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Nickel in PDB 2ok3: X-Ray Structure of Human Cyclophilin J at 2.0 Angstrom

Enzymatic activity of X-Ray Structure of Human Cyclophilin J at 2.0 Angstrom

All present enzymatic activity of X-Ray Structure of Human Cyclophilin J at 2.0 Angstrom:
5.2.1.8;

Protein crystallography data

The structure of X-Ray Structure of Human Cyclophilin J at 2.0 Angstrom, PDB code: 2ok3 was solved by Z.Xia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.11 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 40.577, 40.577, 170.682, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 25.5

Nickel Binding Sites:

The binding sites of Nickel atom in the X-Ray Structure of Human Cyclophilin J at 2.0 Angstrom (pdb code 2ok3). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the X-Ray Structure of Human Cyclophilin J at 2.0 Angstrom, PDB code: 2ok3:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2ok3

Go back to Nickel Binding Sites List in 2ok3
Nickel binding site 1 out of 2 in the X-Ray Structure of Human Cyclophilin J at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of X-Ray Structure of Human Cyclophilin J at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni801

b:55.0
occ:1.00
O A:HOH948 2.1 38.0 1.0
O A:HOH936 2.2 42.6 1.0
ND1 A:HIS6 2.4 34.8 1.0
O A:HOH955 2.7 43.2 1.0
O A:HOH961 2.8 44.5 1.0
CG A:HIS6 3.3 33.6 1.0
CE1 A:HIS6 3.3 35.4 1.0
O A:HOH953 3.4 50.2 1.0
CB A:HIS6 3.6 31.6 1.0
OD1 A:ASP11 4.0 32.1 1.0
OD2 A:ASP11 4.0 34.0 1.0
CG A:ASP11 4.4 32.7 1.0
NE2 A:HIS6 4.4 35.7 1.0
CD2 A:HIS6 4.5 34.7 1.0
CA A:HIS6 4.7 31.2 1.0
OD1 A:ASP151 4.7 40.7 1.0

Nickel binding site 2 out of 2 in 2ok3

Go back to Nickel Binding Sites List in 2ok3
Nickel binding site 2 out of 2 in the X-Ray Structure of Human Cyclophilin J at 2.0 Angstrom


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of X-Ray Structure of Human Cyclophilin J at 2.0 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni802

b:44.5
occ:1.00
O A:HOH940 2.0 34.4 1.0
NE2 A:HIS148 2.1 32.2 1.0
O A:HOH938 2.3 35.1 1.0
O A:HOH939 2.3 40.0 1.0
O A:HOH937 2.5 43.5 1.0
CD2 A:HIS148 3.0 30.0 1.0
CE1 A:HIS148 3.1 32.0 1.0
OD2 A:ASP146 4.0 34.8 1.0
O A:HOH867 4.0 33.9 1.0
O A:HOH922 4.1 44.6 1.0
CG A:HIS148 4.1 30.5 1.0
ND1 A:HIS148 4.2 31.5 1.0
CB A:ASP146 4.5 31.7 1.0
CG A:ASP146 4.7 33.6 1.0
CG2 A:ILE41 4.7 24.0 1.0

Reference:

J.Chen, S.Chen, L.Huang, X.Zhao, J.Tan, C.Huang, H.Saiyin, M.Zhang, X.Zeng, J.Xi, B.Wan, Y.Zhao, Z.Xia, H.Jiang, Q.Yi, J.O.Liu, L.Yu. Targeting Cyclophilin J, A Novel Peptidyl-Prolyl Isomerase, Can Induce Cellular G1/S Arrest and Repress the Growth of Hepatocellular Carcinoma To Be Published.
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