Atomistry » Sodium » PDB 3cq8-3dfh » 3d7j
Atomistry »
  Sodium »
    PDB 3cq8-3dfh »
      3d7j »

Sodium in PDB 3d7j: SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor

Protein crystallography data

The structure of SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor, PDB code: 3d7j was solved by J.E.Spoonamore, S.A.Roberts, A.Heroux, V.Bandarian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.34 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.400, 88.000, 120.900, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 22.4

Other elements in 3d7j:

The structure of SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor (pdb code 3d7j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor, PDB code: 3d7j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3d7j

Go back to Sodium Binding Sites List in 3d7j
Sodium binding site 1 out of 2 in the SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na133

b:20.3
occ:1.00
O A:HOH260 2.3 30.7 1.0
O A:ARG109 2.3 16.6 1.0
O A:HOH206 2.5 25.2 1.0
C A:ARG109 3.5 17.0 1.0
O A:HOH207 3.9 24.5 1.0
O A:LEU111 4.0 15.8 1.0
CA A:GLY110 4.1 15.5 1.0
N A:GLY110 4.2 16.1 1.0
O A:HOH205 4.4 25.5 1.0
O A:HOH269 4.4 30.9 1.0
C A:GLY110 4.5 15.3 1.0
OXT A:LEU132 4.5 20.6 1.0
O A:LEU132 4.5 19.7 1.0
CA A:ARG109 4.6 17.1 1.0
O A:HOH277 4.7 40.1 1.0
N A:LEU111 4.8 15.2 1.0
C A:LEU132 4.8 19.1 1.0
O A:GLY110 5.0 15.6 1.0

Sodium binding site 2 out of 2 in 3d7j

Go back to Sodium Binding Sites List in 3d7j
Sodium binding site 2 out of 2 in the SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na134

b:23.4
occ:1.00
O A:HOH276 2.2 24.6 1.0
O A:GLN25 2.4 15.9 1.0
O A:HOH183 2.4 22.0 1.0
O A:HOH185 2.5 25.7 1.0
O A:HOH273 3.4 30.6 1.0
C A:GLN25 3.4 14.9 1.0
CB A:GLN25 4.1 15.5 1.0
CA A:GLN25 4.2 15.9 1.0
N A:ARG26 4.4 15.1 1.0
O A:PHE16 4.5 16.4 1.0
CA A:ARG26 4.5 15.7 1.0
O A:HOH215 4.6 22.9 1.0
OG A:SER15 4.6 17.5 1.0
CB A:SER15 4.7 15.6 1.0
O A:HOH184 4.8 17.9 1.0

Reference:

J.E.Spoonamore, S.A.Roberts, A.Heroux, V.Bandarian. Structure of A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor. Acta Crystallogr.,Sect.F V. 64 875 2008.
ISSN: ESSN 1744-3091
PubMed: 18931427
DOI: 10.1107/S1744309108027048
Page generated: Tue Dec 15 06:08:32 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy