Nickel in PDB 4gaz: Crystal Structure of A Jumonji Domain-Containing Protein JMJD5

All present enzymatic activity of Crystal Structure of A Jumonji Domain-Containing Protein JMJD5:
1.14.11.27;

The structure of Crystal Structure of A Jumonji Domain-Containing Protein JMJD5, PDB code: 4gaz was solved by H.Wang, X.Zhou, X.Zhang, Y.Tao, N.Chen, J.Zang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.18 / 2.81
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.431, 69.431, 270.052, 90.00, 90.00, 120.00
R / Rfree (%)	22.1 / 27.4

The binding sites of Nickel atom in the Crystal Structure of A Jumonji Domain-Containing Protein JMJD5 (pdb code 4gaz). 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 A Jumonji Domain-Containing Protein JMJD5, PDB code: 4gaz:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of A Jumonji Domain-Containing Protein JMJD5


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 A Jumonji Domain-Containing Protein JMJD5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:81.8 occ:1.00 O1 A:OGA502 2.2 87.2 1.0 O2' A:OGA502 2.3 72.8 1.0 NE2 A:HIS321 2.3 69.4 1.0 OD2 A:ASP323 2.5 75.1 1.0 NE2 A:HIS400 2.7 74.1 1.0 OD1 A:ASP323 2.8 72.3 1.0 C1 A:OGA502 2.8 77.7 1.0 C2 A:OGA502 2.9 79.4 1.0 CG A:ASP323 3.0 74.1 1.0 CE1 A:HIS321 3.2 71.9 1.0 CD2 A:HIS321 3.3 69.1 1.0 O A:HOH1009 3.6 80.8 1.0 CE1 A:HIS400 3.6 81.5 1.0 CD2 A:HIS400 3.7 73.2 1.0 O2 A:OGA502 4.0 67.8 1.0 N1 A:OGA502 4.3 70.2 1.0 ND1 A:HIS321 4.3 68.1 1.0 CZ2 A:TRP414 4.4 71.0 1.0 CG A:HIS321 4.4 73.0 1.0 CB A:ASP323 4.5 74.1 1.0 ND1 A:HIS400 4.7 74.0 1.0 CG A:HIS400 4.8 69.2 1.0 CH2 A:TRP310 4.9 68.5 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of A Jumonji Domain-Containing Protein JMJD5


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 A Jumonji Domain-Containing Protein JMJD5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:84.0 occ:1.00 O2' B:OGA502 2.2 74.6 1.0 NE2 B:HIS321 2.3 73.7 1.0 O1 B:OGA502 2.4 80.6 1.0 OD2 B:ASP323 2.5 76.8 1.0 NE2 B:HIS400 2.7 74.9 1.0 C2 B:OGA502 2.9 77.4 1.0 OD1 B:ASP323 2.9 73.8 1.0 C1 B:OGA502 3.0 77.5 1.0 CG B:ASP323 3.1 76.8 1.0 CE1 B:HIS321 3.2 74.6 1.0 CD2 B:HIS321 3.3 73.8 1.0 CE1 B:HIS400 3.4 80.5 1.0 CD2 B:HIS400 3.8 72.8 1.0 CZ2 B:TRP414 4.0 64.1 1.0 O2 B:OGA502 4.2 73.2 1.0 N1 B:OGA502 4.3 72.1 1.0 ND1 B:HIS321 4.4 74.5 1.0 CG B:HIS321 4.5 80.0 1.0 CB B:ASP323 4.5 81.0 1.0 ND1 B:HIS400 4.6 78.3 1.0 NE1 B:TRP414 4.6 76.1 1.0 CE2 B:TRP414 4.7 68.0 1.0 CG B:HIS400 4.8 80.4 1.0 CH2 B:TRP310 4.9 67.3 1.0 C4 B:OGA502 4.9 74.0 1.0 CH2 B:TRP414 5.0 64.8 1.0

H.Wang, X.Zhou, X.Zhang, Y.Tao, N.Chen, J.Zang. Crystal Structure of A Jumonji Domain-Containing Protein JMJD5 To Be Published.