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Sodium in PDB 1zh8: Crystal Structure of Oxidoreductase (TM0312) From Thermotoga Maritima at 2.50 A Resolution

Protein crystallography data

The structure of Crystal Structure of Oxidoreductase (TM0312) From Thermotoga Maritima at 2.50 A Resolution, PDB code: 1zh8 was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.849, 63.088, 101.172, 90.00, 104.88, 90.00
R / Rfree (%) 19.4 / 23.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Oxidoreductase (TM0312) From Thermotoga Maritima at 2.50 A Resolution (pdb code 1zh8). 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 Oxidoreductase (TM0312) From Thermotoga Maritima at 2.50 A Resolution, PDB code: 1zh8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1zh8

Go back to Sodium Binding Sites List in 1zh8
Sodium binding site 1 out of 2 in the Crystal Structure of Oxidoreductase (TM0312) From Thermotoga Maritima at 2.50 A Resolution


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 Oxidoreductase (TM0312) From Thermotoga Maritima at 2.50 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na329

b:40.2
occ:1.00
O A:LEU216 2.1 42.6 1.0
O A:GLY218 2.4 47.3 1.0
OD1 A:ASP211 2.4 43.0 1.0
O A:SER213 2.5 37.6 1.0
OD2 A:ASP220 2.6 42.0 1.0
CG A:ASP211 3.2 47.2 1.0
C A:LEU216 3.3 43.4 1.0
OD2 A:ASP211 3.6 49.2 1.0
C A:GLY218 3.6 44.6 1.0
O A:HOH497 3.6 60.8 1.0
C A:SER213 3.6 38.6 1.0
CG A:ASP220 3.7 35.5 1.0
N A:GLY218 4.0 41.9 1.0
CB A:LEU216 4.0 40.6 1.0
CA A:LEU216 4.0 42.8 1.0
N A:SER213 4.1 37.0 1.0
N A:LEU216 4.1 42.4 1.0
CB A:ASP220 4.2 35.9 1.0
C A:GLY217 4.3 42.8 1.0
CB A:ASP211 4.3 43.8 1.0
CA A:SER213 4.3 39.6 1.0
N A:GLY217 4.3 43.6 1.0
CA A:ASP211 4.4 42.5 1.0
CA A:GLY218 4.4 43.0 1.0
N A:LEU212 4.5 37.9 1.0
C A:ASP211 4.5 40.5 1.0
N A:MSE219 4.6 43.7 0.5
N A:MSE219 4.6 43.7 0.5
CA A:GLY217 4.6 43.0 1.0
C A:MSE219 4.6 41.0 0.5
OD1 A:ASP220 4.6 43.5 1.0
C A:MSE219 4.6 41.1 0.5
CB A:SER213 4.7 39.2 1.0
CA A:MSE219 4.7 42.6 0.5
N A:PRO214 4.7 38.5 1.0
CA A:MSE219 4.7 42.4 0.5
N A:ASP220 4.8 39.1 1.0
O A:GLY217 4.8 40.9 1.0
O A:MSE219 4.9 41.8 0.5
CA A:PRO214 4.9 39.4 1.0
O A:MSE219 5.0 42.0 0.5

Sodium binding site 2 out of 2 in 1zh8

Go back to Sodium Binding Sites List in 1zh8
Sodium binding site 2 out of 2 in the Crystal Structure of Oxidoreductase (TM0312) From Thermotoga Maritima at 2.50 A Resolution


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 Oxidoreductase (TM0312) From Thermotoga Maritima at 2.50 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na329

b:57.2
occ:1.00
OD1 B:ASP211 2.1 40.6 1.0
O B:LEU216 2.4 43.0 1.0
O B:GLY218 2.4 45.6 1.0
O B:SER213 2.5 37.6 1.0
OD2 B:ASP220 2.7 42.0 1.0
CG B:ASP211 3.3 47.0 1.0
C B:LEU216 3.5 42.5 1.0
C B:SER213 3.6 38.1 1.0
CG B:ASP220 3.6 36.7 1.0
C B:GLY218 3.6 44.0 1.0
O B:HOH446 3.8 54.9 1.0
N B:SER213 3.9 35.9 1.0
OD2 B:ASP211 4.0 47.8 1.0
CB B:LEU216 4.0 40.6 1.0
CA B:LEU216 4.1 41.7 1.0
N B:GLY218 4.1 41.0 1.0
CB B:ASP220 4.1 35.4 1.0
CA B:SER213 4.2 38.5 1.0
CB B:ASP211 4.2 44.4 1.0
N B:LEU216 4.2 41.1 1.0
CA B:ASP211 4.3 43.3 1.0
N B:LEU212 4.3 38.3 1.0
C B:ASP211 4.4 41.3 1.0
C B:GLY217 4.4 41.4 1.0
CB B:SER213 4.4 38.4 1.0
CA B:GLY218 4.5 43.0 1.0
N B:GLY217 4.5 43.0 1.0
OD1 B:ASP220 4.6 44.4 1.0
N B:MSE219 4.6 43.0 1.0
C B:MSE219 4.6 39.8 1.0
N B:ASP220 4.6 37.8 1.0
CA B:MSE219 4.7 41.7 1.0
N B:PRO214 4.7 37.1 1.0
CA B:GLY217 4.8 42.8 1.0
O B:GLY217 4.9 40.1 1.0
C B:LEU212 4.9 34.9 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Tue Dec 15 05:44:31 2020

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