Nickel in PDB 2xml: Crystal Structure of Human JMJD2C Catalytic Domain

The structure of Crystal Structure of Human JMJD2C Catalytic Domain, PDB code: 2xml was solved by W.W.Yue, C.Gileadi, T.Krojer, A.C.W.Pike, F.Von Delft, S.Ng, L.Carpenter, C.Arrowsmith, J.Weigelt, A.Edwards, C.Bountra, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.572 / 2.55
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.660, 95.870, 100.690, 90.00, 90.00, 90.00
R / Rfree (%)	19.61 / 25.4

The structure of Crystal Structure of Human JMJD2C Catalytic Domain also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Nickel atom in the Crystal Structure of Human JMJD2C Catalytic Domain (pdb code 2xml). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Human JMJD2C Catalytic Domain, PDB code: 2xml:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Human JMJD2C Catalytic Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Human JMJD2C Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1348 b:12.7 occ:1.00 O A:HOH2084 2.1 15.7 1.0 NE2 A:HIS278 2.2 4.7 1.0 OE2 A:GLU192 2.2 14.6 1.0 NE2 A:HIS190 2.2 12.8 1.0 O2' A:OGA601 2.2 27.5 1.0 O1 A:OGA601 2.3 10.4 1.0 CE1 A:HIS278 2.9 9.6 1.0 C1 A:OGA601 3.0 28.2 1.0 C2 A:OGA601 3.0 23.4 1.0 CE1 A:HIS190 3.0 18.4 1.0 CD A:GLU192 3.1 13.1 1.0 CD2 A:HIS190 3.3 12.1 1.0 CD2 A:HIS278 3.3 11.1 1.0 OE1 A:GLU192 3.4 8.2 1.0 ND1 A:HIS278 4.1 17.5 1.0 OG A:SER198 4.1 13.9 1.0 ND1 A:HIS190 4.2 8.0 1.0 O2 A:OGA601 4.2 23.5 1.0 N1 A:OGA601 4.2 19.9 1.0 CG A:HIS190 4.3 10.2 1.0 CG A:HIS278 4.4 13.9 1.0 CG A:GLU192 4.4 18.1 1.0 CB A:SER198 4.8 5.0 1.0 CG2 A:THR272 4.9 10.2 1.0 OG1 A:THR272 4.9 2.5 1.0 C4 A:OGA601 5.0 31.4 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Human JMJD2C Catalytic Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Human JMJD2C Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1348 b:12.0 occ:1.00 NE2 B:HIS190 2.1 14.9 1.0 OE2 B:GLU192 2.1 16.5 1.0 NE2 B:HIS278 2.2 5.6 1.0 O2' B:OGA601 2.2 25.1 1.0 O1 B:OGA601 2.2 15.0 1.0 O B:HOH2072 2.2 12.0 1.0 C2 B:OGA601 2.9 31.8 1.0 CE1 B:HIS278 2.9 12.2 1.0 C1 B:OGA601 2.9 26.0 1.0 CE1 B:HIS190 2.9 15.2 1.0 CD B:GLU192 3.1 14.9 1.0 CD2 B:HIS190 3.2 16.5 1.0 CD2 B:HIS278 3.3 15.8 1.0 OE1 B:GLU192 3.3 7.9 1.0 ND1 B:HIS190 4.1 12.9 1.0 ND1 B:HIS278 4.1 18.4 1.0 O2 B:OGA601 4.2 12.6 1.0 N1 B:OGA601 4.2 31.9 1.0 OG B:SER198 4.2 10.4 1.0 CG B:HIS190 4.2 10.8 1.0 CG B:HIS278 4.3 14.4 1.0 CG B:GLU192 4.4 21.5 1.0 C4 B:OGA601 4.9 28.8 1.0 CB B:SER198 4.9 2.6 1.0 NZ B:LYS243 4.9 43.3 1.0 CG2 B:THR272 5.0 11.8 1.0 OG1 B:THR272 5.0 5.0 1.0

L.Hillringhaus, W.W.Yue, N.R.Rose, S.S.Ng, C.Gileadi, C.Loenarz, S.H.Bello, J.E.Bray, C.J.Schofield, U.Oppermann. Structural and Evolutionary Basis For the Dual Substrate Selectivity of Human KDM4 Histone Demethylase Family. J.Biol.Chem. V. 286 41616 2011.
ISSN: ISSN 0021-9258
PubMed: 21914792
DOI: 10.1074/JBC.M111.283689