Magnesium in PDB 5ybi: Structure of the Bacterial Pathogens Atpase with Substrate Amppnp
Enzymatic activity of Structure of the Bacterial Pathogens Atpase with Substrate Amppnp
All present enzymatic activity of Structure of the Bacterial Pathogens Atpase with Substrate Amppnp:
3.6.3.14;
Protein crystallography data
The structure of Structure of the Bacterial Pathogens Atpase with Substrate Amppnp, PDB code: 5ybi
was solved by
Z.X.Mu,
X.P.Gao,
S.Cui,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.00 /
2.27
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.017,
105.017,
146.642,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.9 /
22.7
|
Magnesium Binding Sites:
Magnesium binding site 1 out
of 38 in 5ybi
Go back to
Magnesium Binding Sites List in 5ybi
Magnesium binding site 1 out
of 38 in the Structure of the Bacterial Pathogens Atpase with Substrate Amppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of the Bacterial Pathogens Atpase with Substrate Amppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg506
b:59.8
occ:1.00
|
HOB2
|
A:ANP505
|
1.6
|
50.9
|
0.7
|
O2B
|
A:ANP505
|
2.4
|
42.4
|
0.7
|
O1G
|
A:ANP505
|
2.5
|
54.5
|
0.7
|
O2A
|
A:ANP505
|
2.6
|
51.9
|
0.7
|
HG1
|
A:THR166
|
2.6
|
41.5
|
1.0
|
O
|
A:HOH683
|
2.6
|
32.4
|
1.0
|
OG1
|
A:THR166
|
2.7
|
34.6
|
1.0
|
N3B
|
A:ANP505
|
3.1
|
44.2
|
0.7
|
HOG2
|
A:ANP505
|
3.1
|
65.1
|
0.7
|
HB
|
A:THR166
|
3.2
|
46.7
|
1.0
|
PG
|
A:ANP505
|
3.2
|
61.2
|
0.7
|
PB
|
A:ANP505
|
3.3
|
37.9
|
0.7
|
O
|
A:HOH622
|
3.4
|
36.6
|
1.0
|
CB
|
A:THR166
|
3.4
|
38.9
|
1.0
|
O2G
|
A:ANP505
|
3.6
|
54.2
|
0.7
|
HZ2
|
A:LYS165
|
3.6
|
45.0
|
1.0
|
HG21
|
A:THR166
|
3.8
|
39.6
|
1.0
|
PA
|
A:ANP505
|
3.8
|
56.8
|
0.7
|
HNB1
|
A:ANP505
|
3.9
|
53.1
|
0.7
|
O3A
|
A:ANP505
|
4.0
|
48.0
|
0.7
|
HZ1
|
A:LYS165
|
4.0
|
45.0
|
1.0
|
OE1
|
A:GLU195
|
4.1
|
57.1
|
1.0
|
HG2
|
A:GLU192
|
4.1
|
40.0
|
1.0
|
CG2
|
A:THR166
|
4.2
|
33.0
|
1.0
|
NZ
|
A:LYS165
|
4.2
|
37.5
|
1.0
|
H
|
A:THR166
|
4.3
|
45.4
|
1.0
|
OE2
|
A:GLU192
|
4.3
|
48.9
|
1.0
|
HZ3
|
A:LYS165
|
4.5
|
45.0
|
1.0
|
O1B
|
A:ANP505
|
4.6
|
38.6
|
0.7
|
O1A
|
A:ANP505
|
4.6
|
44.7
|
0.7
|
O3G
|
A:ANP505
|
4.7
|
49.6
|
0.7
|
HG23
|
A:THR166
|
4.7
|
39.6
|
1.0
|
CA
|
A:THR166
|
4.7
|
37.1
|
1.0
|
HOG3
|
A:ANP505
