Magnesium in PDB 8b37: Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate
Enzymatic activity of Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate
All present enzymatic activity of Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate:
7.1.3.1;
Protein crystallography data
The structure of Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate, PDB code: 8b37
was solved by
J.Strauss,
C.Wilkinson,
K.Vidilaseris,
O.Ribeiro,
J.Liu,
J.Hillier,
A.Malinen,
B.Gehl,
L.C.Jeuken,
A.R.Pearson,
A.Goldman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.97 /
3.84
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
107.19,
88.02,
116.75,
90,
106.95,
90
|
R / Rfree (%)
|
28.9 /
31.1
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate
(pdb code 8b37). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the
Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate, PDB code: 8b37:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 10 in 8b37
Go back to
Magnesium Binding Sites List in 8b37
Magnesium binding site 1 out
of 10 in the Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate
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 Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg801
b:83.7
occ:1.00
|
O5
|
A:2PN806
|
1.9
|
99.0
|
1.0
|
O
|
A:HOH903
|
2.2
|
86.7
|
1.0
|
OD1
|
A:ASP194
|
2.8
|
91.5
|
1.0
|
OD2
|
A:ASP198
|
2.8
|
91.1
|
1.0
|
MG
|
A:MG803
|
2.9
|
87.1
|
1.0
|
P2
|
A:2PN806
|
3.1
|
100.0
|
1.0
|
O6
|
A:2PN806
|
3.3
|
100.1
|
1.0
|
OD2
|
A:ASP194
|
3.3
|
89.7
|
1.0
|
OE1
|
A:GLU209
|
3.4
|
106.6
|
1.0
|
CG
|
A:ASP194
|
3.5
|
91.2
|
1.0
|
OD2
|
A:ASP676
|
3.6
|
90.6
|
1.0
|
CG
|
A:ASP198
|
3.8
|
91.6
|
1.0
|
OD1
|
A:ASP198
|
3.9
|
93.4
|
1.0
|
O
|
A:HOH904
|
4.0
|
93.8
|
1.0
|
O4
|
A:2PN806
|
4.0
|
100.1
|
1.0
|
OD2
|
A:ASP672
|
4.1
|
89.6
|
1.0
|
O3
|
A:2PN806
|
4.3
|
97.0
|
1.0
|
N1
|
A:2PN806
|
4.3
|
99.2
|
1.0
|
NZ
|
A:LYS651
|
4.5
|
89.1
|
1.0
|
OD2
|
A:ASP220
|
4.6
|
97.6
|
1.0
|
CD
|
A:GLU209
|
4.6
|
108.2
|
1.0
|
CG
|
A:ASP676
|
4.6
|
89.4
|
1.0
|
OD1
|
A:ASP672
|
4.7
|
87.1
|
1.0
|
CG
|
A:ASP672
|
4.8
|
88.3
|
1.0
|
CB
|
A:ASP194
|
4.9
|
89.4
|
1.0
|
|
Magnesium binding site 2 out
of 10 in 8b37
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Magnesium Binding Sites List in 8b37
Magnesium binding site 2 out
of 10 in the Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate
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 Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg802
