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Sodium in PDB 3oyo: Crystal Structure of Hemopexin Fold Protein CP4 From Cow Pea

Protein crystallography data

The structure of Crystal Structure of Hemopexin Fold Protein CP4 From Cow Pea, PDB code: 3oyo was solved by V.Gaur, V.Chanana, D.M.Salunke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.22 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.087, 60.138, 67.574, 90.00, 111.18, 90.00
R / Rfree (%) 20.5 / 24.6

Other elements in 3oyo:

The structure of Crystal Structure of Hemopexin Fold Protein CP4 From Cow Pea also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hemopexin Fold Protein CP4 From Cow Pea (pdb code 3oyo). 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 Hemopexin Fold Protein CP4 From Cow Pea, PDB code: 3oyo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3oyo

Go back to Sodium Binding Sites List in 3oyo
Sodium binding site 1 out of 2 in the Crystal Structure of Hemopexin Fold Protein CP4 From Cow Pea


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 Hemopexin Fold Protein CP4 From Cow Pea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na230

b:17.2
occ:1.00
N A:HIS69 3.3 10.6 1.0
N A:ARG125 3.4 8.9 1.0
N A:ALA178 3.5 11.1 1.0
CA A:PHE68 3.7 9.0 1.0
CA A:PHE124 3.8 7.8 1.0
CB A:HIS69 3.9 18.3 1.0
CA A:PHE177 3.9 9.3 1.0
CB A:PHE68 3.9 6.8 1.0
CB A:ARG125 4.0 9.5 1.0
C A:PHE68 4.1 8.5 1.0
C A:PHE124 4.1 8.9 1.0
CB A:PHE177 4.1 10.2 1.0
CB A:PHE124 4.2 8.0 1.0
CA A:PHE10 4.2 11.2 1.0
CA A:HIS69 4.2 11.2 1.0
O A:HOH231 4.2 15.2 1.0
C A:PHE177 4.3 9.7 1.0
N A:ARG11 4.3 12.9 1.0
CB A:ALA178 4.3 11.6 1.0
CA A:ARG125 4.3 9.9 1.0
CB A:PHE10 4.3 9.5 1.0
O A:ALA123 4.3 7.3 1.0
CA A:ALA178 4.5 12.3 1.0
O A:ALA9 4.6 9.9 1.0
O A:HIS69 4.7 7.3 1.0
O A:SER67 4.7 3.6 1.0
C A:PHE10 4.8 12.1 1.0
O A:CYS176 4.9 7.6 1.0
N A:PHE124 4.9 7.8 1.0
N A:PHE68 5.0 8.2 1.0
NH1 A:ARG11 5.0 34.8 1.0
C A:HIS69 5.0 11.0 1.0

Sodium binding site 2 out of 2 in 3oyo

Go back to Sodium Binding Sites List in 3oyo
Sodium binding site 2 out of 2 in the Crystal Structure of Hemopexin Fold Protein CP4 From Cow Pea


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 Hemopexin Fold Protein CP4 From Cow Pea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na230

b:19.2
occ:1.00
N B:ALA178 3.5 14.5 1.0
N B:HIS69 3.6 10.2 1.0
N B:ARG125 3.7 11.5 1.0
CA B:PHE177 3.8 10.1 1.0
N B:ARG11 3.8 14.9 1.0
CA B:PHE10 3.9 10.5 1.0
CA B:PHE68 3.9 11.8 1.0
CB B:PHE177 4.0 10.6 1.0
CA B:PHE124 4.0 10.0 1.0
O B:HOH231 4.1 16.4 1.0
CB B:PHE10 4.2 8.0 1.0
C B:PHE177 4.2 11.4 1.0
CB B:PHE68 4.2 8.2 1.0
CB B:ARG125 4.2 13.8 1.0
CB B:ALA178 4.2 6.9 1.0
CB B:HIS69 4.2 20.6 1.0
CB B:PHE124 4.3 13.5 1.0
C B:PHE68 4.3 12.8 1.0
O B:ALA9 4.4 9.1 1.0
C B:PHE10 4.4 11.2 1.0
CA B:ALA178 4.4 15.4 1.0
C B:PHE124 4.5 11.0 1.0
O B:ALA123 4.5 9.0 1.0
CA B:HIS69 4.5 11.1 1.0
ND1 B:HIS69 4.6 30.8 1.0
CA B:ARG125 4.6 12.6 1.0
O B:CYS176 4.7 8.2 1.0
O B:SER67 4.7 3.0 1.0
CB B:ARG11 4.9 22.8 1.0
CG B:HIS69 4.9 25.3 1.0
O B:HIS69 4.9 6.2 1.0
N B:PHE10 5.0 9.0 1.0
CA B:ARG11 5.0 17.0 1.0
O B:ALA178 5.0 17.7 1.0
N B:PHE177 5.0 9.9 1.0

Reference:

V.Gaur, V.Chanana, A.Jain, D.M.Salunke. The Structure of A Haemopexin-Fold Protein From Cow Pea (Vigna Unguiculata) Suggests Functional Diversity of Haemopexins in Plants Acta Crystallogr.,Sect.F V. 67 193 2011.
ISSN: ESSN 1744-3091
PubMed: 21301085
DOI: 10.1107/S1744309110051250
Page generated: Tue Dec 15 06:20:35 2020

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