|
4.8
|
59.5
|
0.7
|
HG3
|
A:LYS165
|
4.8
|
53.5
|
1.0
|
N
|
A:THR166
|
4.9
|
37.8
|
1.0
|
HG22
|
A:THR166
|
4.9
|
39.6
|
1.0
|
CG
|
A:GLU192
|
4.9
|
33.3
|
1.0
|
HB3
|
A:GLU192
|
4.9
|
38.6
|
1.0
|
|
Magnesium binding site 2 out
of 38 in 5ybi
Go back to
Magnesium Binding Sites List in 5ybi
Magnesium binding site 2 out
of 38 in the Structure of the Bacterial Pathogens Atpase with Substrate Amppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of the Bacterial Pathogens Atpase with Substrate Amppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg507
b:42.3
occ:1.00
|
HB3
|
A:ASP324
|
1.6
|
53.4
|
1.0
|
CB
|
A:ASP324
|
2.3
|
44.5
|
1.0
|
HB2
|
A:ASP324
|
2.4
|
53.4
|
1.0
|
O
|
B:HOH745
|
2.5
|
33.9
|
1.0
|
HZ2
|
B:LYS293
|
2.6
|
71.1
|
1.0
|
O
|
B:HOH661
|
2.7
|
36.8
|
1.0
|
HA
|
B:SER127
|
2.9
|
37.3
|
1.0
|
CG
|
A:ASP324
|
3.0
|
34.2
|
1.0
|
OD2
|
A:ASP324
|
3.0
|
16.9
|
1.0
|
HZ1
|
B:LYS293
|
3.2
|
71.1
|
1.0
|
NZ
|
B:LYS293
|
3.3
|
59.2
|
1.0
|
HB2
|
B:SER127
|
3.5
|
38.7
|
1.0
|
HB2
|
A:ARG350
|
3.5
|
36.6
|
1.0
|
CA
|
A:ASP324
|
3.6
|
37.1
|
1.0
|
HA
|
A:ASP324
|
3.6
|
44.5
|
1.0
|
HZ3
|
B:LYS293
|
3.7
|
71.1
|
1.0
|
HB3
|
A:ARG350
|
3.7
|
36.6
|
1.0
|
CA
|
B:SER127
|
3.7
|
31.1
|
1.0
|
CB
|
B:SER127
|
3.9
|
32.3
|
1.0
|
O
|
B:SER127
|
4.0
|
32.9
|
1.0
|
HB3
|
B:SER127
|
4.0
|
38.7
|
1.0
|
OD1
|
A:ASP324
|
4.0
|
34.0
|
1.0
|
CB
|
A:ARG350
|
4.1
|
30.5
|
1.0
|
HD2
|
A:ARG350
|
4.1
|
48.8
|
1.0
|
HD3
|
A:ARG350
|
4.1
|
48.8
|
1.0
|
HG13
|
A:VAL351
|
4.2
|
36.6
|
1.0
|
C
|
B:SER127
|
4.3
|
39.7
|
1.0
|
HE3
|
B:LYS293
|
4.4
|
49.3
|
1.0
|
N
|
A:ASP324
|
4.4
|
24.0
|
1.0
|
CE
|
B:LYS293
|
4.5
|
41.1
|
1.0
|
HH21
|
A:ARG154
|
4.5
|
30.8
|
1.0
|
CD
|
A:ARG350
|
4.5
|
40.7
|
1.0
|
HG12
|
A:VAL351
|
4.5
|
36.6
|
1.0
|
O
|
A:LEU323
|
4.6
|
24.4
|
1.0
|
HE1
|
B:TYR126
|
4.6
|
61.3
|
1.0
|
C
|
A:ASP324
|
4.6
|
24.8
|
1.0
|
HD1
|
B:TYR126
|
4.6
|
69.9
|
1.0
|
HH11
|
A:ARG350
|
4.6
|
53.4
|
1.0
|
O
|
A:ASP324
|
4.7
|
29.6
|
1.0
|
O
|
A:ARG350
|
4.8
|
31.2
|
1.0
|
HD2
|
B:LYS293
|
4.8
|
44.3
|
1.0
|
CG1
|
A:VAL351
|
4.8
|
30.5
|
1.0
|
N
|
B:SER127
|
4.8
|
35.6
|
1.0
|
H
|
A:ASP324
|
4.9
|
28.8
|
1.0
|
O
|
A:HOH604
|
4.9
|
19.3
|
1.0
|
C
|
A:LEU323
|
4.9
|
27.2
|
1.0
|
O
|
B:TYR126
|
4.9
|
35.1
|
1.0
|
CG
|
A:ARG350