b:103.5
occ:1.00
|
O4
|
A:2PN806
|
1.8
|
100.1
|
1.0
|
O
|
A:HOH904
|
2.0
|
93.8
|
1.0
|
OD1
|
A:ASP446
|
2.1
|
105.5
|
1.0
|
O
|
A:HOH901
|
2.3
|
95.7
|
1.0
|
CG
|
A:ASP446
|
2.9
|
107.7
|
1.0
|
OD2
|
A:ASP446
|
2.9
|
107.6
|
1.0
|
MG
|
A:MG804
|
2.9
|
101.0
|
1.0
|
P2
|
A:2PN806
|
3.2
|
100.0
|
1.0
|
O6
|
A:2PN806
|
3.6
|
100.1
|
1.0
|
OD1
|
A:ASP220
|
3.8
|
108.2
|
1.0
|
OD2
|
A:ASP224
|
3.8
|
102.0
|
1.0
|
O5
|
A:2PN806
|
3.9
|
99.0
|
1.0
|
OD2
|
A:ASP210
|
4.1
|
116.7
|
1.0
|
OD1
|
A:ASN221
|
4.1
|
104.9
|
1.0
|
O
|
A:HOH903
|
4.1
|
86.7
|
1.0
|
CB
|
A:ASP446
|
4.3
|
106.3
|
1.0
|
OD1
|
A:ASP210
|
4.4
|
116.5
|
1.0
|
N1
|
A:2PN806
|
4.4
|
99.2
|
1.0
|
O
|
A:ASP446
|
4.4
|
112.4
|
1.0
|
CG
|
A:ASP224
|
4.6
|
104.7
|
1.0
|
OD1
|
A:ASP224
|
4.6
|
105.9
|
1.0
|
HA
|
A:ASP446
|
4.6
|
121.9
|
1.0
|
CG
|
A:ASP220
|
4.6
|
105.4
|
1.0
|
CG
|
A:ASP210
|
4.7
|
117.2
|
1.0
|
OE1
|
A:GLU209
|
4.7
|
106.6
|
1.0
|
O2
|
A:2PN806
|
4.8
|
97.3
|
1.0
|
C
|
A:ASP446
|
4.9
|
111.4
|
1.0
|
CA
|
A:ASP446
|
4.9
|
107.7
|
1.0
|
OD2
|
A:ASP220
|
4.9
|
97.6
|
1.0
|
OD1
|
A:ASP469
|
5.0
|
106.5
|
1.0
|
|
Magnesium binding site 3 out
of 10 in 8b37
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Magnesium Binding Sites List in 8b37
Magnesium binding site 3 out
of 10 in the Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate
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 Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg803
b:87.1
occ:1.00
|
O3
|
A:2PN806
|
1.9
|
97.0
|
1.0
|
OD2
|
A:ASP194
|
2.3
|
89.7
|
1.0
|
O5
|
A:2PN806
|
2.3
|
99.0
|
1.0
|
OD2
|
A:ASP676
|
2.3
|
90.6
|
1.0
|
OD1
|
A:ASP676
|
2.5
|
89.2
|
1.0
|
CG
|
A:ASP676
|
2.6
|
89.4
|
1.0
|
MG
|
A:MG801
|
2.9
|
83.7
|
1.0
|
P1
|
A:2PN806
|
3.1
|
99.2
|
1.0
|
N1
|
A:2PN806
|
3.3
|
99.2
|
1.0
|
P2
|
A:2PN806
|
3.4
|
100.0
|
1.0
|
CG
|
A:ASP194
|
3.4
|
91.2
|
1.0
|
NZ
|
A:LYS191
|
3.5
|
89.1
|
1.0
|
OD1
|
A:ASP194
|
3.8
|
91.5
|
1.0
|
CB
|
A:ASP676
|
3.9
|
88.6
|
1.0
|
OD1
|
A:ASP672
|
4.0
|
87.1
|
1.0
|
O1
|
A:2PN806
|
4.1
|
97.5
|
1.0
|
O2
|
A:2PN806
|
4.1
|
97.3
|
1.0
|
O6
|
A:2PN806
|
4.2
|
100.1
|
1.0
|
O4
|
A:2PN806
|
4.5
|
100.1
|
1.0
|
CB
|
A:ASP194
|
4.7
|
89.4
|
1.0
|
CA
|
A:ASP676
|
4.7
|
87.8
|
1.0
|
MG
|
A:MG804
|
4.7
|
101.0
|
1.0
|
OD2
|
A:ASP198
|
4.8
|
91.1
|
1.0
|
OD2
|
A:ASP648
|
4.8
|
96.5
|
1.0
|
O
|
A:HOH903
|
4.8
|
86.7
|
1.0
|
HB3
|
A:ASP194
|
4.8
|
101.3
|
1.0
|
HB2
|
A:ASP194
|
4.8
|
101.3
|
1.0
|
CE
|
A:LYS191
|
4.9
|
87.7
|
1.0
|
OD2
|
A:ASP672
|
4.9
