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Magnesium in PDB 4av6: Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium

Enzymatic activity of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium

All present enzymatic activity of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium, PDB code: 4av6 was solved by T.Kajander, J.Kellosalo, K.Kogan, K.Pokharel, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.832 / 4.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.800, 112.266, 109.714, 90.00, 103.00, 90.00
R / Rfree (%) 29.52 / 36.5

Other elements in 4av6:

The structure of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium also contains other interesting chemical elements:

Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium (pdb code 4av6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium, PDB code: 4av6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4av6

Go back to Magnesium Binding Sites List in 4av6
Magnesium binding site 1 out of 8 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium


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 Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1729

b:0.4
occ:1.00
 OD1 A:ASP202 2.3 0.9 1.0
OD2 A:ASP202 2.7 0.6 1.0
O3 A:PO41727 2.7 0.3 1.0
CG A:ASP202 2.8 0.5 1.0
O2 A:PO41727 2.8 0.5 1.0
OD2 A:ASP228 2.8 0.8 1.0
OD2 A:ASP206 3.0 0.6 1.0
P A:PO41727 3.3 0.6 1.0
OD2 A:ASP688 3.9 0.7 1.0
CG A:ASP206 4.0 0.9 1.0
MG A:MG1731 4.0 0.7 1.0
CG A:ASP228 4.0 0.8 1.0
CB A:ASP202 4.2 0.8 1.0
OD1 A:ASP206 4.2 1.0 1.0
OD2 A:ASP692 4.2 0.7 1.0
O4 A:PO41727 4.3 0.6 1.0
MG A:MG1730 4.3 0.7 1.0
O1 A:PO41727 4.4 0.7 1.0
OD1 A:ASP228 4.6 0.2 1.0
CA A:ASP202 4.7 0.1 1.0
O A:ASP202 4.7 0.8 1.0
NZ A:LYS663 4.9 0.6 1.0

Magnesium binding site 2 out of 8 in 4av6

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Magnesium binding site 2 out of 8 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium


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 Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1730

b:0.7
occ:1.00
 OD2 A:ASP232 2.7 0.3 1.0
O1 A:PO41727 2.7 0.7 1.0
OD1 A:ASP465 3.3 0.9 1.0
P A:PO41727 3.4 0.6 1.0
O3 A:PO41727 3.5 0.3 1.0
MG A:MG1732 3.5 0.5 1.0
O2 A:PO41727 3.5 0.5 1.0
CG A:ASP232 3.7 0.9 1.0
OD2 A:ASP228 3.8 0.8 1.0
OD1 A:ASP232 4.2 0.3 1.0
ND2 A:ASN229 4.2 0.1 1.0
CG A:ASP228 4.2 0.8 1.0
MG A:MG1729 4.3 0.4 1.0
CG A:ASP465 4.3 0.4 1.0
CG A:ASN229 4.5 0.9 1.0
OD2 A:ASP465 4.6 0.0 1.0
CA A:ASN229 4.6 0.5 1.0
O A:ASP228 4.7 0.4 1.0
CB A:ASP228 4.7 0.4 1.0
OD1 A:ASP228 4.8 0.2 1.0
OD1 A:ASN229 4.8 0.9 1.0
N A:ASN229 4.8 0.2 1.0
C A:ASP228 4.8 0.2 1.0
O4 A:PO41727 4.8 0.6 1.0
CB A:ASP232 5.0 0.9 1.0

Magnesium binding site 3 out of 8 in 4av6

Go back to Magnesium Binding Sites List in 4av6
Magnesium binding site 3 out of 8 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium


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 Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1731

