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 |
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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:
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