|
4.9
|
33.8
|
1.0
|
C
|
A:ARG350
|
5.0
|
28.5
|
1.0
|
|
Magnesium binding site 3 out
of 38 in 5ybi
Go back to
Magnesium Binding Sites List in 5ybi
Magnesium binding site 3 out
of 38 in the Structure of the Bacterial Pathogens Atpase with Substrate Amppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of the Bacterial Pathogens Atpase with Substrate Amppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg508
b:49.1
occ:1.00
|
H
|
A:SER220
|
2.6
|
33.0
|
1.0
|
HA
|
A:SER219
|
3.3
|
35.8
|
1.0
|
HB2
|
A:SER219
|
3.4
|
33.6
|
1.0
|
O
|
A:HOH729
|
3.4
|
26.6
|
1.0
|
N
|
A:SER220
|
3.5
|
27.5
|
1.0
|
HB2
|
A:SER220
|
3.5
|
35.1
|
1.0
|
OG
|
A:SER220
|
3.7
|
33.1
|
1.0
|
HG
|
A:SER220
|
3.8
|
39.7
|
1.0
|
CA
|
A:SER219
|
4.0
|
29.8
|
1.0
|
CB
|
A:SER220
|
4.0
|
29.2
|
1.0
|
CB
|
A:SER219
|
4.1
|
28.0
|
1.0
|
C
|
A:SER219
|
4.3
|
28.2
|
1.0
|
O
|
A:HOH747
|
4.4
|
45.2
|
1.0
|
CA
|
A:SER220
|
4.4
|
22.9
|
1.0
|
HB3
|
A:SER219
|
4.4
|
33.6
|
1.0
|
H
|
A:VAL221
|
4.9
|
29.3
|
1.0
|
HB3
|
A:ASP260
|
4.9
|
37.7
|
1.0
|
HA
|
A:SER220
|
4.9
|
27.5
|
1.0
|
HB3
|
A:SER220
|
4.9
|
35.1
|
1.0
|
|
Magnesium binding site 4 out
of 38 in 5ybi
Go back to
Magnesium Binding Sites List in 5ybi
Magnesium binding site 4 out
of 38 in the Structure of the Bacterial Pathogens Atpase with Substrate Amppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of the Bacterial Pathogens Atpase with Substrate Amppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg509
b:45.5
occ:1.00
|
O
|
A:HOH739
|
2.2
|
38.5
|
1.0
|
HD22
|
A:LEU414
|
3.1
|
39.0
|
1.0
|
O
|
A:GLY415
|
3.4
|
45.6
|
1.0
|
O
|
A:HOH689
|
3.4
|
44.1
|
1.0
|
HB3
|
A:LEU414
|
3.7
|
50.8
|
1.0
|
O
|
A:HOH637
|
4.0
|
43.4
|
1.0
|
CD2
|
A:LEU414
|
4.0
|
32.5
|
1.0
|
CE1
|
A:PHE416
|
4.1
|
40.4
|
1.0
|
CZ
|
A:PHE416
|
4.2
|
38.8
|
1.0
|
HD23
|
A:LEU414
|
4.3
|
39.0
|
1.0
|
HE1
|
A:PHE416
|
4.3
|
48.4
|
1.0
|
H
|
A:GLY415
|
4.3
|
55.5
|
1.0
|
HZ
|
A:PHE416
|
4.4
|
46.5
|
1.0
|
HD13
|
A:LEU414
|
4.4
|
47.1
|
1.0
|
C
|
A:GLY415
|
4.4
|
46.4
|
1.0
|
CD1
|
A:PHE416
|
4.4
|
42.6
|
1.0
|
HA
|
A:PHE416
|
4.5
|
44.6
|
1.0
|
CE2
|
A:PHE416
|
4.5
|
43.4
|
1.0
|
CB
|
A:LEU414
|
4.5
|
42.4
|
1.0
|
HD21
|
A:LEU414
|
4.6
|
39.0
|
1.0
|
HA
|
A:LEU414
|
4.6
|
50.6
|
1.0
|
N
|
A:GLY415
|
4.7
|
46.2
|
1.0