b:0.7
occ:1.00
 OD1 A:ASP692 2.5 0.7 1.0
OD2 A:ASP202 2.6 0.6 1.0
OD2 A:ASP692 2.8 0.7 1.0
O2 A:PO41728 2.8 0.3 1.0
O3 A:PO41727 2.9 0.3 1.0
OD2 A:ASP660 3.0 0.2 1.0
CG A:ASP692 3.0 0.8 1.0
O3 A:PO41728 3.1 0.8 1.0
OD1 A:ASP688 3.4 0.7 1.0
P A:PO41728 3.6 0.1 1.0
NZ A:LYS695 3.6 0.6 1.0
O4 A:PO41727 3.6 0.6 1.0
OD2 A:ASP688 3.7 0.7 1.0
NZ A:LYS199 3.8 0.5 1.0
CG A:ASP202 3.8 0.5 1.0
P A:PO41727 3.9 0.6 1.0
CG A:ASP688 3.9 0.2 1.0
MG A:MG1729 4.0 0.4 1.0
CG A:ASP660 4.2 0.4 1.0
ND2 A:ASN492 4.2 0.5 1.0
CE A:LYS199 4.3 0.7 1.0
CE A:LYS695 4.4 0.8 1.0
MG A:MG1732 4.4 0.5 1.0
OD1 A:ASP202 4.5 0.9 1.0
CB A:ASP692 4.5 0.3 1.0
OD2 A:ASP696 4.5 0.6 1.0
O4 A:PO41728 4.6 0.3 1.0
O1 A:PO41728 4.6 0.3 1.0
O2 A:PO41727 4.7 0.5 1.0
CB A:ASP660 4.7 0.3 1.0
CB A:ASP202 4.8 0.8 1.0
O A:ASP688 4.9 0.2 1.0

Magnesium binding site 4 out of 8 in 4av6

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Magnesium binding site 4 out of 8 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium


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 Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1732

b:0.5
occ:1.00
 OD1 A:ASP232 2.0 0.3 1.0
CG A:ASP232 2.4 0.9 1.0
OD2 A:ASP232 2.4 0.3 1.0
O3 A:PO41727 2.6 0.3 1.0
O1 A:PO41727 2.7 0.7 1.0
O1 A:PO41728 2.9 0.3 1.0
OD1 A:ASP465 3.0 0.9 1.0
P A:PO41727 3.1 0.6 1.0
CG A:ASP465 3.3 0.4 1.0
OD2 A:ASP465 3.3 0.0 1.0
MG A:MG1730 3.5 0.7 1.0
CB A:ASP232 3.7 0.9 1.0
P A:PO41728 3.7 0.1 1.0
O2 A:PO41728 3.7 0.3 1.0
O3 A:PO41728 3.8 0.8 1.0
O4 A:PO41727 3.8 0.6 1.0
CA A:ASP232 4.4 0.6 1.0
NZ A:LYS199 4.4 0.5 1.0
CB A:ASP465 4.4 0.5 1.0
MG A:MG1731 4.4 0.7 1.0
O2 A:PO41727 4.4 0.5 1.0
OD2 A:ASP202 4.6 0.6 1.0

Magnesium binding site 5 out of 8 in 4av6

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Magnesium binding site 5 out of 8 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium


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 Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1729

b:0.1
occ:1.00
 OD2 B:ASP206 2.3 1.0 1.0
O2 B:PO41727 2.7 0.4 1.0
OD1 B:ASP202 2.7 0.4 1.0
CG B:ASP206 3.1 0.9 1.0
OD1 B:ASP206 3.2 1.0 1.0
O3 B:PO41727 3.3 0.2 1.0
OD2 B:ASP688 3.4 0.4 1.0
OD2 B:ASP202 3.5 0.1 1.0
CG B:ASP202 3.5 0.5 1.0
P B:PO41727 3.6 0.3 1.0
OD2 B:ASP228 3.7 0.5 1.0
CE B:LYS663 4.1 0.9 1.0
NZ B:LYS663 4.1 1.0 1.0
CB B:ASP206 4.5 0.0 1.0
O4 B:PO41727 4.6 0.0 1.0
O1 B:PO41727 4.6 0.8 1.0
MG B:MG1731 4.7 0.8 1.0
CG B:ASP688 4.7 0.1 1.0
OD2 B:ASP692 4.7 0.9 1.0
MG B:MG1730 4.8 0.9 1.0
CG B:ASP228 4.9 0.8 1.0
O B:ASP202 4.9 0.7 1.0
CB B:ASP202 5.0 0.4 1.0

Magnesium binding site 6 out of 8 in 4av6

Go back to Magnesium Binding Sites List in 4av6
Magnesium binding site 6 out of 8 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium


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 Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1730

b:0.9
occ:1.00
 O1 B:PO41727 2.9 0.8 1.0
O2 B:PO41727 3.4 0.4 1.0
P B:PO41727 3.7 0.3 1.0
CA B:GLY469 4.3 0.2 1.0
O3 B:PO41727 4.4 0.2 1.0
OD2 B:ASP232 4.5 0.7 1.0
OD2 B:ASP228 4.5 0.5 1.0
OD1 B:ASP465 4.6 0.7 1.0
N B:GLY469 4.7 0.2 1.0
OD2 B:ASP488 4.7 0.8 1.0
MG B:MG1729 4.8 0.1 1.0
NZ B:LYS664 4.9 0.7 1.0
OD1 B:ASN229 4.9 0.7 1.0
O4 B:PO41727 5.0 0.0 1.0

