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Sodium in PDB 4wcn: Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori

Protein crystallography data

The structure of Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori, PDB code: 4wcn was solved by A.C.Chan, M.E.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.15 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.230, 66.830, 145.050, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.8

Other elements in 4wcn:

The structure of Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Iodine (I) 44 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori (pdb code 4wcn). 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 Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori, PDB code: 4wcn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4wcn

Go back to Sodium Binding Sites List in 4wcn
Sodium binding site 1 out of 2 in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori


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 Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na543

b:26.8
occ:1.00
I A:IOD534 2.8 26.8 0.3
HG2 A:PRO302 2.8 44.7 1.0
HD2 A:LYS300 3.1 50.1 1.0
HB3 A:LYS300 3.1 46.4 1.0
HD2 A:PRO302 3.2 47.0 1.0
HD3 A:LYS300 3.5 50.1 1.0
CG A:PRO302 3.6 37.3 1.0
CD A:LYS300 3.7 41.8 1.0
CD A:PRO302 3.8 39.1 1.0
CB A:LYS300 3.9 38.7 1.0
HB2 A:LYS300 4.0 46.4 1.0
HD3 A:PRO302 4.1 47.0 1.0
HB2 A:PRO302 4.2 42.0 1.0
HG3 A:PRO302 4.3 44.7 1.0
CG A:LYS300 4.3 40.8 1.0
CB A:PRO302 4.5 35.0 1.0
HG3 A:LYS300 4.7 49.0 1.0
HE3 A:LYS300 4.9 54.0 1.0
CE A:LYS300 5.0 45.0 1.0

Sodium binding site 2 out of 2 in 4wcn

Go back to Sodium Binding Sites List in 4wcn
Sodium binding site 2 out of 2 in the Crystal Structure of Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori


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 Tripeptide Bound Cell Shape Determinant CSD4 Protein From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na544

b:26.8
occ:0.50
HH21 A:ARG135 2.2 27.9 1.0
NH2 A:ARG135 3.0 23.2 1.0
HA A:ILE186 3.2 28.2 1.0
HE A:ARG135 3.4 31.0 1.0
HH22 A:ARG135 3.4 27.9 1.0
I A:IOD502 3.5 34.7 1.0
CZ A:ARG135 3.9 22.2 1.0
HG13 A:ILE186 3.9 31.6 1.0
NE A:ARG135 4.0 25.8 1.0
O A:PRO185 4.1 20.3 1.0
CA A:ILE186 4.2 23.5 1.0
HB3 A:GLU188 4.6 28.7 1.0
C A:PRO185 4.6 22.1 1.0
N A:ILE186 4.7 24.9 1.0
O A:ILE186 4.8 16.6 1.0
CG1 A:ILE186 4.8 26.4 1.0
C A:ILE186 4.8 17.8 1.0
HE1 A:HIS190 4.9 34.1 1.0

Reference:

A.C.Chan, K.M.Blair, Y.Liu, E.Frirdich, E.C.Gaynor, M.E.Tanner, N.R.Salama, M.E.Murphy. Helical Shape of Helicobacter Pylori Requires An Atypical Glutamine As A Zinc Ligand in the Carboxypeptidase CSD4 J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.624734
Page generated: Tue Dec 15 09:24:56 2020

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