|
89.6
|
1.0
|
CG
|
A:ASP672
|
4.9
|
88.3
|
1.0
|
NZ
|
A:LYS679
|
4.9
|
84.7
|
1.0
|
|
Magnesium binding site 4 out
of 10 in 8b37
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Magnesium Binding Sites List in 8b37
Magnesium binding site 4 out
of 10 in the Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate
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 Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg804
b:101.0
occ:1.00
|
O4
|
A:2PN806
|
2.1
|
100.1
|
1.0
|
OD2
|
A:ASP446
|
2.2
|
107.6
|
1.0
|
O2
|
A:2PN806
|
2.2
|
97.3
|
1.0
|
OD1
|
A:ASP224
|
2.3
|
105.9
|
1.0
|
MG
|
A:MG802
|
2.9
|
103.5
|
1.0
|
CG
|
A:ASP224
|
3.0
|
104.7
|
1.0
|
P2
|
A:2PN806
|
3.0
|
100.0
|
1.0
|
OD2
|
A:ASP224
|
3.1
|
102.0
|
1.0
|
P1
|
A:2PN806
|
3.2
|
99.2
|
1.0
|
CG
|
A:ASP446
|
3.3
|
107.7
|
1.0
|
N1
|
A:2PN806
|
3.3
|
99.2
|
1.0
|
O5
|
A:2PN806
|
3.4
|
99.0
|
1.0
|
OD1
|
A:ASP220
|
3.4
|
108.2
|
1.0
|
OD1
|
A:ASP446
|
3.7
|
105.5
|
1.0
|
O3
|
A:2PN806
|
3.8
|
97.0
|
1.0
|
O
|
A:HOH904
|
4.2
|
93.8
|
1.0
|
OD2
|
A:ASP220
|
4.2
|
97.6
|
1.0
|
CG
|
A:ASP220
|
4.2
|
105.4
|
1.0
|
CB
|
A:ASP224
|
4.4
|
106.2
|
1.0
|
O6
|
A:2PN806
|
4.4
|
100.1
|
1.0
|
O1
|
A:2PN806
|
4.5
|
97.5
|
1.0
|
CB
|
A:ASP446
|
4.5
|
106.3
|
1.0
|
O
|
A:HOH901
|
4.6
|
95.7
|
1.0
|
HA
|
A:ASP224
|
4.7
|
121.9
|
1.0
|
MG
|
A:MG803
|
4.7
|
87.1
|
1.0
|
OD2
|
A:ASP194
|
4.8
|
89.7
|
1.0
|
|
Magnesium binding site 5 out
of 10 in 8b37
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Magnesium Binding Sites List in 8b37
Magnesium binding site 5 out
of 10 in the Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate
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 Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg805
b:92.0
occ:1.00
|
OD2
|
A:ASP648
|
1.8
|
96.5
|
1.0
|
ND2
|
A:ASN473
|
2.2
|
96.7
|
1.0
|
N1
|
A:2PN806
|
2.4
|
99.2
|
1.0
|
CG
|
A:ASP648
|
2.5
|
96.1
|
1.0
|
OD1
|
A:ASP648
|
2.6
|
97.6
|
1.0
|
CG
|
A:ASN473
|
2.8
|
93.6
|
1.0
|
OD1
|
A:ASN473
|
2.9
|
92.0
|
1.0
|
O6
|
A:2PN806
|
3.4
|
100.1
|
1.0
|
O1
|
A:2PN806
|
3.5
|
97.5
|
1.0
|
OD2
|
A:ASP469
|
3.5
|
107.8
|
1.0
|
P2
|
A:2PN806
|
3.5
|
100.0
|
1.0
|
P1
|
A:2PN806
|
3.5
|
99.2
|
1.0
|
CB
|
A:ASP648
|
4.0
|
95.5
|
1.0
|
CB
|
A:ASN473
|
4.1
|
94.3
|
1.0
|
HB3
|
A:ASP648
|
4.2
|
99.0
|
1.0
|
CG
|
A:ASP469
|
4.3
|
107.6
|
1.0
|
HB2
|
A:ASP648
|
4.3
|
99.0
|
1.0
|
OD1
|
A:ASP469
|
4.4
|
106.5
|
1.0
|
O4
|
A:2PN806
|
4.4
|
100.1
|
1.0
|
O3
|
A:2PN806
|
4.5
|
97.0
|
1.0
|
O2
|
A:2PN806
|