Magnesium binding site 7 out of 8 in 4av6

Go back to Magnesium Binding Sites List in 4av6
Magnesium binding site 7 out of 8 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium


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 Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1731

b:0.8
occ:1.00
 OD1 B:ASP692 2.5 0.6 1.0
OD2 B:ASP692 2.7 0.9 1.0
OD2 B:ASP202 2.7 0.1 1.0
OD2 B:ASP660 2.8 0.8 1.0
OD1 B:ASP688 2.9 0.9 1.0
CG B:ASP692 2.9 0.3 1.0
O3 B:PO41727 3.0 0.2 1.0
O3 B:PO41728 3.2 0.4 1.0
NZ B:LYS695 3.3 1.0 1.0
O4 B:PO41727 3.3 0.0 1.0
OD2 B:ASP688 3.4 0.4 1.0
CG B:ASP688 3.5 0.1 1.0
P B:PO41727 3.7 0.3 1.0
O2 B:PO41728 3.7 0.9 1.0
NZ B:LYS199 3.9 0.6 1.0
CG B:ASP202 3.9 0.5 1.0
CG B:ASP660 3.9 0.9 1.0
P B:PO41728 4.1 0.2 1.0
ND2 B:ASN492 4.2 0.9 1.0
CE B:LYS695 4.3 0.0 1.0
MG B:MG1732 4.4 0.7 1.0
CB B:ASP660 4.4 0.8 1.0
O2 B:PO41727 4.4 0.4 1.0
CB B:ASP692 4.4 0.9 1.0
CE B:LYS199 4.5 0.3 1.0
O B:ASP688 4.6 0.6 1.0
OD1 B:ASP202 4.6 0.4 1.0
MG B:MG1729 4.7 0.1 1.0
OD2 B:ASP696 4.7 0.6 1.0
O4 B:PO41728 4.8 0.1 1.0
CB B:ASP202 4.9 0.4 1.0
CB B:ASP688 5.0 0.9 1.0
OD1 B:ASP660 5.0 0.2 1.0

Magnesium binding site 8 out of 8 in 4av6

Go back to Magnesium Binding Sites List in 4av6
Magnesium binding site 8 out of 8 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium


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 Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase at 4 A in Complex with Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1732

b:0.7
occ:1.00
 OD1 B:ASP232 2.1 0.9 1.0
O1 B:PO41727 2.6 0.8 1.0
CG B:ASP232 2.6 0.8 1.0
O3 B:PO41727 2.7 0.2 1.0
OD2 B:ASP232 2.8 0.7 1.0
O2 B:PO41728 2.8 0.9 1.0
O1 B:PO41728 2.9 0.9 1.0
P B:PO41727 2.9 0.3 1.0
OD2 B:ASP465 3.0 0.4 1.0
OD1 B:ASP465 3.0 0.7 1.0
P B:PO41728 3.1 0.2 1.0
O3 B:PO41728 3.1 0.4 1.0
O4 B:PO41727 3.2 0.0 1.0
CG B:ASP465 3.3 0.4 1.0
CB B:ASP232 3.9 0.8 1.0
NZ B:LYS199 4.4 0.6 1.0
MG B:MG1731 4.4 0.8 1.0
O2 B:PO41727 4.4 0.4 1.0
OD2 B:ASP202 4.5 0.1 1.0
CB B:ASP465 4.6 1.0 1.0
CA B:ASP232 4.6 0.9 1.0
O4 B:PO41728 4.6 0.1 1.0
OD1 B:ASP488 4.7 0.5 1.0
ND2 B:ASN492 4.9 0.9 1.0

Reference:

J.Kellosalo, T.Kajander, K.Kogan, K.Pokharel, A.Goldman. The Structure and Catalytic Cycle of A Sodium-Pumping Pyrophosphatase. Science V. 337 473 2012.
ISSN: ISSN 0036-8075
PubMed: 22837527
DOI: 10.1126/SCIENCE.1222505
Page generated: Thu Aug 15 14:45:40 2024

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