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Sodium in PDB 3geg: Fingerprint and Structural Analysis of A Scor Enzyme with Its Bound Cofactor From Clostridium Thermocellum

Protein crystallography data

The structure of Fingerprint and Structural Analysis of A Scor Enzyme with Its Bound Cofactor From Clostridium Thermocellum, PDB code: 3geg was solved by R.Huether, Z.J.Liu, H.Xu, B.C.Wang, V.Pletnev, Q.Mao, T.Umland, W.Duax, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.94 / 2.10
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 124.272, 124.272, 161.208, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20

Sodium Binding Sites:

The binding sites of Sodium atom in the Fingerprint and Structural Analysis of A Scor Enzyme with Its Bound Cofactor From Clostridium Thermocellum (pdb code 3geg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Fingerprint and Structural Analysis of A Scor Enzyme with Its Bound Cofactor From Clostridium Thermocellum, PDB code: 3geg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3geg

Go back to Sodium Binding Sites List in 3geg
Sodium binding site 1 out of 2 in the Fingerprint and Structural Analysis of A Scor Enzyme with Its Bound Cofactor From Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Fingerprint and Structural Analysis of A Scor Enzyme with Its Bound Cofactor From Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na251

b:47.8
occ:1.00
O A:LEU49 2.8 29.3 1.0
O A:ALA43 2.8 36.0 1.0
O A:HOH382 2.9 36.4 1.0
O A:HOH358 3.1 39.5 1.0
O A:ARG46 3.1 34.5 1.0
C A:ALA43 3.5 35.7 1.0
CB A:ALA43 3.7 32.5 1.0
C A:ARG46 3.9 30.6 1.0
O A:HOH306 3.9 33.6 1.0
C A:LEU49 4.0 30.5 1.0
CA A:ALA43 4.1 32.9 1.0
N A:ARG46 4.3 32.5 1.0
N A:LYS44 4.5 35.1 1.0
N A:PRO47 4.6 36.4 1.0
CA A:ARG46 4.6 28.8 1.0
CA A:PRO47 4.6 41.4 1.0
O A:HOH325 4.7 41.5 1.0
N A:GLU45 4.7 31.7 1.0
CA A:LYS44 4.7 32.8 1.0
N A:LEU49 4.7 29.9 1.0
CA A:LEU49 4.8 28.9 1.0
CB A:LEU49 4.9 26.3 1.0
C A:PRO47 4.9 39.9 1.0
O A:PRO47 4.9 39.0 1.0
C A:LYS44 4.9 32.0 1.0
N A:PHE50 4.9 28.3 1.0
CA A:PHE50 4.9 28.3 1.0
CB A:ARG46 5.0 29.9 1.0

Sodium binding site 2 out of 2 in 3geg

Go back to Sodium Binding Sites List in 3geg
Sodium binding site 2 out of 2 in the Fingerprint and Structural Analysis of A Scor Enzyme with Its Bound Cofactor From Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Fingerprint and Structural Analysis of A Scor Enzyme with Its Bound Cofactor From Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na250

b:40.9
occ:1.00
O B:ALA43 2.7 30.1 1.0
O B:LEU49 2.7 27.5 1.0
O B:ARG46 2.8 32.2 1.0
O B:HOH372 2.8 39.8 1.0
O B:HOH384 2.9 51.0 1.0
O B:HOH362 3.0 34.4 1.0
C B:ARG46 3.5 29.3 1.0
C B:ALA43 3.6 33.1 1.0
C B:LEU49 3.8 28.1 1.0
CB B:ALA43 3.9 35.2 1.0
N B:ARG46 4.0 30.0 1.0
CA B:ALA43 4.1 31.0 1.0
N B:PRO47 4.2 38.9 1.0
CA B:PRO47 4.3 41.0 1.0
CA B:ARG46 4.3 28.6 1.0
N B:LEU49 4.3 24.9 1.0
C B:PRO47 4.4 40.9 1.0
O B:HOH322 4.4 34.2 1.0
CA B:LEU49 4.5 24.5 1.0
O B:PRO47 4.5 40.7 1.0
CB B:LEU49 4.6 26.9 1.0
CB B:ARG46 4.6 27.5 1.0
N B:LYS44 4.6 32.5 1.0
N B:GLU45 4.7 32.8 1.0
N B:PHE50 4.9 26.2 1.0
C B:LYS44 4.9 33.5 1.0
CA B:LYS44 4.9 31.7 1.0

Reference:

R.Huether, Z.J.Liu, H.Xu, B.C.Wang, V.Z.Pletnev, Q.Mao, W.L.Duax, T.C.Umland. Sequence Fingerprint and Structural Analysis of the Scor Enzyme A3DFK9 From Clostridium Thermocellum. Proteins V. 78 603 2010.
ISSN: ISSN 0887-3585
PubMed: 19774618
DOI: 10.1002/PROT.22584
Page generated: Mon Oct 7 10:15:08 2024

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