Nickel in PDB 5fyi: Crystal Structure of Human JMJD2A in Complex with Pyruvate

The structure of Crystal Structure of Human JMJD2A in Complex with Pyruvate, PDB code: 5fyi 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)	29.77 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.450, 148.830, 57.060, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23.6

The structure of Crystal Structure of Human JMJD2A in Complex with Pyruvate 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 Pyruvate (pdb code 5fyi). 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 Pyruvate, PDB code: 5fyi:
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 Pyruvate


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 Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:42.5 occ:1.00 OE2 A:GLU190 2.1 33.5 1.0 O1 A:PYR1355 2.2 38.1 0.8 NE2 A:HIS276 2.2 30.6 1.0 O A:HOH2083 2.3 35.5 1.0 NE2 A:HIS188 2.3 40.6 1.0 O3 A:PYR1355 2.4 33.9 0.8 C1 A:PYR1355 2.9 44.1 0.8 C2 A:PYR1355 3.0 43.6 0.8 CE1 A:HIS188 3.0 35.1 1.0 CD2 A:HIS276 3.1 32.2 1.0 CD A:GLU190 3.2 36.7 1.0 CE1 A:HIS276 3.3 33.7 1.0 CD2 A:HIS188 3.3 37.0 1.0 OE1 A:GLU190 3.6 36.2 1.0 O2 A:PYR1355 4.1 39.3 0.8 ND1 A:HIS188 4.2 35.0 1.0 OG A:SER196 4.3 37.3 1.0 CG A:HIS276 4.3 32.0 1.0 ND1 A:HIS276 4.4 30.9 1.0 CG A:HIS188 4.4 36.6 1.0 C3 A:PYR1355 4.4 42.8 0.8 CG A:GLU190 4.5 32.5 1.0 C3 A:PYR1356 4.5 51.7 0.6 O2 A:EDO1365 4.7 62.3 1.0 CG2 A:THR270 5.0 36.1 1.0 CB A:SER196 5.0 33.2 1.0

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


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 Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:42.1 occ:1.00 OE2 B:GLU190 2.2 34.4 1.0 O1 B:PYR1354 2.2 29.5 0.9 O3 B:PYR1354 2.3 36.2 0.9 NE2 B:HIS276 2.3 35.9 1.0 NE2 B:HIS188 2.3 34.4 1.0 O B:HOH2090 2.4 37.0 1.0 C1 B:PYR1354 2.9 41.6 0.9 C2 B:PYR1354 2.9 37.1 0.9 CD B:GLU190 3.2 35.9 1.0 CE1 B:HIS276 3.2 35.1 1.0 CE1 B:HIS188 3.2 41.6 1.0 CD2 B:HIS188 3.2 39.1 1.0 CD2 B:HIS276 3.3 35.6 1.0 OE1 B:GLU190 3.5 34.2 1.0 O2 B:PYR1354 4.1 43.9 0.9 OG B:SER196 4.3 37.4 1.0 ND1 B:HIS188 4.3 38.5 1.0 ND1 B:HIS276 4.3 35.2 1.0 CG B:HIS188 4.4 30.2 1.0 C3 B:PYR1354 4.4 37.4 0.9 CG B:HIS276 4.4 37.4 1.0 O1 B:EDO1364 4.5 56.7 1.0 CG B:GLU190 4.5 28.9 1.0 C3 B:PYR1355 4.9 50.4 0.6 CG2 B:THR270 4.9 32.7 1.0 CB B:SER196 5.0 31.8 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 Pyruvate To Be Published.