Nickel in PDB 6g5w: Crystal Structure of KDM4A with Compound Yp-03-038

The structure of Crystal Structure of KDM4A with Compound Yp-03-038, PDB code: 6g5w was solved by P.H.Malecki, D.M.Carter, U.Gohlke, E.Specker, M.Nazare, M.S.Weiss, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.57 / 1.83
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.362, 148.574, 56.390, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.8

The structure of Crystal Structure of KDM4A with Compound Yp-03-038 also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Nickel atom in the Crystal Structure of KDM4A with Compound Yp-03-038 (pdb code 6g5w). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of KDM4A with Compound Yp-03-038, PDB code: 6g5w:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of KDM4A with Compound Yp-03-038


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 KDM4A with Compound Yp-03-038 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:60.3 occ:0.80 NE2 A:HIS215 2.3 34.1 1.0 O A:HOH707 2.5 71.4 1.0 O A:HOH712 2.6 54.2 1.0 O A:HOH703 3.1 52.9 1.0 CE1 A:HIS215 3.2 30.9 1.0 CD2 A:HIS215 3.4 35.1 1.0 O A:HOH521 3.9 46.6 1.0 OE1 A:GLU214 3.9 44.4 1.0 ND1 A:HIS215 4.4 30.5 1.0 O B:HOH667 4.4 45.4 1.0 CG A:HIS215 4.5 30.4 1.0 CD A:GLU214 4.7 55.5 1.0 CG A:GLU214 4.9 43.6 1.0 CAH B:ENZ407 5.0 59.4 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of KDM4A with Compound Yp-03-038


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 KDM4A with Compound Yp-03-038 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni403 b:26.6 occ:1.00 OE1 A:GLU190 2.0 25.1 1.0 O4 A:CIT406 2.0 26.9 1.0 O A:HOH502 2.0 32.1 1.0 NE2 A:HIS188 2.1 25.4 1.0 O A:HOH571 2.1 27.4 1.0 NE2 A:HIS276 2.1 27.2 1.0 CE1 A:HIS188 2.9 28.6 1.0 CE1 A:HIS276 3.0 32.0 1.0 C5 A:CIT406 3.0 34.0 1.0 CD A:GLU190 3.0 30.8 1.0 CD2 A:HIS188 3.1 28.8 1.0 CD2 A:HIS276 3.2 25.7 1.0 O3 A:CIT406 3.3 39.4 1.0 OE2 A:GLU190 3.4 26.8 1.0 ND1 A:HIS188 4.1 25.1 1.0 O A:HOH667 4.1 46.5 1.0 O A:HOH603 4.1 37.5 1.0 ND1 A:HIS276 4.2 27.9 1.0 CG A:HIS188 4.2 22.7 1.0 OG A:SER196 4.3 30.0 1.0 CG A:HIS276 4.3 26.6 1.0 CG A:GLU190 4.3 25.5 1.0 C4 A:CIT406 4.4 32.5 1.0 O A:HOH666 4.9 26.5 0.5 NZ A:LYS241 4.9 95.1 1.0 CB A:SER196 4.9 26.2 1.0 O7 A:CIT406 5.0 40.9 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of KDM4A with Compound Yp-03-038


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of KDM4A with Compound Yp-03-038 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni402 b:28.2 occ:1.00 OE1 B:GLU190 2.1 25.3 1.0 O B:HOH501 2.1 30.6 1.0 O4 B:CIT406 2.1 26.3 1.0 NE2 B:HIS276 2.1 23.6 1.0 NE2 B:HIS188 2.2 25.9 1.0 O B:HOH544 2.2 27.2 1.0 C5 B:CIT406 2.9 33.1 1.0 CE1 B:HIS276 2.9 25.6 1.0 CE1 B:HIS188 3.0 28.8 1.0 O3 B:CIT406 3.1 42.1 1.0 CD B:GLU190 3.1 36.9 1.0 CD2 B:HIS188 3.2 27.3 1.0 CD2 B:HIS276 3.2 22.8 1.0 OE2 B:GLU190 3.5 29.8 1.0 O B:HOH631 4.1 36.9 1.0 ND1 B:HIS276 4.1 24.1 1.0 ND1 B:HIS188 4.1 23.4 1.0 O B:HOH647 4.2 40.2 1.0 CG B:HIS188 4.3 23.4 1.0 CG B:HIS276 4.3 21.9 1.0 OG B:SER196 4.4 31.3 1.0 C4 B:CIT406 4.4 27.2 1.0 CG B:GLU190 4.4 29.3 1.0 NZ B:LYS241 4.7 94.2 1.0 O7 B:CIT406 4.9 48.4 1.0 CB B:SER196 4.9 28.4 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of KDM4A with Compound Yp-03-038


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of KDM4A with Compound Yp-03-038 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni403 b:36.7 occ:1.00 O5 A:CIT407 1.9 38.4 1.0 NAE B:ENZ407 2.1 33.1 1.0 O7 A:CIT407 2.2 34.6 1.0 NAJ B:ENZ407 2.2 44.4 1.0 O2 A:CIT407 2.2 32.0 1.0 O B:HOH661 2.2 39.9 1.0 C6 A:CIT407 2.7 55.6 1.0 C3 A:CIT407 2.9 45.1 1.0 NAI B:ENZ407 2.9 51.4 1.0 CAC B:ENZ407 2.9 52.3 1.0 CAG B:ENZ407 3.1 39.0 1.0 C1 A:CIT407 3.1 39.6 1.0 CAL B:ENZ407 3.3 59.1 1.0 C2 A:CIT407 3.5 42.7 1.0 CAA B:ENZ407 3.8 51.5 1.0 O6 A:CIT407 3.9 47.5 1.0 CAK B:ENZ407 4.1 63.8 1.0 O3 A:CIT407 4.2 81.2 1.0 O1 A:CIT407 4.2 37.4 1.0 CAM B:ENZ407 4.2 65.5 1.0 CAD B:ENZ407 4.2 75.5 1.0 O B:HOH667 4.3 45.4 1.0 C4 A:CIT407 4.3 48.7 1.0 CAH B:ENZ407 4.4 59.4 1.0 CG B:GLU115 4.5 56.8 1.0 C5 A:CIT407 4.7 69.4 1.0 OE1 B:GLU115 4.8 76.6 1.0 CE1 A:HIS215 4.8 30.9 1.0 CAF B:ENZ407 4.8 80.4 1.0 ND1 A:HIS215 4.9 30.5 1.0 CD A:ARG218 4.9 58.8 1.0 CB B:PHE114 4.9 39.8 1.0 CD B:GLU115 4.9 66.3 1.0

P.H.Malecki, D.M.Carter, U.Gohlke, E.Specker, M.Nazare, M.S.Weiss, U.Heinemann. Crystal Structure of KDM4A with Compound Yp-03-038 To Be Published.