Nickel in PDB 3kvb: Structure of KIAA1718 Jumonji Domain in Complex with N- Oxalylglycine

The structure of Structure of KIAA1718 Jumonji Domain in Complex with N- Oxalylglycine, PDB code: 3kvb was solved by J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.67 / 2.69
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	78.300, 78.300, 289.100, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 26.7

The binding sites of Nickel atom in the Structure of KIAA1718 Jumonji Domain in Complex with N- Oxalylglycine (pdb code 3kvb). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of KIAA1718 Jumonji Domain in Complex with N- Oxalylglycine, PDB code: 3kvb:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of KIAA1718 Jumonji Domain in Complex with N- Oxalylglycine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of KIAA1718 Jumonji Domain in Complex with N- Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni489 b:66.0 occ:1.00 O2' A:OGA5798 1.9 0.2 1.0 O2 A:OGA5798 2.0 0.6 1.0 NE2 A:HIS354 2.4 46.0 1.0 OD1 A:ASP284 2.4 48.7 1.0 NE2 A:HIS282 2.5 42.2 1.0 C2 A:OGA5798 2.6 0.2 1.0 C1 A:OGA5798 2.6 0.2 1.0 CE1 A:HIS354 3.3 43.6 1.0 CE1 A:HIS282 3.3 42.1 1.0 CD2 A:HIS354 3.4 42.0 1.0 CG A:ASP284 3.4 49.4 1.0 CD2 A:HIS282 3.5 40.6 1.0 OD2 A:ASP284 3.8 53.3 1.0 O1 A:OGA5798 3.8 0.2 1.0 N1 A:OGA5798 3.9 0.7 1.0 ND1 A:HIS354 4.4 43.4 1.0 ND1 A:HIS282 4.5 42.1 1.0 CG A:HIS354 4.5 41.7 1.0 CG A:HIS282 4.6 40.0 1.0 CB A:ASP284 4.7 43.4 1.0 O2 A:OXY491 4.7 77.9 1.0 C4 A:OGA5798 4.8 0.7 1.0

Nickel binding site 2 out of 2 in the Structure of KIAA1718 Jumonji Domain in Complex with N- Oxalylglycine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of KIAA1718 Jumonji Domain in Complex with N- Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni490 b:68.1 occ:1.00 N A:LEU370 3.1 35.2 1.0 OG A:SER249 3.2 31.3 1.0 N A:TRP250 3.3 38.0 1.0 N A:VAL251 3.4 39.3 1.0 CA A:PHE369 3.6 36.1 1.0 CG2 A:VAL251 3.8 37.7 1.0 C A:PHE369 3.8 35.6 1.0 CB A:PHE369 3.8 38.4 1.0 O A:LEU370 3.8 34.4 1.0 CB A:SER249 3.9 37.6 1.0 CB A:VAL251 3.9 41.3 1.0 CB A:TRP250 4.0 34.4 1.0 CA A:SER249 4.0 39.5 1.0 C A:SER249 4.0 39.1 1.0 CA A:LEU370 4.0 34.7 1.0 CB A:LEU370 4.0 35.4 1.0 CA A:TRP250 4.0 36.1 1.0 C A:TRP250 4.2 37.3 1.0 CA A:VAL251 4.3 41.9 1.0 CG A:LEU370 4.4 37.0 1.0 C A:LEU370 4.4 34.8 1.0 CZ A:PHE396 4.4 64.0 1.0 CE1 A:PHE396 4.5 64.1 1.0 O A:ASN368 4.7 37.4 1.0 N A:PHE369 4.8 36.3 1.0 CD1 A:LEU370 4.8 36.5 1.0

J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, X.Cheng. Enzymatic and Structural Insights For Substrate Specificity of A Family of Jumonji Histone Lysine Demethylases. Nat.Struct.Mol.Biol. V. 17 38 2010.
ISSN: ISSN 1545-9993
PubMed: 20023638
DOI: 10.1038/NSMB.1753