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Magnesium in PDB 4av3: Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase with Metal Ions in Active Site

Enzymatic activity of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase with Metal Ions in Active Site

All present enzymatic activity of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase with Metal Ions in Active Site:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase with Metal Ions in Active Site, PDB code: 4av3 was solved by T.Kajander, K.Kogan, J.Kellosalo, K.Pokharel, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.520, 107.779, 102.521, 90.00, 108.50, 90.00
R / Rfree (%) 20.5 / 24.5

Other elements in 4av3:

The structure of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase with Metal Ions in Active Site also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase with Metal Ions in Active Site (pdb code 4av3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase with Metal Ions in Active Site, PDB code: 4av3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4av3

Go back to Magnesium Binding Sites List in 4av3
Magnesium binding site 1 out of 2 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase with Metal Ions in Active Site


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 with Metal Ions in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg727

b:0.5
occ:1.00
 OD1 A:ASP465 2.3 0.0 1.0
OD2 A:ASP232 2.3 0.7 1.0
ND2 A:ASN229 2.8 99.5 1.0
CG A:ASP465 3.2 0.2 1.0
OD2 A:ASP465 3.4 0.8 1.0
CG A:ASP232 3.6 0.1 1.0
CG A:ASN229 3.9 0.1 1.0
CA A:ASN229 4.2 95.1 1.0
OD1 A:ASP232 4.4 0.2 1.0
CB A:ASP232 4.5 96.2 1.0
CB A:ASN229 4.5 99.0 1.0
ND2 A:ASN466 4.5 0.2 1.0
O A:ASP465 4.6 0.8 1.0
CB A:ASP465 4.6 96.7 1.0
O A:ASP228 4.6 90.9 1.0
N A:ASN229 4.7 95.3 1.0
OD1 A:ASN229 4.8 0.9 1.0
C A:ASP465 4.8 0.8 1.0
C A:ASP228 4.9 97.7 1.0

Magnesium binding site 2 out of 2 in 4av3

Go back to Magnesium Binding Sites List in 4av3
Magnesium binding site 2 out of 2 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase with Metal Ions in Active Site


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 with Metal Ions in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg727

b:96.0
occ:1.00
 OD1 B:ASP465 2.3 98.7 1.0
OD2 B:ASP232 2.5 0.4 1.0
ND2 B:ASN229 2.9 0.8 1.0
CG B:ASP465 3.1 96.5 1.0
OD2 B:ASP465 3.3 94.1 1.0
CG B:ASP232 3.7 0.7 1.0
CG B:ASN229 4.1 0.7 1.0
CA B:ASN229 4.4 99.8 1.0
ND2 B:ASN466 4.5 0.9 1.0
O B:ASP465 4.5 0.9 1.0
OD1 B:ASP232 4.5 0.1 1.0
CB B:ASP465 4.6 94.4 1.0
CB B:ASP232 4.7 97.4 1.0
CB B:ASN229 4.7 0.5 1.0
C B:ASP465 4.8 0.5 1.0
O B:ASP228 4.9 97.8 1.0
N B:ASN229 4.9 99.0 1.0
OD1 B:ASN229 5.0 0.3 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 14:45:29 2024

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