Nickel in PDB 5fyc: Crystal Structure of Human JMJD2A in Complex with Succinate

The structure of Crystal Structure of Human JMJD2A in Complex with Succinate, PDB code: 5fyc was solved by R.Nowak, J.Kopec, C.Johansson, A.Szykowska, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.10 / 2.26
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.650, 149.440, 57.280, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.9

The structure of Crystal Structure of Human JMJD2A in Complex with Succinate also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of Human JMJD2A in Complex with Succinate (pdb code 5fyc). 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 JMJD2A in Complex with Succinate, PDB code: 5fyc:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Human JMJD2A in Complex with Succinate


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 JMJD2A in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:36.4 occ:1.00 O A:HOH2084 2.0 43.1 1.0 OE2 A:GLU190 2.1 34.2 1.0 NE2 A:HIS276 2.2 29.9 1.0 O A:HOH2080 2.3 31.7 1.0 NE2 A:HIS188 2.3 34.4 1.0 O3 A:FUM1354 2.3 34.7 1.0 CE1 A:HIS188 3.1 32.8 1.0 CD A:GLU190 3.1 33.4 1.0 C2 A:FUM1354 3.1 44.9 1.0 CE1 A:HIS276 3.2 31.1 1.0 CD2 A:HIS276 3.2 37.0 1.0 CD2 A:HIS188 3.4 36.5 1.0 O1 A:FUM1354 3.4 39.6 1.0 OE1 A:GLU190 3.5 32.6 1.0 ND1 A:HIS188 4.2 32.8 1.0 O A:HOH2081 4.3 42.5 1.0 ND1 A:HIS276 4.3 33.4 1.0 CG A:HIS276 4.3 33.0 1.0 OG A:SER196 4.3 34.5 1.0 CG A:HIS188 4.4 34.7 1.0 C4 A:FUM1354 4.4 45.5 1.0 CG A:GLU190 4.4 32.0 1.0 CB A:SER196 5.0 32.4 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Human JMJD2A in Complex with Succinate


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 JMJD2A in Complex with Succinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:36.8 occ:1.00 OE2 B:GLU190 2.1 34.9 1.0 O8 B:FUM1354 2.2 29.5 1.0 NE2 B:HIS188 2.2 26.0 1.0 O B:HOH2093 2.3 39.8 1.0 O B:HOH2098 2.3 39.6 1.0 NE2 B:HIS276 2.4 30.4 1.0 CE1 B:HIS188 3.1 28.4 1.0 CD B:GLU190 3.2 34.1 1.0 C6 B:FUM1354 3.2 32.8 1.0 CE1 B:HIS276 3.2 31.2 1.0 CD2 B:HIS188 3.3 30.0 1.0 CD2 B:HIS276 3.4 29.5 1.0 O7 B:FUM1354 3.4 36.0 1.0 OE1 B:GLU190 3.5 30.0 1.0 O B:HOH2092 4.0 40.6 1.0 ND1 B:HIS188 4.2 29.3 1.0 CG B:HIS188 4.4 27.1 1.0 ND1 B:HIS276 4.4 31.0 1.0 OG B:SER196 4.4 41.6 1.0 CG B:HIS276 4.5 31.6 1.0 CG B:GLU190 4.5 30.9 1.0 C5 B:FUM1354 4.5 34.2 1.0 CB B:SER196 5.0 33.3 1.0

R.Nowak, J.Kopec, C.Johansson, A.Szykowska, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann. Crystal Structure of Human JMJD2A in Complex with Succinate To Be Published.