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Sodium in PDB 5lzq: Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion

Enzymatic activity of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion

All present enzymatic activity of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion:
3.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion, PDB code: 5lzq was solved by C.Wilkinson, J.Kellosalo, T.Kajander, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.75 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.421, 106.763, 161.913, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 27.3

Other elements in 5lzq:

The structure of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion (pdb code 5lzq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion, PDB code: 5lzq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5lzq

Go back to Sodium Binding Sites List in 5lzq
Sodium binding site 1 out of 2 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na807

b:0.7
occ:1.00
 OE1 A:GLU246 2.4 0.7 1.0
OG A:SER247 2.4 0.5 1.0
OD1 A:ASP243 2.5 0.3 1.0
OD1 A:ASP703 2.5 0.1 1.0
O A:ASP243 2.8 0.6 1.0
CG A:ASP703 3.4 0.2 1.0
NZ A:LYS707 3.4 0.1 1.0
CD A:GLU246 3.6 0.1 1.0
OD2 A:ASP703 3.6 99.0 1.0
CB A:SER247 3.6 0.4 1.0
C A:ASP243 3.6 0.3 1.0
N A:SER247 3.7 0.5 1.0
CG A:ASP243 3.7 0.4 1.0
CE A:LYS707 3.7 0.7 1.0
CG1 A:ILE704 3.8 97.2 1.0
CD1 A:ILE704 3.8 0.4 1.0
CA A:SER247 3.9 0.7 1.0
CA A:ASP243 4.1 0.2 1.0
O A:ASP703 4.1 85.0 1.0
C A:GLU246 4.2 0.5 1.0
CB A:GLU246 4.3 0.4 1.0
C A:ASP703 4.3 94.5 1.0
CA A:ILE704 4.4 0.6 1.0
N A:ILE704 4.4 0.5 1.0
OE2 A:GLU246 4.4 0.9 1.0
CB A:ASP243 4.5 0.3 1.0
OD2 A:ASP243 4.6 0.7 1.0
CG A:GLU246 4.6 0.6 1.0
N A:LEU244 4.7 0.6 1.0
O A:GLU246 4.7 0.2 1.0
CB A:ILE704 4.7 0.3 1.0
CB A:ASP703 4.8 97.1 1.0
CA A:GLU246 4.8 0.6 1.0

Sodium binding site 2 out of 2 in 5lzq

Go back to Sodium Binding Sites List in 5lzq
Sodium binding site 2 out of 2 in the Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Thermotoga Maritima Sodium Pumping Membrane Integral Pyrophosphatase in Complex with Imidodiphosphate and Magnesium, and with Bound Sodium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na807

b:0.8
occ:1.00
 OG B:SER247 2.4 0.9 1.0
OE1 B:GLU246 2.4 0.3 1.0
OD1 B:ASP243 2.5 0.3 1.0
OD1 B:ASP703 2.6 0.2 1.0
O B:ASP243 2.8 0.2 1.0
NZ B:LYS707 3.3 0.3 1.0
CG B:ASP703 3.5 0.6 1.0
CE B:LYS707 3.6 0.7 1.0
C B:ASP243 3.6 0.1 1.0
CB B:SER247 3.6 0.3 1.0
CD B:GLU246 3.6 0.1 1.0
N B:SER247 3.7 0.8 1.0
OD2 B:ASP703 3.7 0.2 1.0
CG B:ASP243 3.7 0.7 1.0
CG1 B:ILE704 3.7 0.0 1.0
CD1 B:ILE704 3.8 0.3 1.0
CA B:SER247 3.9 0.3 1.0
CA B:ASP243 4.0 0.5 1.0
O B:ASP703 4.2 0.4 1.0
C B:GLU246 4.2 0.4 1.0
CB B:GLU246 4.3 0.2 1.0
CA B:ILE704 4.3 0.6 1.0
N B:ILE704 4.4 0.3 1.0
C B:ASP703 4.4 0.2 1.0
OE2 B:GLU246 4.4 0.9 1.0
CB B:ASP243 4.5 0.5 1.0
OD2 B:ASP243 4.6 0.6 1.0
CG B:GLU246 4.6 0.6 1.0
N B:LEU244 4.6 0.1 1.0
CB B:ILE704 4.7 0.3 1.0
O B:GLU246 4.7 0.6 1.0
CA B:GLU246 4.8 0.2 1.0
CB B:ASP703 4.9 0.2 1.0

Reference:

K.M.Li, C.Wilkinson, J.Kellosalo, J.Y.Tsai, T.Kajander, L.J.Jeuken, Y.J.Sun, A.Goldman. Membrane Pyrophosphatases From Thermotoga Maritima and Vigna Radiata Suggest A Conserved Coupling Mechanism. Nat Commun V. 7 13596 2016.
ISSN: ESSN 2041-1723
PubMed: 27922000
DOI: 10.1038/NCOMMS13596
Page generated: Tue Dec 15 11:14:49 2020

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