|
CG
|
A:PHE416
|
4.8
|
41.1
|
1.0
|
HD1
|
A:PHE416
|
4.8
|
51.1
|
1.0
|
CG
|
A:LEU414
|
4.8
|
41.5
|
1.0
|
CD2
|
A:PHE416
|
4.8
|
44.6
|
1.0
|
OE1
|
A:GLN420
|
4.8
|
38.5
|
1.0
|
HE2
|
A:PHE416
|
4.9
|
52.0
|
1.0
|
|
Magnesium binding site 5 out
of 38 in 5ybi
Go back to
Magnesium Binding Sites List in 5ybi
Magnesium binding site 5 out
of 38 in the Structure of the Bacterial Pathogens Atpase with Substrate Amppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of the Bacterial Pathogens Atpase with Substrate Amppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg510
b:42.6
occ:1.00
|
H
|
A:LYS291
|
2.1
|
36.0
|
1.0
|
N
|
A:LYS291
|
2.9
|
30.0
|
1.0
|
HA2
|
A:GLY290
|
3.0
|
33.1
|
1.0
|
HG13
|
A:ILE132
|
3.2
|
34.6
|
1.0
|
HA3
|
A:GLY290
|
3.2
|
33.1
|
1.0
|
HB2
|
A:LYS291
|
3.2
|
42.6
|
1.0
|
O
|
A:HOH671
|
3.3
|
30.4
|
1.0
|
CA
|
A:GLY290
|
3.4
|
27.6
|
1.0
|
O
|
A:ALA130
|
3.5
|
37.4
|
1.0
|
HD11
|
A:ILE132
|
3.6
|
34.4
|
1.0
|
HH11
|
A:ARG129
|
3.6
|
37.7
|
1.0
|
HA3
|
A:GLY152
|
3.6
|
28.9
|
1.0
|
C
|
A:GLY290
|
3.6
|
28.0
|
1.0
|
HH
|
B:TYR126
|
3.7
|
66.4
|
1.0
|
OH
|
B:TYR126
|
3.7
|
55.4
|
1.0
|
O
|
A:LYS291
|
3.7
|
31.4
|
1.0
|
HG12
|
A:ILE132
|
3.7
|
34.6
|
1.0
|
HB3
|
A:LYS291
|
3.8
|
42.6
|
1.0
|
CB
|
A:LYS291
|
3.8
|
35.5
|
1.0
|
CA
|
A:LYS291
|
3.8
|
33.7
|
1.0
|
HB3
|
A:ARG129
|
3.8
|
41.5
|
1.0
|
CG1
|
A:ILE132
|
3.8
|
28.8
|
1.0
|
O
|
A:GLY152
|
3.9
|
23.9
|
1.0
|
HD3
|
A:ARG129
|
3.9
|
41.2
|
1.0
|
CZ
|
B:TYR126
|
4.2
|
44.7
|
1.0
|
CD1
|
A:ILE132
|
4.2
|
28.7
|
1.0
|
C
|
A:LYS291
|
4.2
|
26.6
|
1.0
|
CA
|
A:GLY152
|
4.4
|
24.1
|
1.0
|
NH1
|
A:ARG129
|
4.4
|
31.4
|
1.0
|
C
|
A:GLY152
|
4.4
|
22.4
|
1.0
|
HG2
|
A:ARG129
|
4.5
|
35.5
|
1.0
|
HD12
|
A:ILE132
|
4.6
|
34.4
|
1.0
|
HA2
|
A:GLY152
|
4.6
|
28.9
|
1.0
|
HH12
|
A:ARG129
|
4.6
|
37.7
|
1.0
|
HE2
|
B:TYR126
|
4.6
|
52.2
|
1.0
|
HA
|
A:LYS291
|
4.6
|
40.4
|
1.0
|
CE2
|
B:TYR126
|
4.6
|
43.5
|
1.0
|
H
|
A:ALA130
|
4.6
|
43.0
|
1.0
|
C
|
A:ALA130
|
4.7
|
34.7
|
1.0
|
CB
|
A:ARG129
|
4.7
|
34.6
|
1.0
|
CE1
|
B:TYR126
|
4.7
|
51.1
|
1.0
|
CD
|
A:ARG129
|
4.8
|
34.3
|
1.0
|
HE1
|
B:TYR126
|
4.8
|
61.3
|
1.0
|
N
|
A:GLY290
|
4.8
|
23.7
|
1.0
|
O
|
A:GLY290
|
4.8
|
31.0
|
1.0
|
CG
|
A:ARG129
|
4.9
|
29.6
|
1.0
|
H
|
A:ILE132
|
4.9
|
47.7
|
1.0
