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Sodium in PDB 3ged: Fingerprint and Structural Analysis of A Apo Scor Enzyme From Clostridium Thermocellum

Protein crystallography data

The structure of Fingerprint and Structural Analysis of A Apo Scor Enzyme From Clostridium Thermocellum, PDB code: 3ged 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) 49.68 / 1.70
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 124.287, 124.287, 162.608, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Fingerprint and Structural Analysis of A Apo Scor Enzyme From Clostridium Thermocellum (pdb code 3ged). 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 Apo Scor Enzyme From Clostridium Thermocellum, PDB code: 3ged:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3ged

Go back to Sodium Binding Sites List in 3ged
Sodium binding site 1 out of 2 in the Fingerprint and Structural Analysis of A Apo Scor Enzyme 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 Apo Scor Enzyme From Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na251

b:32.6
occ:1.00
O A:LEU49 2.4 33.1 1.0
O A:ARG46 2.5 36.5 1.0
O A:ALA43 2.5 32.9 1.0
O A:HOH350 2.5 39.2 1.0
O A:HOH360 2.7 45.5 1.0
O A:HOH291 2.9 43.5 1.0
C A:ARG46 3.3 35.3 1.0
C A:ALA43 3.5 31.4 1.0
C A:LEU49 3.6 31.1 1.0
CB A:ALA43 3.9 36.1 1.0
N A:ARG46 3.9 37.9 1.0
CA A:ALA43 4.0 30.9 1.0
CA A:ARG46 4.1 35.0 1.0
N A:PRO47 4.1 39.5 1.0
N A:LEU49 4.1 29.4 1.0
CA A:PRO47 4.2 42.6 1.0
CA A:LEU49 4.3 28.8 1.0
CB A:ARG46 4.3 34.3 1.0
CB A:LEU49 4.3 28.5 1.0
O A:HOH385 4.3 38.3 1.0
C A:PRO47 4.4 41.5 1.0
O A:HOH280 4.4 36.0 1.0
O A:PRO47 4.6 40.0 1.0
N A:LYS44 4.6 33.8 1.0
N A:PHE50 4.6 29.7 1.0
N A:GLU45 4.8 34.5 1.0
CA A:PHE50 4.8 31.9 1.0
CA A:LYS44 4.9 35.1 1.0
C A:LYS44 4.9 37.0 1.0
N A:ASN48 5.0 33.3 1.0

Sodium binding site 2 out of 2 in 3ged

Go back to Sodium Binding Sites List in 3ged
Sodium binding site 2 out of 2 in the Fingerprint and Structural Analysis of A Apo Scor Enzyme 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 Apo Scor Enzyme From Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na250

b:29.4
occ:1.00
O B:LEU49 2.3 28.9 1.0
O B:ARG46 2.5 33.5 1.0
O B:ALA43 2.5 30.0 1.0
O B:HOH441 2.5 40.1 1.0
O B:HOH472 2.7 37.9 1.0
O B:HOH497 2.9 37.5 1.0
C B:ARG46 3.3 31.7 1.0
C B:ALA43 3.5 32.1 1.0
C B:LEU49 3.5 26.2 1.0
CB B:ALA43 3.8 32.5 1.0
N B:ARG46 4.0 31.3 1.0
CA B:ALA43 4.0 27.3 1.0
CA B:ARG46 4.1 31.8 1.0
N B:LEU49 4.1 25.7 1.0
N B:PRO47 4.1 33.9 1.0
CA B:PRO47 4.2 36.1 1.0
CA B:LEU49 4.2 25.4 1.0
CB B:LEU49 4.3 28.1 1.0
CB B:ARG46 4.3 32.3 1.0
O B:HOH488 4.4 68.0 1.0
C B:PRO47 4.4 38.2 1.0
O B:HOH473 4.4 63.9 1.0
O B:HOH289 4.5 40.5 1.0
N B:PHE50 4.5 26.3 1.0
N B:LYS44 4.6 35.1 1.0
O B:HOH357 4.6 37.8 1.0
O B:PRO47 4.6 34.5 1.0
CA B:PHE50 4.8 25.9 1.0
N B:GLU45 4.8 31.0 1.0
CA B:LYS44 4.9 36.2 1.0
C B:LYS44 4.9 35.8 1.0
N B:ASN48 4.9 33.1 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: Tue Dec 15 06:12:26 2020

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