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

Protein crystallography data

The structure of Crystal Structure of Product Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori, PDB code: 4wcl 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) 42.76 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.030, 66.770, 144.570, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19.5

Other elements in 4wcl:

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

Zinc (Zn) 3 atoms
Iodine (I) 33 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Product Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori (pdb code 4wcl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Product Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori, PDB code: 4wcl:

Sodium binding site 1 out of 1 in 4wcl

Go back to Sodium Binding Sites List in 4wcl
Sodium binding site 1 out of 1 in the Crystal Structure of Product Bound Cell Shape Determinant Protein CSD4 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 Product Bound Cell Shape Determinant Protein CSD4 From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na536

b:28.6
occ:0.53
HE1 A:HIS38 2.5 31.6 1.0
HB3 A:ASP34 3.1 43.1 1.0
HB3 A:ARG33 3.2 40.0 1.0
CE1 A:HIS38 3.3 26.3 1.0
I A:IOD522 3.3 36.2 0.5
HE2 A:HIS38 3.5 30.5 1.0
HA A:ASP34 3.5 37.7 1.0
HB2 A:ARG33 3.6 40.0 1.0
NE2 A:HIS38 3.7 25.4 1.0
CB A:ARG33 3.8 33.3 1.0
CB A:ASP34 3.9 35.9 1.0
N A:ASP34 3.9 30.8 1.0
CA A:ASP34 4.0 31.4 1.0
C A:ARG33 4.0 32.1 1.0
O A:ARG33 4.1 28.9 1.0
H A:ASP34 4.2 37.0 1.0
HB2 A:ASP34 4.2 43.1 1.0
HD3 A:ARG33 4.3 41.3 1.0
ND1 A:HIS38 4.5 23.6 1.0
HB2 A:ASN120 4.6 47.6 1.0
CA A:ARG33 4.6 32.3 1.0
HD2 A:ARG33 4.6 41.3 1.0
CD A:ARG33 4.8 34.4 1.0
HD1 A:HIS38 4.8 28.3 1.0
CG A:ARG33 5.0 33.2 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 09:22:33 2020

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