The binding sites of Zinc atom in the structure of Crystal Structure of Rabggtase(Delta Lrr; Delta Ig)in Complex With Mono-Prenylated Peptide Ser-Cys-Ser-Cys(Gg) Derivated From RAB7 (pdb code 3dsv). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3dsv structure was solved by Z.GUO, S.YU, R.S.GOODY, K.ALEXANDROV, W.BLANKENFELDT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 29.2-2.1 | Space group | P212121 | a (A) | 67.035 | b (A) | 90.613 | c (A) | 114.376 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | 14.9 | Rfree (%) | 21.1 |
|
Zinc binding site 1 out of 1 in 3dsv
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3dsv. 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: His2, B: Asp238, B: Cys240, B: Asp280, B: Phe289, B: His290, | conact list:
Atom | Atom | Distance (A) | Zn | NE2 A:His2 | 2.20 | Zn | ND1 A:His2 | 4.30 | Zn | CD2 A:His2 | 2.67 | Zn | CE1 A:His2 | 3.45 | Zn | CG A:His2 | 3.98 | Zn | CB B:Asp238 | 4.17 | Zn | OD2 B:Asp238 | 2.25 | Zn | OD1 B:Asp238 | 2.59 | Zn | CG B:Asp238 | 2.73 | Zn | N B:Cys240 | 4.07 | Zn | CB B:Cys240 | 3.36 | Zn | SG B:Cys240 | 2.28 | Zn | CA B:Cys240 | 4.30 | Zn | CB B:Asp280 | 4.20 | Zn | CA B:Asp280 | 4.95 | Zn | CD1 B:Phe289 | 4.68 | Zn | CE1 B:Phe289 | 4.06 | Zn | NE2 B:His290 | 2.20 | Zn | ND1 B:His290 | 4.32 | Zn | CD2 B:His290 | 3.10 | Zn | CE1 B:His290 | 3.24 | Zn | CG B:His290 | 4.29 |
| interactive model:
|
|