Nickel in the structure of Structure of KIAA1718 Jumonji Domain in Complex With N- Oxalylglycine (pdb 3kvb)

The binding sites of Nickel atom in the structure of Structure of KIAA1718 Jumonji Domain in Complex With N- Oxalylglycine (pdb code 3kvb). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 3kvb structure was solved by J.R.HORTON, A.K.UPADHYAY, H.H.QI, X.ZHANG, Y.SHI, X.CHENG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 33.7-2.7 Space group P6122 a (A) 78.300 b (A) 78.300 c (A) 289.100 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 21.6 Rfree (%) 26.7 Nickel Binding Sites: Nickel binding site 1 out of 2 in 3kvb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 3kvb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His282, A: Asp284, A: His354, A: Oxy491, A: Oga5798, conact list: Atom Atom Distance (A) Ni NE2 A:His282 2.48 Ni ND1 A:His282 4.47 Ni CD2 A:His282 3.54 Ni CE1 A:His282 3.31 Ni CG A:His282 4.62 Ni CB A:Asp284 4.73 Ni OD2 A:Asp284 3.79 Ni OD1 A:Asp284 2.37 Ni CG A:Asp284 3.42 Ni NE2 A:His354 2.36 Ni ND1 A:His354 4.41 Ni CD2 A:His354 3.39 Ni CE1 A:His354 3.26 Ni CG A:His354 4.50 Ni O2 A:Oxy491 4.74 Ni N1 A:Oga5798 3.92 Ni O2 A:Oga5798 2.04 Ni C4 A:Oga5798 4.78 Ni C1 A:Oga5798 2.62 Ni O1 A:Oga5798 3.80 Ni O2' A:Oga5798 1.93 Ni C2 A:Oga5798 2.59 interactive model: Nickel binding site 2 out of 2 in 3kvb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 3kvb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Ser249, A: Trp250, A: Val251, A: Asn368, A: Phe369, A: Leu370, A: Phe396, conact list: Atom Atom Distance (A) Ni CB A:Ser249 3.91 Ni OG A:Ser249 3.21 Ni C A:Ser249 4.01 Ni CA A:Ser249 3.99 Ni N A:Trp250 3.35 Ni CB A:Trp250 3.96 Ni C A:Trp250 4.21 Ni CA A:Trp250 4.03 Ni N A:Val251 3.40 Ni CB A:Val251 3.93 Ni CG2 A:Val251 3.76 Ni CA A:Val251 4.28 Ni O A:Asn368 4.74 Ni N A:Phe369 4.82 Ni CB A:Phe369 3.84 Ni C A:Phe369 3.83 Ni CA A:Phe369 3.58 Ni O A:Leu370 3.85 Ni N A:Leu370 3.06 Ni CB A:Leu370 4.02 Ni CD1 A:Leu370 4.83 Ni C A:Leu370 4.37 Ni CG A:Leu370 4.36 Ni CA A:Leu370 4.01 Ni CZ A:Phe396 4.37 Ni CE1 A:Phe396 4.48 interactive model: