Nickel in PDB 7jm5: Crystal Structure of KDM4B in Complex with QC6352

All present enzymatic activity of Crystal Structure of KDM4B in Complex with QC6352:
1.14.11.66;

The structure of Crystal Structure of KDM4B in Complex with QC6352, PDB code: 7jm5 was solved by S.W.White, M.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.03 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.825, 97.107, 80.068, 90, 106.52, 90
R / Rfree (%)	19.6 / 24.4

The structure of Crystal Structure of KDM4B in Complex with QC6352 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Nickel atom in the Crystal Structure of KDM4B in Complex with QC6352 (pdb code 7jm5). 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 KDM4B in Complex with QC6352, PDB code: 7jm5:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of KDM4B in Complex with QC6352


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 KDM4B in Complex with QC6352 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:49.8 occ:1.00 NE2 A:HIS277 2.0 67.8 1.0 NE2 A:HIS189 2.0 68.4 1.0 OE2 A:GLU191 2.0 83.8 1.0 N4 A:9DJ402 2.0 107.2 1.0 O A:HOH501 2.2 52.1 1.0 O A:HOH503 2.3 48.4 1.0 CE1 A:HIS189 2.6 65.1 1.0 CE1 A:HIS277 2.9 64.0 1.0 C5 A:9DJ402 2.9 93.2 1.0 C3 A:9DJ402 2.9 94.3 1.0 CD2 A:HIS277 3.0 62.0 1.0 CD A:GLU191 3.1 73.7 1.0 CD2 A:HIS189 3.2 63.9 1.0 OE1 A:GLU191 3.6 81.8 1.0 ND1 A:HIS189 3.8 63.0 1.0 ND1 A:HIS277 4.0 61.1 1.0 CG A:HIS277 4.1 59.4 1.0 CG A:HIS189 4.1 60.5 1.0 C6 A:9DJ402 4.2 86.9 1.0 C2 A:9DJ402 4.2 86.8 1.0 CG A:GLU191 4.3 58.7 1.0 C1 A:9DJ402 4.7 85.1 1.0 OG A:SER197 4.7 54.4 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of KDM4B in Complex with QC6352


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 KDM4B in Complex with QC6352 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:62.3 occ:1.00 N4 B:9DJ403 2.0 105.5 1.0 NE2 B:HIS277 2.0 69.5 1.0 OE2 B:GLU191 2.0 83.9 1.0 NE2 B:HIS189 2.0 77.0 1.0 O B:HOH501 2.0 77.2 1.0 O B:HOH502 2.4 67.0 1.0 C3 B:9DJ403 2.8 90.0 1.0 CE1 B:HIS189 2.8 70.7 1.0 CD2 B:HIS277 2.9 66.5 1.0 C5 B:9DJ403 2.9 94.9 1.0 CD B:GLU191 3.0 72.1 1.0 CE1 B:HIS277 3.0 65.9 1.0 CD2 B:HIS189 3.1 70.6 1.0 OE1 B:GLU191 3.4 79.3 1.0 ND1 B:HIS189 4.0 69.4 1.0 CG B:HIS277 4.0 64.2 1.0 ND1 B:HIS277 4.1 65.6 1.0 CG B:HIS189 4.1 68.2 1.0 C2 B:9DJ403 4.1 79.0 1.0 C6 B:9DJ403 4.2 84.9 1.0 CG B:GLU191 4.3 63.1 1.0 OG B:SER197 4.6 48.1 1.0 C1 B:9DJ403 4.7 85.1 1.0 NZ B:LYS242 5.0 101.0 1.0

S.Singh, A.Abu-Zaid, H.Jin, J.Fang, Q.Wu, T.Wang, H.Feng, W.Quarni, Y.Shao, L.Maxham, A.Abdolvahabi, M.K.Yun, S.Vaithiyalingam, H.Tan, J.Bowling, V.Honnell, B.Young, Y.Guo, R.Bajpai, S.M.Pruett-Miller, G.C.Grosveld, M.Hatley, B.Xu, Y.Fan, G.Wu, E.Y.Chen, T.Chen, P.W.Lewis, Z.Rankovic, Y.Li, A.J.Murphy, J.Easton, J.Peng, X.Chen, R.Wang, S.W.White, A.M.Davidoff, J.Yang. Targeting KDM4 For Treating PAX3-FOXO1-Driven Alveolar Rhabdomyosarcoma. Sci Transl Med V. 14 Q2096 2022.
ISSN: ESSN 1946-6242
PubMed: 35857643
DOI: 10.1126/SCITRANSLMED.ABQ2096