
CB
|
A:GLU358
|
4.8
|
61.9
|
1.0
|
|
Magnesium binding site 9 out
of 20 in 5ybh
Go back to
Magnesium Binding Sites List in 5ybh
Magnesium binding site 9 out
of 20 in the Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg503
b:38.0
occ:1.00
|
HZ1
|
B:LYS205
|
2.0
|
50.2
|
1.0
|
|
HA2
|
B:GLY177
|
2.5
|
43.3
|
1.0
|
|
NZ
|
B:LYS205
|
2.8
|
41.9
|
1.0
|
|
O
|
B:ALA178
|
2.8
|
39.9
|
1.0
|
|
HE2
|
B:LYS205
|
3.0
|
41.2
|
1.0
|
|
HE1
|
B:TYR181
|
3.0
|
32.5
|
1.0
|
|
HZ2
|
B:LYS205
|
3.0
|
50.2
|
1.0
|
|
HD3
|
B:LYS205
|
3.2
|
41.2
|
1.0
|
|
OH
|
B:TYR181
|
3.3
|
34.4
|
1.0
|
|
CE
|
B:LYS205
|
3.3
|
34.3
|
1.0
|
|
CA
|
B:GLY177
|
3.3
|
36.1
|
1.0
|
|
C
|
B:GLY177
|
3.5
|
34.9
|
1.0
|
|
HZ3
|
B:LYS205
|
3.5
|
50.2
|
1.0
|
|
H
|
B:ALA178
|
3.5
|
43.1
|
1.0
|
|
N
|
B:ALA178
|
3.5
|
35.9
|
1.0
|
|
O
|
B:SER176
|
3.7
|
32.7
|
1.0
|
|
HD3
|
B:ARG208
|
3.7
|
53.9
|
1.0
|
|
CD
|
B:LYS205
|
3.8
|
34.3
|
1.0
|
|
CE1
|
B:TYR181
|
3.8
|
27.1
|
1.0
|
|
HE
|
B:ARG208
|
3.9
|
68.7
|
1.0
|
|
C
|
B:ALA178
|
3.9
|
37.4
|
1.0
|
|
HH
|
B:TYR181
|
3.9
|
41.2
|
1.0
|
|
NE
|
B:ARG208
|
4.0
|
57.2
|
1.0
|
|
HA3
|
B:GLY177
|
4.0
|
43.3
|
1.0
|
|
CZ
|
B:TYR181
|
4.0
|
29.7
|
1.0
|
|
N
|
B:GLY177
|
4.1
|
37.2
|
1.0
|
|
O
|
B:GLY177
|
4.2
|
38.6
|
1.0
|
|
HE3
|
B:LYS205
|
4.2
|
41.2
|
1.0
|
|
CD
|
B:ARG208
|
4.2
|
44.9
|
1.0
|
|
C
|
B:SER176
|
4.3
|
37.4
|
1.0
|
|
HD2
|
B:ARG208
|
4.3
|
53.9
|
1.0
|
|
CA
|
B:ALA178
|
4.3
|
36.8
|
1.0
|
|
HD2
|
B:LYS205
|
4.3
|
41.2
|
1.0
|
|
O
|
B:HOH680
|
4.4
|
47.0
|
1.0
|
|
CZ
|
B:ARG208
|
4.4
|
67.0
|
1.0
|
|
HG2
|
B:LYS205
|
4.6
|
51.3
|
1.0
|
|
HH21
|
B:ARG208
|
4.7
|
74.3
|
1.0
|
|
HB3
|
B:ALA178
|
4.7
|
39.2
|
1.0
|
|
NH2
|
B:ARG208
|
4.8
|
62.0
|
1.0
|
|
H
|
B:GLY177
|
4.8
|
44.6
|
1.0
|
|
HA
|
B:ASP179
|
4.8
|
44.7
|
1.0
|
|
CG
|
B:LYS205
|
4.8
|
42.8
|
1.0
|
|
N
|
B:ASP179
|
5.0
|
36.4
|
1.0
|
|
Magnesium binding site 10 out
of 20 in 5ybh
Go back to
Magnesium Binding Sites List in 5ybh
Magnesium binding site 10 out
of 20 in the Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Structural of the Highly Conserved Atpase From Type III Secretion System of Bacterial Pathogens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg504
b:34.5
occ:1.00
|
HB2
|
B:SER250
|
2.1
|
38.4
|
1.0
|
|
HH11
|
B:ARG253
|
2.3
|
46.2
|
1.0
|
|
HB3
|
B:SER250
|
2.3
|
38.4
|
1.0
|
|
HG
|
B:SER250
|
2.4
|
34.8
|
1.0
|
|
