Nickel in PDB 2vd7: Crystal Structure of JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid

The structure of Crystal Structure of JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid, PDB code: 2vd7 was solved by S.S.Ng, F.Von Delft, E.S.Pilka, K.L.Kavanagh, M.A.Mcdonough, P.Savitsky, C.H.Arrowsmith, J.Weigelt, A.Edwards, M.Sundstrom, C.J.Schofield, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.63 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.285, 149.121, 57.566, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21.9

The structure of Crystal Structure of JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid (pdb code 2vd7). 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 JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid, PDB code: 2vd7:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid


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 JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:26.5 occ:1.00 O21 A:PD21356 2.1 30.7 1.0 OE2 A:GLU190 2.2 42.1 1.0 NE2 A:HIS188 2.2 39.0 1.0 NE2 A:HIS276 2.2 37.4 1.0 N1 A:PD21356 2.2 29.4 1.0 O A:HOH2096 2.2 34.7 1.0 C21 A:PD21356 2.9 30.3 1.0 C2 A:PD21356 3.0 30.9 1.0 CE1 A:HIS276 3.0 37.0 1.0 CE1 A:HIS188 3.1 35.1 1.0 CD A:GLU190 3.1 40.0 1.0 CD2 A:HIS188 3.2 34.7 1.0 C6 A:PD21356 3.2 30.1 1.0 CD2 A:HIS276 3.3 32.9 1.0 OE1 A:GLU190 3.4 40.5 1.0 O A:HOH2091 3.8 35.4 1.0 O22 A:PD21356 4.0 30.7 1.0 O A:HOH2121 4.1 30.6 1.0 ND1 A:HIS188 4.2 35.9 1.0 ND1 A:HIS276 4.2 36.6 1.0 CG A:HIS188 4.3 35.6 1.0 C3 A:PD21356 4.3 30.1 1.0 CG A:HIS276 4.4 34.5 1.0 OG A:SER196 4.4 38.4 1.0 O A:HOH2141 4.5 43.5 1.0 CG A:GLU190 4.5 39.1 1.0 C5 A:PD21356 4.5 29.5 1.0 ND2 A:ASN198 4.9 34.3 0.5 C4 A:PD21356 4.9 30.6 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid


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 JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:27.5 occ:1.00 O B:HOH2100 2.0 30.9 1.0 NE2 B:HIS188 2.1 35.8 1.0 OE2 B:GLU190 2.1 45.0 1.0 NE2 B:HIS276 2.1 37.8 1.0 N1 B:PD21356 2.2 32.4 1.0 O21 B:PD21356 2.2 34.3 1.0 C21 B:PD21356 3.0 34.6 1.0 C2 B:PD21356 3.0 35.0 1.0 CE1 B:HIS276 3.0 36.7 1.0 CE1 B:HIS188 3.1 37.3 1.0 CD2 B:HIS188 3.1 37.9 1.0 C6 B:PD21356 3.2 31.8 1.0 CD2 B:HIS276 3.2 35.8 1.0 CD B:GLU190 3.2 43.4 1.0 O B:HOH2185 3.3 53.5 1.0 OE1 B:GLU190 3.6 42.9 1.0 O22 B:PD21356 4.1 35.1 1.0 ND1 B:HIS188 4.2 34.4 1.0 ND1 B:HIS276 4.2 37.5 1.0 CG B:HIS188 4.2 37.1 1.0 CG B:HIS276 4.3 37.1 1.0 O B:HOH2132 4.3 26.0 1.0 C3 B:PD21356 4.3 34.4 1.0 OG B:SER196 4.4 42.3 1.0 C5 B:PD21356 4.4 32.2 1.0 CG B:GLU190 4.5 40.8 1.0 O B:HOH2149 4.5 62.1 1.0 C4 B:PD21356 4.9 33.7 1.0

N.R.Rose, S.S.Ng, J.Mecinovic, B.M.Lienard, S.H.Bello, Z.Sun, M.A.Mcdonough, U.Oppermann, C.J.Schofield. Inhibitor Scaffolds For 2-Oxoglutarate-Dependent Histone Lysine Demethylases. J. Med. Chem. V. 51 7053 2008.
ISSN: ISSN 1520-4804
PubMed: 18942826
DOI: 10.1021/JM800936S