|
HD13
|
A:ILE132
|
5.0
|
34.4
|
1.0
|
|
Magnesium binding site 6 out
of 38 in 5ybi
Go back to
Magnesium Binding Sites List in 5ybi
Magnesium binding site 6 out
of 38 in the Structure of the Bacterial Pathogens Atpase with Substrate Amppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of the Bacterial Pathogens Atpase with Substrate Amppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg511
b:52.0
occ:1.00
|
O
|
A:HOH740
|
2.2
|
56.8
|
1.0
|
HZ3
|
A:LYS293
|
2.7
|
60.6
|
1.0
|
HA
|
A:ALA130
|
2.9
|
42.8
|
1.0
|
H
|
A:ALA131
|
3.1
|
41.8
|
1.0
|
HZ2
|
A:LYS293
|
3.3
|
60.6
|
1.0
|
HG2
|
A:LYS293
|
3.3
|
41.1
|
1.0
|
NZ
|
A:LYS293
|
3.4
|
50.5
|
1.0
|
HB1
|
A:ALA130
|
3.5
|
42.5
|
1.0
|
HZ1
|
A:LYS293
|
3.8
|
60.6
|
1.0
|
CA
|
A:ALA130
|
3.8
|
35.7
|
1.0
|
HB2
|
A:ALA130
|
3.9
|
42.5
|
1.0
|
CB
|
A:ALA130
|
3.9
|
35.4
|
1.0
|
N
|
A:ALA131
|
3.9
|
34.8
|
1.0
|
O
|
A:HOH668
|
4.2
|
41.5
|
1.0
|
CG
|
A:LYS293
|
4.3
|
34.3
|
1.0
|
C
|
A:ALA130
|
4.4
|
34.7
|
1.0
|
HB3
|
A:ALA131
|
4.5
|
45.4
|
1.0
|
HG3
|
A:LYS293
|
4.6
|
41.1
|
1.0
|
CE
|
A:LYS293
|
4.6
|
45.3
|
1.0
|
HA
|
A:LYS293
|
4.7
|
48.8
|
1.0
|
O
|
A:ARG129
|
4.7
|
40.1
|
1.0
|
HB2
|
A:ALA131
|
4.7
|
45.4
|
1.0
|
HD3
|
A:LYS293
|
4.7
|
51.9
|
1.0
|
CD
|
A:LYS293
|
4.8
|
43.3
|
1.0
|
HB3
|
A:ALA130
|
4.8
|
42.5
|
1.0
|
N
|
A:ALA130
|
4.9
|
35.8
|
1.0
|
CB
|
A:ALA131
|
4.9
|
37.9
|
1.0
|
HE2
|
A:LYS293
|
5.0
|
54.4
|
1.0
|
|
Magnesium binding site 7 out
of 38 in 5ybi
Go back to
Magnesium Binding Sites List in 5ybi
Magnesium binding site 7 out
of 38 in the Structure of the Bacterial Pathogens Atpase with Substrate Amppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structure of the Bacterial Pathogens Atpase with Substrate Amppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg512
b:48.0
occ:1.00
|
SE
|
A:MSE171
|
2.0
|
28.8
|
1.0
|
HB3
|
A:PRO340
|
2.2
|
45.5
|
1.0
|
HD3
|
A:PRO340
|
2.3
|
47.6
|
1.0
|
HN61
|
A:ANP505
|
2.6
|
59.9
|
0.7
|
HG3
|
A:PRO340
|
2.7
|
51.4
|
1.0
|
CB
|
A:PRO340
|
2.9
|
38.0
|
1.0
|
HE1
|
A:MSE171
|
2.9
|
42.5
|
1.0
|
CD
|
A:PRO340
|
2.9
|
39.6
|
1.0
|
CG
|
A:PRO340
|
3.0
|
42.8
|
1.0
|
CE
|
A:MSE171
|
3.1
|
35.4
|
1.0
|
HN62
|
A:ANP505
|
3.1
|
59.9
|
0.7
|
N6
|
A:ANP505
|
3.2
|
49.9
|
0.7
|
N
|
A:PRO340
|
3.5
|
41.6
|
1.0
