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Calcium in PDB 5mj7: Structure of the C. Elegans Nucleoside Hydrolase

Protein crystallography data

The structure of Structure of the C. Elegans Nucleoside Hydrolase, PDB code: 5mj7 was solved by W.Versees, R.K.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.93 / 1.65
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.578, 84.578, 260.911, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 15.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the C. Elegans Nucleoside Hydrolase (pdb code 5mj7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of the C. Elegans Nucleoside Hydrolase, PDB code: 5mj7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5mj7

Go back to Calcium Binding Sites List in 5mj7
Calcium binding site 1 out of 2 in the Structure of the C. Elegans Nucleoside Hydrolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the C. Elegans Nucleoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:16.2
occ:1.00
O A:ILE133 2.3 20.9 1.0
OD2 A:ASP254 2.4 21.7 1.0
O1 A:TRS402 2.4 18.3 1.0
OD1 A:ASP18 2.5 21.6 1.0
OD1 A:ASP13 2.5 20.9 1.0
O A:HOH522 2.5 21.1 1.0
OD2 A:ASP18 2.6 21.1 1.0
O2 A:TRS402 2.7 19.5 1.0
CG A:ASP18 2.9 21.4 1.0
CG A:ASP254 3.4 21.6 1.0
C1 A:TRS402 3.5 17.0 1.0
C A:ILE133 3.5 20.7 1.0
CG A:ASP13 3.6 20.9 1.0
C2 A:TRS402 3.6 15.6 1.0
OD1 A:ASP254 3.8 21.3 1.0
OD2 A:ASP13 3.9 21.1 1.0
C A:TRS402 4.0 17.7 1.0
CB A:ASP18 4.4 21.7 1.0
N A:GLY134 4.4 20.4 1.0
OD1 A:ASP17 4.4 22.6 1.0
CB A:ILE133 4.4 21.3 1.0
CA A:GLY134 4.4 20.3 1.0
CA A:ILE133 4.5 20.8 1.0
CG2 A:VAL15 4.5 23.4 1.0
OD1 A:ASN178 4.6 20.3 1.0
N A:TRS402 4.6 20.7 1.0
N A:ASP13 4.7 20.7 1.0
ND2 A:ASN178 4.7 20.2 1.0
CB A:ASP254 4.7 22.2 1.0
OD2 A:ASP17 4.8 22.7 1.0
CG1 A:ILE133 4.8 21.6 1.0
CG A:ASP17 4.9 22.8 1.0
CB A:ASP13 4.9 20.9 1.0
N A:ASP18 4.9 22.3 1.0
CA A:ASP18 4.9 22.1 1.0

Calcium binding site 2 out of 2 in 5mj7

Go back to Calcium Binding Sites List in 5mj7
Calcium binding site 2 out of 2 in the Structure of the C. Elegans Nucleoside Hydrolase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the C. Elegans Nucleoside Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:16.0
occ:1.00
O B:ILE133 2.3 20.5 1.0
OD2 B:ASP254 2.4 20.1 1.0
OD1 B:ASP13 2.4 20.3 1.0
OD1 B:ASP18 2.4 20.8 1.0
O3 B:TRS402 2.5 18.3 1.0
O B:HOH520 2.5 20.4 1.0
OD2 B:ASP18 2.6 20.2 1.0
O1 B:TRS402 2.7 19.3 1.0
CG B:ASP18 2.8 20.5 1.0
CG B:ASP254 3.5 19.6 1.0
CG B:ASP13 3.5 20.4 1.0
C B:ILE133 3.5 20.3 1.0
C3 B:TRS402 3.5 17.9 1.0
C1 B:TRS402 3.7 19.8 1.0
OD1 B:ASP254 3.8 20.6 1.0
OD2 B:ASP13 3.9 20.7 1.0
C B:TRS402 4.1 19.3 1.0
CB B:ASP18 4.3 20.8 1.0
N B:GLY134 4.4 20.1 1.0
CB B:ILE133 4.4 21.0 1.0
OD1 B:ASP17 4.4 21.8 1.0
CA B:GLY134 4.4 20.0 1.0
CG2 B:VAL15 4.5 21.9 1.0
CA B:ILE133 4.5 20.4 1.0
OD1 B:ASN178 4.7 19.7 1.0
N B:ASP13 4.7 20.1 1.0
N B:TRS402 4.7 19.4 1.0
ND2 B:ASN178 4.7 19.5 1.0
CB B:ASP254 4.8 17.7 1.0
CG1 B:ILE133 4.8 21.4 1.0
OD2 B:ASP17 4.8 21.7 1.0
CB B:ASP13 4.8 20.5 1.0
N B:ASP18 4.9 21.3 1.0
CG B:ASP17 4.9 22.6 1.0
CA B:ASP18 4.9 21.0 1.0

Reference:

R.K.Singh, J.Steyaert, W.Versees. Structural and Biochemical Characterization of the Nucleoside Hydrolase From C. Elegans Reveals the Role of Two Active Site Cysteine Residues in Catalysis. Protein Sci. V. 26 985 2017.
ISSN: ESSN 1469-896X
PubMed: 28218438
DOI: 10.1002/PRO.3141
Page generated: Sat Dec 12 05:37:58 2020

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