The binding sites of Zinc atom in the structure of Crystal Structure of Dna Primase From Pyrococcus Horikoshii (pdb code 1v33). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 1v33 structure was solved by N.ITO, O.NUREKI, M.SHIROUZU, S.YOKOYAMA, F.HANAOKA, RIKENSTRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 33.1-1.8 | Space group | P3221 | a (A) | 76.451 | b (A) | 76.451 | c (A) | 128.894 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 120.00 | Rfactor (%) | 21.9 | Rfree (%) | 24.4 |
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Zinc binding site 1 out of 1 in 1v33
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 1v33. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Arg104, A: Cys106, A: His108, A: Val113, A: Cys114, A: Ile116, A: Cys117, | conact list:
Atom | Atom | Distance (A) | Zn | CD A:Arg104 | 4.72 | Zn | NH1 A:Arg104 | 4.41 | Zn | CB A:Cys106 | 3.37 | Zn | SG A:Cys106 | 2.42 | Zn | CA A:Cys106 | 4.80 | Zn | NE2 A:His108 | 2.23 | Zn | ND1 A:His108 | 4.28 | Zn | CD2 A:His108 | 2.85 | Zn | CE1 A:His108 | 3.36 | Zn | CG A:His108 | 4.07 | Zn | O A:Val113 | 4.93 | Zn | C A:Val113 | 4.14 | Zn | CA A:Val113 | 4.46 | Zn | O A:Cys114 | 4.06 | Zn | N A:Cys114 | 3.46 | Zn | CB A:Cys114 | 3.33 | Zn | SG A:Cys114 | 2.40 | Zn | C A:Cys114 | 4.22 | Zn | CA A:Cys114 | 3.87 | Zn | N A:Ile116 | 4.74 | Zn | CB A:Ile116 | 4.41 | Zn | C A:Ile116 | 4.56 | Zn | CA A:Ile116 | 4.81 | Zn | N A:Cys117 | 3.47 | Zn | CB A:Cys117 | 3.20 | Zn | SG A:Cys117 | 2.43 | Zn | CA A:Cys117 | 3.94 |
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