|
HA
|
A:PRO340
|
3.6
|
47.5
|
1.0
|
CA
|
A:PRO340
|
3.6
|
39.6
|
1.0
|
O
|
A:GLN410
|
3.7
|
40.7
|
1.0
|
HE3
|
A:MSE171
|
3.7
|
42.5
|
1.0
|
HB2
|
A:PRO340
|
3.7
|
45.5
|
1.0
|
HE2
|
A:MSE171
|
3.7
|
42.5
|
1.0
|
CG
|
A:MSE171
|
3.8
|
30.0
|
1.0
|
HD2
|
A:PRO340
|
3.8
|
47.6
|
1.0
|
HA
|
A:LEU168
|
3.9
|
41.8
|
1.0
|
HG2
|
A:PRO340
|
4.0
|
51.4
|
1.0
|
HG3
|
A:MSE171
|
4.0
|
36.0
|
1.0
|
HA
|
A:TYR412
|
4.1
|
37.1
|
1.0
|
HD13
|
A:LEU168
|
4.1
|
43.8
|
1.0
|
HG2
|
A:MSE171
|
4.3
|
36.0
|
1.0
|
C
|
A:PHE339
|
4.3
|
47.0
|
1.0
|
HB2
|
A:MSE171
|
4.4
|
40.0
|
1.0
|
HB3
|
A:GLN410
|
4.4
|
35.1
|
1.0
|
HB3
|
A:PHE339
|
4.4
|
64.6
|
1.0
|
HB3
|
A:PHE167
|
4.4
|
55.2
|
1.0
|
HD13
|
A:ILE140
|
4.5
|
43.9
|
1.0
|
HD12
|
A:LEU168
|
4.5
|
43.8
|
1.0
|
C6
|
A:ANP505
|
4.5
|
57.0
|
0.7
|
CB
|
A:MSE171
|
4.5
|
33.3
|
1.0
|
HB3
|
A:TYR412
|
4.5
|
48.8
|
1.0
|
HB3
|
A:MSE171
|
4.6
|
40.0
|
1.0
|
CA
|
A:LEU168
|
4.7
|
34.9
|
1.0
|
HB2
|
A:LEU168
|
4.8
|
34.8
|
1.0
|
O
|
A:PHE339
|
4.8
|
38.9
|
1.0
|
CD1
|
A:LEU168
|
4.8
|
36.5
|
1.0
|
HG23
|
A:ILE140
|
4.8
|
27.9
|
1.0
|
CA
|
A:TYR412
|
4.8
|
30.9
|
1.0
|
C
|
A:GLN410
|
4.9
|
46.3
|
1.0
|
N
|
A:LEU168
|
4.9
|
30.4
|
1.0
|
HG21
|
A:ILE140
|
5.0
|
27.9
|
1.0
|
HG2
|
A:GLN410
|
5.0
|
40.0
|
1.0
|
HB2
|
A:TYR412
|
5.0
|
48.8
|
1.0
|
|
Magnesium binding site 8 out
of 38 in 5ybi
Go back to
Magnesium Binding Sites List in 5ybi
Magnesium binding site 8 out
of 38 in the Structure of the Bacterial Pathogens Atpase with Substrate Amppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Structure of the Bacterial Pathogens Atpase with Substrate Amppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg513
b:53.6
occ:1.00
|
O
|
A:HOH750
|
2.1
|
68.8
|
1.0
|
H
|
A:TYR418
|
2.3
|
50.4
|
1.0
|
HB
|
A:THR417
|
2.9
|
49.7
|
1.0
|
HD13
|
A:LEU137
|
3.0
|
40.9
|
1.0
|
N
|
A:TYR418
|
3.2
|
42.0
|
1.0
|
HA
|
A:THR417
|
3.3
|
49.4
|
1.0
|
HB3
|
A:TYR418
|
3.4
|
49.5
|
1.0
|
HB2
|
A:TYR418
|
3.5
|
49.5
|
1.0
|
OE1
|
A:GLU419
|
3.5
|
56.5
|
1.0
|
CB
|
A:THR417
|
3.7
|
41.4
|
1.0
|
CD1
|
A:LEU137
|
3.7
|
34.1
|
1.0
|
HD12
|
A:LEU137
|
3.7
|
40.9
|
1.0
|
CB
|
A:TYR418
|
3.8
|
41.2
|
1.0
|
CA
|
A:THR417
|
3.8
|
41.2
|
1.0
|
HD11
|
A:LEU137
|
3.9
|
40.9
|
1.0
|
HG22
|
A:THR417
|
4.0
|
52.3
|
1.0
|
C
|
A:THR417
