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Zinc in PDB 5tvs: JMJD2A in Complex with Ni(II)

Protein crystallography data

The structure of JMJD2A in Complex with Ni(II), PDB code: 5tvs was solved by B.Cascella, S.G.Lee, J.M.Jez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.83 / 2.75
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.689, 101.140, 148.894, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 26.7

Other elements in 5tvs:

The structure of JMJD2A in Complex with Ni(II) also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the JMJD2A in Complex with Ni(II) (pdb code 5tvs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the JMJD2A in Complex with Ni(II), PDB code: 5tvs:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5tvs

Go back to Zinc Binding Sites List in 5tvs
Zinc binding site 1 out of 2 in the JMJD2A in Complex with Ni(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of JMJD2A in Complex with Ni(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:71.6
occ:1.00
SG A:CYS234 1.8 0.6 1.0
NE2 A:HIS240 2.0 66.7 1.0
CB A:CYS234 2.3 78.3 1.0
SG A:CYS308 2.4 60.3 1.0
CE1 A:HIS240 2.6 61.6 1.0
CA A:PHE237 2.8 65.2 1.0
CD2 A:HIS240 2.8 61.5 1.0
O A:ALA236 3.1 59.2 1.0
N A:PHE237 3.2 62.3 1.0
C A:ALA236 3.3 64.5 1.0
ND1 A:HIS240 3.5 65.6 1.0
CB A:PHE237 3.5 67.6 1.0
CG A:HIS240 3.7 58.3 1.0
SG A:CYS306 3.8 86.6 1.0
C A:PHE237 3.9 68.1 1.0
CA A:CYS234 3.9 79.4 1.0
O A:PHE237 4.1 55.7 1.0
CB A:CYS308 4.2 72.5 1.0
N A:ALA236 4.4 71.8 1.0
CA A:ALA236 4.4 69.0 1.0
C A:CYS234 4.4 71.2 1.0
CB A:CYS306 4.5 85.2 1.0
CA A:CYS306 4.5 86.8 1.0
O A:CYS234 4.6 65.8 1.0
N A:CYS234 4.7 82.0 1.0
N A:CYS308 4.8 91.4 1.0
N A:LEU238 4.9 62.5 1.0
N A:HIS240 5.0 54.3 1.0
N A:SER307 5.0 75.2 1.0

Zinc binding site 2 out of 2 in 5tvs

Go back to Zinc Binding Sites List in 5tvs
Zinc binding site 2 out of 2 in the JMJD2A in Complex with Ni(II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of JMJD2A in Complex with Ni(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:71.8
occ:1.00
NE2 B:HIS240 1.7 66.9 1.0
SG B:CYS234 1.9 0.7 1.0
SG B:CYS308 2.0 76.3 1.0
SG B:CYS306 2.1 63.5 1.0
CE1 B:HIS240 2.4 63.2 1.0
CD2 B:HIS240 2.9 65.5 1.0
CB B:CYS308 3.3 64.4 1.0
CB B:CYS234 3.3 66.3 1.0
ND1 B:HIS240 3.6 50.5 1.0
CB B:CYS306 3.7 76.2 1.0
N B:CYS308 3.7 77.6 1.0
CG B:HIS240 3.9 54.7 1.0
CA B:CYS308 4.0 75.6 1.0
CA B:CYS306 4.4 70.4 1.0
CA B:CYS234 4.5 74.8 1.0
CA B:PHE237 4.5 55.2 1.0
N B:SER307 4.5 66.0 1.0
C B:CYS308 4.7 78.2 1.0
N B:CYS234 4.7 68.2 1.0
N B:ARG309 4.7 78.2 1.0
O B:ALA236 4.8 54.6 1.0
C B:CYS306 4.8 61.8 1.0
CG B:ARG309 4.8 79.7 1.0
CB B:PHE237 4.9 53.4 1.0
C B:SER307 4.9 80.2 1.0
N B:PHE237 5.0 59.8 1.0

Reference:

B.Cascella, S.G.Lee, S.Singh, J.M.Jez, L.M.Mirica. The Small Molecule Jib-04 Disrupts O2 Binding in the Fe-Dependent Histone Demethylase KDM4A/JMJD2A. Chem. Commun. (Camb.) V. 53 2174 2017.
ISSN: ESSN 1364-548X
PubMed: 28144654
DOI: 10.1039/C6CC09882G
Page generated: Wed Dec 16 10:57:26 2020

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