Zinc in PDB 1zbd: Structural Basis of Rab Effector Specificity: Crystal Structure of the Small G Protein RAB3A Complexed with the Effector Domain of Rabphilin-3A

The structure of Structural Basis of Rab Effector Specificity: Crystal Structure of the Small G Protein RAB3A Complexed with the Effector Domain of Rabphilin-3A, PDB code: 1zbd was solved by C.Ostermeier, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.00 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.315, 95.619, 47.715, 90.00, 94.49, 90.00
R / Rfree (%)	22.6 / 26.3

The structure of Structural Basis of Rab Effector Specificity: Crystal Structure of the Small G Protein RAB3A Complexed with the Effector Domain of Rabphilin-3A also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Structural Basis of Rab Effector Specificity: Crystal Structure of the Small G Protein RAB3A Complexed with the Effector Domain of Rabphilin-3A (pdb code 1zbd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structural Basis of Rab Effector Specificity: Crystal Structure of the Small G Protein RAB3A Complexed with the Effector Domain of Rabphilin-3A, PDB code: 1zbd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structural Basis of Rab Effector Specificity: Crystal Structure of the Small G Protein RAB3A Complexed with the Effector Domain of Rabphilin-3A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis of Rab Effector Specificity: Crystal Structure of the Small G Protein RAB3A Complexed with the Effector Domain of Rabphilin-3A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:39.8 occ:1.00 SG B:CYS111 2.5 27.2 1.0 SG B:CYS140 2.5 29.5 1.0 SG B:CYS114 2.6 27.4 1.0 SG B:CYS137 2.7 36.7 1.0 CB B:CYS137 3.3 19.9 1.0 CB B:CYS114 3.3 22.8 1.0 CB B:CYS140 3.4 31.1 1.0 CB B:CYS111 3.4 26.6 1.0 N B:CYS114 3.7 25.9 1.0 O B:HOH302 3.9 42.5 1.0 N B:CYS137 3.9 27.0 1.0 CA B:CYS114 4.1 24.2 1.0 CA B:CYS137 4.2 26.7 1.0 N B:CYS140 4.4 27.9 1.0 CA B:CYS140 4.5 28.7 1.0 C B:ASP113 4.7 29.1 1.0 CB B:ASP113 4.7 34.6 1.0 O B:CYS137 4.8 26.9 1.0 CA B:CYS111 4.8 29.0 1.0 C B:CYS137 4.9 24.9 1.0 C B:CYS114 5.0 27.9 1.0

Zinc binding site 2 out of 2 in the Structural Basis of Rab Effector Specificity: Crystal Structure of the Small G Protein RAB3A Complexed with the Effector Domain of Rabphilin-3A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis of Rab Effector Specificity: Crystal Structure of the Small G Protein RAB3A Complexed with the Effector Domain of Rabphilin-3A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:62.5 occ:1.00 SG B:CYS119 2.6 44.2 1.0 SG B:CYS94 2.8 52.6 1.0 SG B:CYS97 2.8 65.4 1.0 SG B:CYS122 2.8 62.7 1.0 CB B:CYS122 3.3 53.1 1.0 CB B:CYS97 3.4 62.5 1.0 CB B:CYS94 3.5 49.9 1.0 CB B:CYS119 3.8 42.0 1.0 N B:CYS97 3.8 61.5 1.0 N B:CYS122 4.2 53.1 1.0 CA B:CYS97 4.3 65.6 1.0 N B:CYS119 4.3 36.4 1.0 CA B:CYS122 4.4 51.3 1.0 CA B:CYS119 4.6 40.5 1.0 CB B:LEU96 4.7 51.5 1.0 N B:GLY98 4.9 70.1 1.0 CB B:LYS121 4.9 57.2 1.0 C B:LEU96 5.0 56.4 1.0 CA B:CYS94 5.0 50.0 1.0 O B:CYS119 5.0 42.7 1.0

C.Ostermeier, A.T.Brunger. Structural Basis of Rab Effector Specificity: Crystal Structure of the Small G Protein RAB3A Complexed with the Effector Domain of Rabphilin-3A. Cell(Cambridge,Mass.) V. 96 363 1999.
ISSN: ISSN 0092-8674
PubMed: 10025402
DOI: 10.1016/S0092-8674(00)80549-8