|
4.0
|
40.3
|
1.0
|
CA
|
A:TYR418
|
4.1
|
42.6
|
1.0
|
H
|
A:GLU419
|
4.2
|
40.8
|
1.0
|
CG2
|
A:THR417
|
4.3
|
43.6
|
1.0
|
CD
|
A:GLU419
|
4.4
|
60.0
|
1.0
|
OE2
|
A:GLU419
|
4.4
|
56.8
|
1.0
|
HG21
|
A:THR417
|
4.7
|
52.3
|
1.0
|
HA
|
A:TYR418
|
4.7
|
51.1
|
1.0
|
OG1
|
A:THR417
|
4.8
|
38.8
|
1.0
|
HB3
|
A:LEU137
|
4.9
|
41.2
|
1.0
|
N
|
A:GLU419
|
4.9
|
34.0
|
1.0
|
|
Magnesium binding site 9 out
of 38 in 5ybi
Go back to
Magnesium Binding Sites List in 5ybi
Magnesium binding site 9 out
of 38 in the Structure of the Bacterial Pathogens Atpase with Substrate Amppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Structure of the Bacterial Pathogens Atpase with Substrate Amppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg514
b:60.5
occ:1.00
|
O
|
A:GLY100
|
2.3
|
50.6
|
1.0
|
O
|
A:HOH639
|
2.6
|
32.5
|
1.0
|
HB2
|
A:GLN86
|
2.7
|
41.0
|
1.0
|
HG11
|
A:VAL96
|
2.8
|
42.6
|
1.0
|
HA2
|
A:GLY100
|
2.9
|
55.1
|
1.0
|
HG13
|
A:VAL96
|
3.0
|
42.6
|
1.0
|
O
|
A:HOH701
|
3.1
|
36.7
|
1.0
|
C
|
A:GLY100
|
3.1
|
47.4
|
1.0
|
CG1
|
A:VAL96
|
3.3
|
35.5
|
1.0
|
HD21
|
A:LEU91
|
3.4
|
46.7
|
1.0
|
CA
|
A:GLY100
|
3.4
|
45.9
|
1.0
|
OE1
|
A:GLN86
|
3.4
|
49.8
|
1.0
|
HA3
|
A:GLY100
|
3.5
|
55.1
|
1.0
|
CB
|
A:GLN86
|
3.6
|
34.1
|
1.0
|
H
|
A:GLN86
|
3.7
|
45.0
|
1.0
|
HG12
|
A:VAL96
|
3.8
|
42.6
|
1.0
|
HG3
|
A:GLN86
|
3.8
|
49.9
|
1.0
|
HG1
|
A:THR85
|
3.8
|
42.4
|
1.0
|
HD22
|
A:LEU91
|
3.9
|
46.7
|
1.0
|
HD11
|
A:LEU91
|
4.0
|
48.5
|
1.0
|
CD
|
A:GLN86
|
4.0
|
48.1
|
1.0
|
CG
|
A:GLN86
|
4.0
|
41.6
|
1.0
|
CD2
|
A:LEU91
|
4.1
|
38.9
|
1.0
|
HB3
|
A:GLN86
|
4.1
|
41.0
|
1.0
|
HG21
|
A:VAL96
|
4.1
|
52.6
|
1.0
|
HG22
|
A:VAL96
|
4.3
|
52.6
|
1.0
|
N
|
A:GLU101
|
4.3
|
45.9
|
1.0
|
OG1
|
A:THR85
|
4.4
|
35.3
|
1.0
|
N
|
A:GLN86
|
4.4
|
37.5
|
1.0
|
HD13
|
A:LEU91
|
4.5
|
48.5
|
1.0
|
HA
|
A:GLU101
|
4.5
|
58.3
|
1.0
|
CG2
|
A:VAL96
|
4.5
|
43.8
|
1.0
|
CB
|
A:VAL96
|
4.5
|
32.4
|
1.0
|
CA
|
A:GLN86
|
4.6
|
39.5
|
1.0
|
CD1
|
A:LEU91
|
4.6
|
40.4
|
1.0
|
HG22
|
A:VAL102
|
4.7
|
46.0
|
1.0
|
HD23
|
A:LEU91
|
4.7
|
46.7
|
1.0
|
N
|
A:GLY100
|
4.8
|
39.5
|
1.0
|
O
|
A:GLN86
|
4.8
|
36.2
|
1.0
|
CA
|
A:GLU101
|
4.9
|
48.5
|
1.0
|
HG23
|
A:VAL102
|
4.9
|
46.0
|
1.0
|
H
|
A:GLY100
|
5.0
|
47.5
|
1.0
|
CG
|
A:LEU91
|
