Atomistry » Nickel » PDB 2w94-2zpl » 2xml
Atomistry »
  Nickel »
    PDB 2w94-2zpl »
      2xml »

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

Protein crystallography data

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

Other elements in 2xml:

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

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

Nickel Binding Sites:

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 2xml

Go back to Nickel Binding Sites List in 2xml
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 2xml

Go back to Nickel Binding Sites List in 2xml
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

Reference:

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
Page generated: Wed Dec 16 01:20:31 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy