Zinc in PDB 4z8y: Crystal Structure of Rab Gtpase SEC4P Mutant - S29V

The structure of Crystal Structure of Rab Gtpase SEC4P Mutant - S29V, PDB code: 4z8y was solved by F.C.Rinadi, R.N.Collins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.30 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.720, 75.450, 66.230, 90.00, 91.58, 90.00
R / Rfree (%)	23.6 / 29.8

The structure of Crystal Structure of Rab Gtpase SEC4P Mutant - S29V also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Rab Gtpase SEC4P Mutant - S29V (pdb code 4z8y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Rab Gtpase SEC4P Mutant - S29V, PDB code: 4z8y:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Rab Gtpase SEC4P Mutant - S29V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Rab Gtpase SEC4P Mutant - S29V within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:18.8 occ:1.00 OD2 A:ASP166 1.8 14.1 1.0 OD1 A:ASP43 2.0 19.2 1.0 O A:HOH404 2.1 20.3 1.0 OD2 A:ASP43 2.6 22.1 1.0 CG A:ASP43 2.6 20.2 1.0 CG A:ASP166 2.8 15.3 1.0 OD1 A:ASP166 3.1 15.5 1.0 O A:HOH364 4.1 21.5 1.0 NH1 A:ARG39 4.1 16.9 1.0 O A:HOH338 4.1 13.6 1.0 CB A:ASP43 4.1 20.5 1.0 CB A:ASP166 4.2 15.4 1.0 CD A:ARG39 4.5 16.2 1.0 CA A:ASP43 4.7 21.2 1.0 O A:HOH315 4.8 24.5 1.0 CZ A:ARG39 5.0 16.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Rab Gtpase SEC4P Mutant - S29V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Rab Gtpase SEC4P Mutant - S29V within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:14.7 occ:1.00 OD2 B:ASP166 1.9 12.6 1.0 O B:HOH366 2.0 14.1 1.0 O A:HOH302 2.1 20.7 1.0 NE2 A:HIS121 2.1 16.8 1.0 OD2 B:ASP43 2.1 13.5 1.0 OD1 B:ASP43 2.2 13.1 1.0 CG B:ASP43 2.5 14.5 1.0 CG B:ASP166 3.0 14.0 1.0 CE1 A:HIS121 3.1 17.5 1.0 CD2 A:HIS121 3.1 18.6 1.0 O A:ILE85 3.2 39.4 1.0 OD1 B:ASP166 3.5 13.8 1.0 CB B:ASP43 4.0 14.9 1.0 ND1 A:HIS121 4.2 17.1 1.0 NH1 B:ARG39 4.2 12.4 1.0 O B:HOH371 4.3 34.1 1.0 CG A:HIS121 4.3 17.4 1.0 CB B:ASP166 4.3 14.4 1.0 O B:HOH357 4.3 20.4 1.0 CG1 A:ILE85 4.4 38.1 1.0 C A:ILE85 4.4 39.1 1.0 CD B:ARG39 4.7 11.4 1.0 CA B:ASP43 4.8 15.6 1.0 CD1 A:ILE85 4.9 34.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Rab Gtpase SEC4P Mutant - S29V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Rab Gtpase SEC4P Mutant - S29V within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:26.3 occ:1.00 OE1 B:GLU182 2.0 21.2 1.0 O B:HOH344 2.8 24.8 1.0 O B:HOH444 2.8 27.5 1.0 CD B:GLU182 2.9 20.2 1.0 OE2 B:GLU182 3.1 18.9 1.0 O B:HOH350 3.9 16.3 1.0 ND2 B:ASN65 4.3 19.8 1.0 CG B:GLU182 4.3 19.9 1.0 CA B:GLU182 4.5 19.9 1.0 O B:HOH416 4.6 19.5 1.0 CB B:GLU182 4.7 19.7 1.0 O B:GLN181 5.0 16.1 1.0

F.C.Rinaldi, M.Packer, R.Collins. New Insights Into the Molecular Mechanism of the Rab Gtpase SEC4P Activation. Bmc Struct.Biol. V. 15 14 2015.
ISSN: ESSN 1472-6807
PubMed: 26263895
DOI: 10.1186/S12900-015-0041-5