CB
|
B:SER250
|
2.5
|
32.0
|
1.0
|
|
O
|
B:ILE186
|
2.6
|
32.7
|
1.0
|
|
O
|
B:HOH651
|
2.6
|
30.6
|
1.0
|
|
HD2
|
B:ARG253
|
2.8
|
46.6
|
1.0
|
|
OG
|
B:SER250
|
2.8
|
29.0
|
1.0
|
|
HG3
|
B:ARG253
|
2.9
|
41.4
|
1.0
|
|
HB2
|
B:ARG253
|
3.0
|
35.6
|
1.0
|
|
NH1
|
B:ARG253
|
3.1
|
38.5
|
1.0
|
|
O
|
B:ASP249
|
3.4
|
23.7
|
1.0
|
|
HD11
|
B:LEU305
|
3.4
|
34.9
|
1.0
|
|
HH12
|
B:ARG253
|
3.4
|
46.2
|
1.0
|
|
HG3
|
B:GLU188
|
3.5
|
40.7
|
1.0
|
|
CG
|
B:ARG253
|
3.5
|
34.5
|
1.0
|
|
CD
|
B:ARG253
|
3.5
|
38.9
|
1.0
|
|
HG2
|
B:GLU188
|
3.5
|
40.7
|
1.0
|
|
CB
|
B:ARG253
|
3.7
|
29.6
|
1.0
|
|
C
|
B:ILE186
|
3.8
|
34.0
|
1.0
|
|
CA
|
B:SER250
|
3.9
|
27.3
|
1.0
|
|
H
|
B:ILE186
|
3.9
|
35.8
|
1.0
|
|
CG
|
B:GLU188
|
4.0
|
33.9
|
1.0
|
|
HB
|
B:ILE186
|
4.0
|
30.9
|
1.0
|
|
H
|
B:ARG253
|
4.1
|
37.8
|
1.0
|
|
CZ
|
B:ARG253
|
4.1
|
43.3
|
1.0
|
|
C
|
B:ASP249
|
4.1
|
31.9
|
1.0
|
|
HB3
|
B:ARG253
|
4.1
|
35.6
|
1.0
|
|
HD12
|
B:LEU305
|
4.2
|
34.9
|
1.0
|
|
CD1
|
B:LEU305
|
4.2
|
29.1
|
1.0
|
|
HD3
|
B:ARG253
|
4.2
|
46.6
|
1.0
|
|
NE
|
B:ARG253
|
4.3
|
46.4
|
1.0
|
|
O
|
B:HOH660
|
4.4
|
35.6
|
1.0
|
|
HG2
|
B:ARG253
|
4.4
|
41.4
|
1.0
|
|
HA
|
B:SER250
|
4.4
|
32.8
|
1.0
|
|
N
|
B:SER250
|
4.4
|
38.0
|
1.0
|
|
HA
|
B:GLU188
|
4.5
|
45.2
|
1.0
|
|
HA3
|
B:GLY187
|
4.5
|
50.0
|
1.0
|
|
C
|
B:GLY187
|
4.5
|
35.8
|
1.0
|
|
N
|
B:ILE186
|
4.5
|
29.8
|
1.0
|
|
CA
|
B:ILE186
|
4.6
|
31.9
|
1.0
|
|
N
|
B:GLU188
|
4.6
|
34.0
|
1.0
|
|
OD1
|
B:ASP249
|
4.7
|
23.7
|
1.0
|
|
N
|
B:GLY187
|
4.7
|
31.0
|
1.0
|
|
O
|
B:SER250
|
4.7
|
30.8
|
1.0
|
|
CB
|
B:ILE186
|
4.7
|
25.8
|
1.0
|
|
H
|
B:GLU188
|
4.7
|
40.7
|
1.0
|
|
OE2
|
B:GLU188
|
4.7
|
36.0
|
1.0
|
|
N
|
B:ARG253
|
4.8
|
31.5
|
1.0
|
|
HD13
|
B:LEU305
|
4.8
|
34.9
|
1.0
|
|
CA
|
B:GLY187
|
4.8
|
41.7
|
1.0
|
|
O
|
B:GLY187
|
4.8
|
38.5
|
1.0
|
|
C
|
B:SER250
|
4.8
|
32.2
|
1.0
|
|
CA
|
B:ARG253
|
4.8
|
31.7
|
1.0
|
|
CD
|
B:GLU188
|
4.9
|
35.2
|
1.0
|
|
CA
|
B:GLU188
|
4.9
|
37.7
|
1.0
|
|
Reference:
X.Gao,
Z.Mu,
X.Yu,
B.Qin,
J.Wojdyla,
M.Wang,
S.Cui.
Structural Insight Into Conformational Changes Induced By Atp Binding in A Type III Secretion-Associated Atpase Fromshigella Flexneri Front Microbiol V. 9 1468 2018.
ISSN: ESSN 1664-302X
PubMed: 30013545
DOI: 10.3389/FMICB.2018.01468
Page generated: Wed Aug 13 00:47:58 2025
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