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Calcium in PDB 1v7x: Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac and Sulfate

Protein crystallography data

The structure of Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac and Sulfate, PDB code: 1v7x was solved by M.Hidaka, Y.Honda, S.Nirasawa, M.Kitaoka, K.Hayashi, T.Wakagi, H.Shoun, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.69 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 140.871, 70.355, 79.939, 90.00, 98.36, 90.00
R / Rfree (%) 16.3 / 19.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac and Sulfate (pdb code 1v7x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac and Sulfate, PDB code: 1v7x:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1v7x

Go back to Calcium Binding Sites List in 1v7x
Calcium binding site 1 out of 2 in the Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac and Sulfate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:34.3
occ:1.00
OD1 A:ASP186 2.3 19.4 1.0
O A:HOH1268 2.4 25.7 1.0
O A:ASN190 2.5 21.1 1.0
O A:LEU187 2.6 16.4 1.0
O A:GLY196 2.7 19.2 1.0
CE1 A:PHE197 3.3 39.5 1.0
C A:LEU187 3.4 15.9 1.0
CG A:ASP186 3.5 20.5 1.0
C A:GLY196 3.6 20.1 1.0
C A:ASN190 3.6 22.7 1.0
CD1 A:PHE197 3.7 37.0 1.0
N A:LEU187 3.7 16.0 1.0
CA A:GLY196 3.9 20.2 1.0
CZ A:PHE197 3.9 39.5 1.0
OD2 A:ASP186 4.1 18.8 1.0
N A:TYR188 4.2 16.3 1.0
CA A:LEU187 4.2 15.7 1.0
O A:HOH1284 4.3 29.2 1.0
CA A:TYR188 4.3 18.4 1.0
N A:ASN190 4.4 20.4 1.0
C A:ASP186 4.4 15.7 1.0
CA A:ASN190 4.5 20.8 1.0
CB A:LEU187 4.5 15.9 1.0
O A:ASP192 4.5 24.7 1.0
CB A:ASN190 4.5 20.6 1.0
C A:TYR188 4.5 18.6 1.0
CG A:PHE197 4.6 31.9 1.0
N A:THR191 4.6 22.9 1.0
CB A:ASP186 4.6 16.5 1.0
CA A:ASP186 4.6 14.8 1.0
O A:TYR188 4.7 18.0 1.0
CA A:THR191 4.7 27.9 1.0
CE2 A:PHE197 4.7 39.1 1.0
N A:PHE197 4.7 20.2 1.0
C A:THR191 4.9 28.7 1.0
CD2 A:PHE197 5.0 32.3 1.0

Calcium binding site 2 out of 2 in 1v7x

Go back to Calcium Binding Sites List in 1v7x
Calcium binding site 2 out of 2 in the Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac and Sulfate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Vibrio Proteolyticus Chitobiose Phosphorylase in Complex with Glcnac and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:37.1
occ:1.00
O A:HOH1115 2.3 20.8 1.0
O A:HOH1327 2.4 28.1 1.0
OD2 A:ASP793 2.5 27.1 1.0
O A:GLY791 2.6 26.4 1.0
CG A:ASP793 3.3 23.3 1.0
C A:GLY791 3.4 25.6 1.0
OD1 A:ASP793 3.5 29.0 1.0
CA A:GLY791 3.9 26.6 1.0
O A:SER792 4.1 21.5 1.0
OG1 A:THR756 4.1 19.9 1.0
C A:SER792 4.2 23.1 1.0
N A:SER792 4.3 23.2 1.0
O A:HOH1502 4.5 37.4 1.0
N A:ASP793 4.5 20.7 1.0
CB A:ASP793 4.6 21.6 1.0
CA A:SER792 4.7 21.9 1.0
CA A:ASP793 4.9 21.3 1.0
CB A:THR756 4.9 18.9 1.0

Reference:

M.Hidaka, Y.Honda, M.Kitaoka, S.Nirasawa, K.Hayashi, T.Wakagi, H.Shoun, S.Fushinobu. Chitobiose Phosphorylase From Vibrio Proteolyticus, A Member of Glycosyl Transferase Family 36, Has A Clan Gh-L-Like (Alpha/Alpha)(6) Barrel Fold. Structure V. 12 937 2004.
ISSN: ISSN 0969-2126
PubMed: 15274915
DOI: 10.1016/J.STR.2004.03.027
Page generated: Sat Dec 12 03:24:41 2020

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