4.6
|
97.3
|
1.0
|
NZ
|
A:LYS476
|
4.6
|
94.4
|
1.0
|
O5
|
A:2PN806
|
4.6
|
99.0
|
1.0
|
O
|
A:ASP469
|
4.9
|
108.0
|
1.0
|
HA
|
A:SER470
|
4.9
|
114.6
|
1.0
|
HA
|
A:ASN473
|
5.0
|
96.5
|
1.0
|
|
Magnesium binding site 6 out
of 10 in 8b37
Go back to
Magnesium Binding Sites List in 8b37
Magnesium binding site 6 out
of 10 in the Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate
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 Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg801
b:88.6
occ:1.00
|
O4
|
B:2PN806
|
1.9
|
108.6
|
1.0
|
OE1
|
B:GLU209
|
2.5
|
113.2
|
1.0
|
O
|
B:HOH902
|
2.6
|
94.8
|
1.0
|
OD1
|
B:ASP194
|
2.7
|
100.2
|
1.0
|
OD2
|
B:ASP198
|
2.8
|
100.7
|
1.0
|
MG
|
B:MG803
|
2.9
|
95.3
|
1.0
|
P2
|
B:2PN806
|
3.2
|
109.7
|
1.0
|
OD2
|
B:ASP194
|
3.3
|
98.2
|
1.0
|
CG
|
B:ASP194
|
3.4
|
100.1
|
1.0
|
O5
|
B:2PN806
|
3.4
|
108.8
|
1.0
|
CD
|
B:GLU209
|
3.6
|
113.7
|
1.0
|
CG
|
B:ASP198
|
3.6
|
101.6
|
1.0
|
OD1
|
B:ASP198
|
3.7
|
103.7
|
1.0
|
O6
|
B:2PN806
|
3.9
|
111.2
|
1.0
|
OD2
|
B:ASP676
|
3.9
|
95.0
|
1.0
|
OE2
|
B:GLU209
|
4.0
|
112.6
|
1.0
|
OD2
|
B:ASP220
|
4.0
|
103.2
|
1.0
|
OD2
|
B:ASP672
|
4.2
|
98.0
|
1.0
|
O3
|
B:2PN806
|
4.5
|
107.3
|
1.0
|
N1
|
B:2PN806
|
4.5
|
108.8
|
1.0
|
NZ
|
B:LYS651
|
4.7
|
98.6
|
1.0
|
CB
|
B:ASP194
|
4.8
|
99.3
|
1.0
|
O
|
B:ASP194
|
4.9
|
99.1
|
1.0
|
CG
|
B:GLU209
|
4.9
|
115.4
|
1.0
|
MG
|
B:MG802
|
4.9
|
108.4
|
1.0
|
CG
|
B:ASP676
|
5.0
|
93.7
|
1.0
|
|
Magnesium binding site 7 out
of 10 in 8b37
Go back to
Magnesium Binding Sites List in 8b37
Magnesium binding site 7 out
of 10 in the Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate
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 Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg802
b:108.4
occ:1.00
|
O6
|
B:2PN806
|
1.9
|
111.2
|
1.0
|
OD1
|
B:ASP446
|
1.9
|
107.3
|
1.0
|
O
|
B:HOH903
|
2.3
|
102.2
|
1.0
|
CG
|
B:ASP446
|
2.7
|
109.9
|
1.0
|
OD2
|
B:ASP446
|
2.8
|
110.1
|
1.0
|
MG
|
B:MG804
|
2.9
|
106.6
|
1.0
|
P2
|
B:2PN806
|
3.2
|
109.7
|
1.0
|
O5
|
B:2PN806
|
3.5
|
108.8
|
1.0
|
OD2
|
B:ASP224
|
3.7
|
106.7
|
1.0
|
OD2
|
B:ASP210
|
3.7
|
123.3
|
1.0
|
OD1
|
B:ASP210
|
3.8
|
123.7
|
1.0
|
O
|
B:HOH902
|
3.9
|
94.8
|
1.0
|
O4
|
B:2PN806
|
4.0
|
108.6
|
1.0
|
CB
|
B:ASP446
|
4.1
|
108.8
|
1.0
|
OD1
|
B:ASP220
|
4.1
|
114.1
|
1.0
|
CG
|
B:ASP210
|
4.2
|
124.0
|
1.0
|
O
|
B:ASP446
|
4.3
|
114.5
|
1.0
|
HA
|
B:ASP446
|
4.4
|
121.9
|
1.0
|
N1
|
B:2PN806
|
4.4
|
108.8
|
1.0
|
CG
|
B:ASP224
|
