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Sodium in PDB 3trd: Structure of An Alpha-Beta Serine Hydrolase Homologue From Coxiella Burnetii

Protein crystallography data

The structure of Structure of An Alpha-Beta Serine Hydrolase Homologue From Coxiella Burnetii, PDB code: 3trd was solved by J.Cheung, M.C.Franklin, M.Rudolph, M.Cassidy, E.Gary, F.Burshteyn, J.Love, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.26 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.861, 55.905, 62.513, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 20

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of An Alpha-Beta Serine Hydrolase Homologue From Coxiella Burnetii (pdb code 3trd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of An Alpha-Beta Serine Hydrolase Homologue From Coxiella Burnetii, PDB code: 3trd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3trd

Go back to Sodium Binding Sites List in 3trd
Sodium binding site 1 out of 2 in the Structure of An Alpha-Beta Serine Hydrolase Homologue From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of An Alpha-Beta Serine Hydrolase Homologue From Coxiella Burnetii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:15.7
occ:0.85
OXT A:ACT206 2.7 13.3 1.0
N A:HIS37 2.9 8.1 1.0
OG A:SER110 3.0 25.4 1.0
N A:PHE111 3.0 8.9 1.0
CB A:SER110 3.1 17.1 1.0
CB A:HIS37 3.3 8.9 1.0
CB A:PHE111 3.5 7.6 1.0
C A:ACT206 3.5 13.1 1.0
CA A:HIS37 3.6 8.5 1.0
CH3 A:ACT206 3.7 11.7 1.0
CB A:PRO36 3.8 7.8 1.0
CA A:PHE111 3.8 9.8 1.0
C A:PRO36 3.8 8.1 1.0
CA A:PRO36 3.9 9.1 1.0
C A:SER110 3.9 7.2 1.0
CA A:SER110 4.1 12.4 1.0
CG A:HIS37 4.2 10.5 1.0
OH A:TYR137 4.2 15.7 1.0
CD2 A:HIS37 4.4 13.0 1.0
O A:ACT206 4.6 13.4 1.0
O A:PHE109 4.8 9.8 1.0
CG A:PHE111 4.9 9.8 1.0
NE2 A:HIS187 4.9 9.8 1.0
C A:HIS37 5.0 9.4 1.0
O A:PRO36 5.0 7.2 1.0

Sodium binding site 2 out of 2 in 3trd

Go back to Sodium Binding Sites List in 3trd
Sodium binding site 2 out of 2 in the Structure of An Alpha-Beta Serine Hydrolase Homologue From Coxiella Burnetii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of An Alpha-Beta Serine Hydrolase Homologue From Coxiella Burnetii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na209

b:13.7
occ:1.00
O A:HOH253 2.6 40.0 1.0
O A:SER74 2.8 13.2 1.0
O A:GLY72 2.8 16.4 1.0
O A:HOH354 2.8 26.6 1.0
O A:GLY70 3.2 19.6 1.0
C A:GLY70 3.6 14.3 1.0
C A:SER74 3.8 15.6 1.0
C A:GLY72 3.9 13.1 1.0
CA A:GLY70 4.0 9.5 1.0
N A:SER74 4.2 11.2 1.0
O A:HOH243 4.3 35.1 1.0
N A:VAL71 4.3 11.5 1.0
C A:LYS73 4.3 12.6 1.0
C A:VAL71 4.4 11.2 1.0
N A:GLY72 4.5 12.1 1.0
CA A:GLN75 4.5 14.6 1.0
O A:VAL71 4.6 11.3 1.0
N A:GLN75 4.6 13.4 1.0
CA A:LYS73 4.6 13.5 1.0
CA A:SER74 4.6 12.2 1.0
N A:LYS73 4.7 14.0 1.0
N A:GLY70 4.7 11.4 1.0
O A:LYS73 4.7 17.0 1.0
CA A:VAL71 4.8 9.9 1.0
CA A:GLY72 4.8 13.6 1.0

Reference:

M.C.Franklin, J.Cheung, M.J.Rudolph, F.Burshteyn, M.Cassidy, E.Gary, B.Hillerich, Z.K.Yao, P.R.Carlier, M.Totrov, J.D.Love. Structural Genomics For Drug Design Against the Pathogen Coxiella Burnetii. Proteins V. 83 2124 2015.
ISSN: ISSN 0887-3585
PubMed: 26033498
DOI: 10.1002/PROT.24841
Page generated: Mon Oct 7 13:19:51 2024

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