Nickel in PDB 5f5i: Crystal Structure of Human JMJD2A Complexed with KDOOA011340

The structure of Crystal Structure of Human JMJD2A Complexed with KDOOA011340, PDB code: 5f5i was solved by T.Krojer, M.Vollmar, L.Crawley, A.Szykowska, C.Gileadi, C.Johansson, K.England, H.Yang, N.Burgess-Brown, P.Brennan, C.Bountra, C.H.Arrowsmith, A.Edwards, U.Oppermann, F.Von Delft, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.01 / 2.63
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.030, 149.580, 57.920, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.3

The structure of Crystal Structure of Human JMJD2A Complexed with KDOOA011340 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of Human JMJD2A Complexed with KDOOA011340 (pdb code 5f5i). 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 Complexed with KDOOA011340, PDB code: 5f5i:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Human JMJD2A Complexed with KDOOA011340


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 Complexed with KDOOA011340 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:45.8 occ:1.00 OE1 A:GLU190 2.1 36.8 1.0 N1 A:5V1504 2.3 61.0 1.0 O A:HOH610 2.3 44.8 1.0 N2 A:5V1504 2.4 67.2 1.0 NE2 A:HIS276 2.4 34.2 1.0 NE2 A:HIS188 2.5 34.4 1.0 C7 A:5V1504 2.9 68.8 1.0 CD A:GLU190 3.1 36.1 1.0 C5 A:5V1504 3.2 63.7 1.0 C6 A:5V1504 3.2 64.8 1.0 CE1 A:HIS276 3.2 34.1 1.0 C4 A:5V1504 3.2 59.9 1.0 CD2 A:HIS188 3.4 34.0 1.0 CE1 A:HIS188 3.4 34.3 1.0 OE2 A:GLU190 3.4 36.6 1.0 CD2 A:HIS276 3.5 34.3 1.0 OG A:SER196 4.3 38.0 1.0 C8 A:5V1504 4.4 69.5 1.0 ND1 A:HIS276 4.4 34.0 1.0 ND1 A:HIS188 4.4 34.0 1.0 CG A:GLU190 4.5 35.4 1.0 CG A:HIS188 4.5 33.7 1.0 C14 A:5V1504 4.5 62.4 1.0 O A:HOH666 4.5 42.6 1.0 C3 A:5V1504 4.6 60.4 1.0 CG A:HIS276 4.6 34.0 1.0 CB A:SER196 4.9 38.2 1.0 CG2 A:THR270 4.9 37.0 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Human JMJD2A Complexed with KDOOA011340


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 Complexed with KDOOA011340 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:45.5 occ:1.00 N1 B:5V1504 2.2 47.1 1.0 OE1 B:GLU190 2.2 37.0 1.0 O B:HOH613 2.3 26.9 1.0 N2 B:5V1504 2.5 50.7 1.0 NE2 B:HIS276 2.5 32.9 1.0 NE2 B:HIS188 2.5 35.3 1.0 C5 B:5V1504 3.1 50.6 1.0 C7 B:5V1504 3.1 51.5 1.0 C4 B:5V1504 3.1 47.2 1.0 C6 B:5V1504 3.2 49.7 1.0 CD B:GLU190 3.2 37.6 1.0 CE1 B:HIS276 3.3 32.7 1.0 CE1 B:HIS188 3.4 35.2 1.0 CD2 B:HIS188 3.5 35.1 1.0 OE2 B:GLU190 3.5 37.6 1.0 CD2 B:HIS276 3.5 32.6 1.0 OG B:SER196 4.3 38.9 1.0 C14 B:5V1504 4.4 50.5 1.0 C3 B:5V1504 4.4 47.9 1.0 ND1 B:HIS188 4.5 35.2 1.0 ND1 B:HIS276 4.5 32.5 1.0 CG B:HIS188 4.5 35.0 1.0 C8 B:5V1504 4.5 52.1 1.0 CG B:GLU190 4.6 37.6 1.0 CG B:HIS276 4.6 32.2 1.0 OD1 B:ASN198 4.9 40.2 0.5 CB B:SER196 4.9 39.2 1.0 CG2 B:THR270 4.9 36.3 1.0 C2 B:5V1504 5.0 49.1 1.0

V.Bavetsias, R.M.Lanigan, G.F.Ruda, B.Atrash, M.G.Mclaughlin, A.Tumber, N.Y.Mok, Y.V.Le Bihan, S.Dempster, K.J.Boxall, F.Jeganathan, S.B.Hatch, P.Savitsky, S.Velupillai, T.Krojer, K.S.England, J.Sejberg, C.Thai, A.Donovan, A.Pal, G.Scozzafava, J.M.Bennett, A.Kawamura, C.Johansson, A.Szykowska, C.Gileadi, N.A.Burgess-Brown, F.Von Delft, U.Oppermann, Z.Walters, J.Shipley, F.I.Raynaud, S.M.Westaway, R.K.Prinjha, O.Fedorov, R.Burke, C.J.Schofield, I.M.Westwood, C.Bountra, S.Muller, R.L.Van Montfort, P.E.Brennan, J.Blagg. 8-Substituted Pyrido[3,4-D]Pyrimidin-4(3H)-One Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors. J.Med.Chem. V. 59 1388 2016.
ISSN: ISSN 0022-2623
PubMed: 26741168
DOI: 10.1021/ACS.JMEDCHEM.5B01635