4.5
|
109.6
|
1.0
|
OD1
|
B:ASP224
|
4.6
|
110.5
|
1.0
|
OD1
|
B:ASN221
|
4.6
|
109.4
|
1.0
|
OD1
|
B:ASP469
|
4.6
|
107.3
|
1.0
|
CA
|
B:ASP446
|
4.7
|
110.0
|
1.0
|
C
|
B:ASP446
|
4.7
|
114.0
|
1.0
|
CG
|
B:ASP220
|
4.8
|
111.4
|
1.0
|
O2
|
B:2PN806
|
4.9
|
109.6
|
1.0
|
OD2
|
B:ASP220
|
4.9
|
103.2
|
1.0
|
MG
|
B:MG801
|
4.9
|
88.6
|
1.0
|
|
Magnesium binding site 8 out
of 10 in 8b37
Go back to
Magnesium Binding Sites List in 8b37
Magnesium binding site 8 out
of 10 in the Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate
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 Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg803
b:95.3
occ:1.00
|
O3
|
B:2PN806
|
2.0
|
107.3
|
1.0
|
O4
|
B:2PN806
|
2.1
|
108.6
|
1.0
|
OD2
|
B:ASP194
|
2.4
|
98.2
|
1.0
|
OD2
|
B:ASP676
|
2.4
|
95.0
|
1.0
|
OD1
|
B:ASP676
|
2.8
|
93.7
|
1.0
|
CG
|
B:ASP676
|
2.8
|
93.7
|
1.0
|
MG
|
B:MG801
|
2.9
|
88.6
|
1.0
|
P1
|
B:2PN806
|
3.2
|
109.9
|
1.0
|
P2
|
B:2PN806
|
3.2
|
109.7
|
1.0
|
N1
|
B:2PN806
|
3.3
|
108.8
|
1.0
|
CG
|
B:ASP194
|
3.4
|
100.1
|
1.0
|
NZ
|
B:LYS191
|
3.7
|
93.4
|
1.0
|
OD1
|
B:ASP194
|
3.7
|
100.2
|
1.0
|
O5
|
B:2PN806
|
4.1
|
108.8
|
1.0
|
O2
|
B:2PN806
|
4.1
|
109.6
|
1.0
|
CB
|
B:ASP676
|
4.1
|
92.6
|
1.0
|
OD1
|
B:ASP672
|
4.2
|
96.0
|
1.0
|
O1
|
B:2PN806
|
4.2
|
108.0
|
1.0
|
O6
|
B:2PN806
|
4.3
|
111.2
|
1.0
|
OD2
|
B:ASP672
|
4.4
|
98.0
|
1.0
|
OD2
|
B:ASP648
|
4.6
|
100.2
|
1.0
|
OD2
|
B:ASP198
|
4.7
|
100.7
|
1.0
|
CB
|
B:ASP194
|
4.7
|
99.3
|
1.0
|
CG
|
B:ASP672
|
4.7
|
96.5
|
1.0
|
HB3
|
B:ASP194
|
4.9
|
101.3
|
1.0
|
MG
|
B:MG805
|
4.9
|
101.2
|
1.0
|
HB2
|
B:ASP194
|
4.9
|
101.3
|
1.0
|
NZ
|
B:LYS679
|
4.9
|
94.5
|
1.0
|
MG
|
B:MG804
|
5.0
|
106.6
|
1.0
|
|
Magnesium binding site 9 out
of 10 in 8b37
Go back to
Magnesium Binding Sites List in 8b37
Magnesium binding site 9 out
of 10 in the Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate
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 Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg804
b:106.6
occ:1.00
|
OD2
|
B:ASP446
|
1.9
|
110.1
|
1.0
|
OD1
|
B:ASP224
|
1.9
|
110.5
|
1.0
|
O6
|
B:2PN806
|
2.1
|
111.2
|
1.0
|
CG
|
B:ASP224
|
2.5
|
109.6
|
1.0
|
O2
|
B:2PN806
|
2.5
|
109.6
|
1.0
|
OD2
|
B:ASP224
|
2.6
|
106.7
|
1.0
|
MG
|
B:MG802
|
2.9
|
108.4
|
1.0
|
CG
|
B:ASP446
|
3.0
|
109.9
|
1.0
|
P2
|
B:2PN806
|
3.3
|
109.7
|
1.0
|
OD1
|
B:ASP220
|
3.3
|
114.1
|
1.0
|
OD1
|
B:ASP446
|
3.5
|
107.3
|
1.0
|
P1
|
B:2PN806
|
3.6
|
109.9
|
1.0
|
N1
|