5.0
|
42.4
|
1.0
|
HG2
|
A:GLN86
|
5.0
|
49.9
|
1.0
|
|
Magnesium binding site 10 out
of 38 in 5ybi
Go back to
Magnesium Binding Sites List in 5ybi
Magnesium binding site 10 out
of 38 in the Structure of the Bacterial Pathogens Atpase with Substrate Amppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Structure of the Bacterial Pathogens Atpase with Substrate Amppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg515
b:48.5
occ:1.00
|
HE
|
A:ARG368
|
2.0
|
53.5
|
1.0
|
NE
|
A:ARG368
|
2.8
|
44.6
|
1.0
|
HB3
|
A:LEU146
|
3.0
|
39.4
|
1.0
|
HD3
|
A:ARG368
|
3.1
|
47.5
|
1.0
|
O
|
A:LEU146
|
3.2
|
34.2
|
1.0
|
HD21
|
A:LEU147
|
3.2
|
35.3
|
1.0
|
HH21
|
A:ARG368
|
3.3
|
44.3
|
1.0
|
HB2
|
A:SER344
|
3.3
|
49.6
|
1.0
|
HD23
|
A:LEU147
|
3.3
|
35.3
|
1.0
|
CD
|
A:ARG368
|
3.5
|
39.5
|
1.0
|
O
|
A:SER344
|
3.7
|
36.1
|
1.0
|
CD2
|
A:LEU147
|
3.7
|
29.4
|
1.0
|
CZ
|
A:ARG368
|
3.7
|
49.7
|
1.0
|
NH2
|
A:ARG368
|
3.8
|
36.9
|
1.0
|
HD13
|
A:LEU146
|
3.8
|
46.2
|
1.0
|
HG
|
A:LEU147
|
3.9
|
31.2
|
1.0
|
CB
|
A:LEU146
|
3.9
|
32.8
|
1.0
|
HG2
|
A:ARG368
|
4.0
|
49.7
|
1.0
|
C
|
A:LEU146
|
4.1
|
28.8
|
1.0
|
HB2
|
A:LEU146
|
4.2
|
39.4
|
1.0
|
CB
|
A:SER344
|
4.2
|
41.3
|
1.0
|
HD2
|
A:ARG368
|
4.3
|
47.5
|
1.0
|
CG
|
A:ARG368
|
4.3
|
41.4
|
1.0
|
O
|
A:HOH694
|
4.4
|
28.6
|
1.0
|
C
|
A:SER344
|
4.4
|
41.1
|
1.0
|
CG
|
A:LEU147
|
4.4
|
26.0
|
1.0
|
HA
|
A:SER344
|
4.5
|
51.5
|
1.0
|
O
|
A:SER347
|
4.5
|
38.9
|
1.0
|
HD22
|
A:LEU147
|
4.5
|
35.3
|
1.0
|
CA
|
A:LEU146
|
4.5
|
30.3
|
1.0
|
HA
|
A:LEU146
|
4.6
|
36.4
|
1.0
|
CD1
|
A:LEU146
|
4.6
|
38.5
|
1.0
|
HH22
|
A:ARG368
|
4.6
|
44.3
|
1.0
|
HD12
|
A:LEU146
|
4.6
|
46.2
|
1.0
|
CA
|
A:SER344
|
4.7
|
42.9
|
1.0
|
HG3
|
A:ARG368
|
4.7
|
49.7
|
1.0
|
HD22
|
A:LEU146
|
4.7
|
50.4
|
1.0
|
HA
|
A:ILE348
|
4.7
|
38.8
|
1.0
|
OG
|
A:SER344
|
4.8
|
47.9
|
1.0
|
CG
|
A:LEU146
|
4.8
|
41.7
|
1.0
|
HB3
|
A:SER344
|
4.8
|
49.6
|
1.0
|
HG
|
A:SER344
|
4.9
|
57.5
|
1.0
|
NH1
|
A:ARG368
|
5.0
|
44.6
|
1.0
|
O
|
A:HOH745
|
5.0
|
40.1
|
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 From Shigella Flexneri Front Microbiol V. 9 1468 2018.
ISSN: ESSN 1664-302X
DOI: 10.3389/FMICB.2018.01468
Page generated: Mon Sep 30 11:04:55 2024
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