B:2PN806
|
3.7
|
108.8
|
1.0
|
O4
|
B:2PN806
|
3.7
|
108.6
|
1.0
|
CB
|
B:ASP224
|
3.8
|
112.1
|
1.0
|
O3
|
B:2PN806
|
4.1
|
107.3
|
1.0
|
CB
|
B:ASP446
|
4.2
|
108.8
|
1.0
|
HA
|
B:ASP224
|
4.3
|
121.9
|
1.0
|
CG
|
B:ASP220
|
4.3
|
111.4
|
1.0
|
O
|
B:HOH903
|
4.4
|
102.2
|
1.0
|
OD2
|
B:ASP220
|
4.5
|
103.2
|
1.0
|
O5
|
B:2PN806
|
4.5
|
108.8
|
1.0
|
CA
|
B:ASP224
|
4.6
|
111.2
|
1.0
|
HA
|
B:ASN221
|
4.7
|
124.1
|
1.0
|
OD2
|
B:ASP194
|
4.8
|
98.2
|
1.0
|
O
|
B:HOH902
|
4.8
|
94.8
|
1.0
|
O1
|
B:2PN806
|
4.8
|
108.0
|
1.0
|
H
|
B:ASP224
|
4.9
|
129.7
|
1.0
|
MG
|
B:MG803
|
5.0
|
95.3
|
1.0
|
|
Magnesium binding site 10 out
of 10 in 8b37
Go back to
Magnesium Binding Sites List in 8b37
Magnesium binding site 10 out
of 10 in the Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Crystal Structure of Pyrobaculum Aerophilum Potassium-Independent Proton Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sulphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg805
b:101.2
occ:1.00
|
N1
|
B:2PN806
|
2.0
|
108.8
|
1.0
|
OD2
|
B:ASP648
|
2.0
|
100.2
|
1.0
|
OD1
|
B:ASN473
|
2.4
|
96.4
|
1.0
|
O1
|
B:2PN806
|
2.4
|
108.0
|
1.0
|
P1
|
B:2PN806
|
2.7
|
109.9
|
1.0
|
CG
|
B:ASN473
|
2.8
|
97.1
|
1.0
|
ND2
|
B:ASN473
|
2.9
|
99.5
|
1.0
|
CG
|
B:ASP648
|
3.2
|
98.7
|
1.0
|
P2
|
B:2PN806
|
3.6
|
109.7
|
1.0
|
NZ
|
B:LYS476
|
3.6
|
104.7
|
1.0
|
O2
|
B:2PN806
|
3.6
|
109.6
|
1.0
|
OD1
|
B:ASP648
|
3.7
|
99.8
|
1.0
|
O3
|
B:2PN806
|
3.9
|
107.3
|
1.0
|
O5
|
B:2PN806
|
4.0
|
108.8
|
1.0
|
CB
|
B:ASN473
|
4.1
|
97.6
|
1.0
|
OD2
|
B:ASP469
|
4.3
|
107.0
|
1.0
|
OD1
|
B:ASP469
|
4.3
|
107.3
|
1.0
|
O6
|
B:2PN806
|
4.3
|
111.2
|
1.0
|
CB
|
B:ASP648
|
4.4
|
97.2
|
1.0
|
HA
|
B:ASN473
|
4.4
|
96.5
|
1.0
|
HB3
|
B:ASP648
|
4.5
|
99.0
|
1.0
|
CE
|
B:LYS476
|
4.5
|
102.6
|
1.0
|
HB2
|
B:ASP648
|
4.6
|
99.0
|
1.0
|
O4
|
B:2PN806
|
4.6
|
108.6
|
1.0
|
CD
|
B:LYS476
|
4.6
|
101.1
|
1.0
|
CG
|
B:ASP469
|
4.7
|
107.5
|
1.0
|
CA
|
B:ASN473
|
4.8
|
100.2
|
1.0
|
O
|
B:ASP469
|
4.8
|
107.7
|
1.0
|
NZ
|
B:LYS679
|
4.9
|
94.5
|
1.0
|
MG
|
B:MG803
|
4.9
|
95.3
|
1.0
|
|
Reference:
J.Strauss,
C.Wilkinson,
K.Vidilaseris,
O.M.De Castro Ribeiro,
J.Liu,
J.Hillier,
M.Wichert,
A.M.Malinen,
B.Gehl,
L.J.Jeuken,
A.R.Pearson,
A.Goldman.
Functional and Structural Asymmetry Suggest A Unifying Principle For Catalysis in Membrane-Bound Pyrophosphatases. Embo Rep. 2024.
ISSN: ESSN 1469-3178
PubMed: 38182815
DOI: 10.1038/S44319-023-00037-X
Page generated: Thu Oct 3 19:08:20 2024
|