Zinc in PDB 4gvl: Crystal Structure of the Gsuk Rck Domain

The structure of Crystal Structure of the Gsuk Rck Domain, PDB code: 4gvl was solved by C.Kong, W.Zeng, S.Ye, L.Chen, D.B.Sauer, Y.Lam, M.G.Derebe, Y.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.45 / 3.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	110.648, 161.693, 310.127, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 26.2

The structure of Crystal Structure of the Gsuk Rck Domain also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of the Gsuk Rck Domain (pdb code 4gvl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Gsuk Rck Domain, PDB code: 4gvl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Gsuk Rck Domain


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 the Gsuk Rck Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:87.1 occ:1.00 ND1 A:HIS391 1.9 88.0 1.0 NE2 A:HIS359 2.2 84.8 1.0 SG A:CYS388 2.3 99.9 1.0 SG A:CYS364 2.3 84.5 1.0 CG A:HIS391 2.9 91.8 1.0 CE1 A:HIS391 2.9 87.0 1.0 CE1 A:HIS359 3.2 88.0 1.0 CB A:HIS391 3.2 95.1 1.0 CD2 A:HIS359 3.3 81.7 1.0 CB A:CYS388 3.3 0.2 1.0 CB A:CYS364 3.5 80.0 1.0 CA A:CYS364 4.0 76.6 1.0 NE2 A:HIS391 4.0 89.3 1.0 CD2 A:HIS391 4.0 91.8 1.0 ND1 A:HIS359 4.3 86.6 1.0 CG A:HIS359 4.4 82.6 1.0 CA A:HIS391 4.5 0.1 1.0 N A:HIS391 4.6 99.5 1.0 O A:CYS364 4.7 76.7 1.0 CA A:CYS388 4.8 0.1 1.0 C A:CYS364 4.8 76.1 1.0 CD1 A:LEU379 4.9 81.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Gsuk Rck Domain


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 the Gsuk Rck Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:76.5 occ:1.00 SG B:CYS388 1.9 82.0 1.0 NE2 B:HIS359 2.1 66.8 1.0 ND1 B:HIS391 2.1 77.1 1.0 SG B:CYS364 2.2 71.8 1.0 CE1 B:HIS359 2.8 68.7 1.0 CG B:HIS391 3.0 78.3 1.0 CE1 B:HIS391 3.0 77.2 1.0 CB B:CYS388 3.1 83.1 1.0 CD2 B:HIS359 3.2 67.8 1.0 CB B:HIS391 3.3 79.1 1.0 CB B:CYS364 3.6 70.0 1.0 CD2 B:HIS391 4.0 78.7 1.0 NE2 B:HIS391 4.0 78.3 1.0 CA B:CYS364 4.0 68.5 1.0 ND1 B:HIS359 4.0 69.0 1.0 CG B:HIS359 4.3 68.8 1.0 N B:HIS391 4.3 0.6 1.0 CA B:CYS388 4.4 86.9 1.0 CA B:HIS391 4.4 81.9 1.0 O B:CYS364 4.6 69.6 1.0 C B:CYS364 4.8 69.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Gsuk Rck Domain


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 the Gsuk Rck Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:0.6 occ:1.00 SG C:CYS388 2.0 0.3 1.0 NE2 C:HIS359 2.1 0.5 1.0 SG C:CYS364 2.1 0.2 1.0 ND1 C:HIS391 2.4 0.9 1.0 CE1 C:HIS359 2.8 0.1 1.0 CB C:CYS388 2.9 0.3 1.0 CG C:HIS391 3.2 0.1 1.0 CD2 C:HIS359 3.3 0.8 1.0 CE1 C:HIS391 3.3 0.6 1.0 CB C:HIS391 3.5 0.8 1.0 CB C:CYS364 3.5 0.6 1.0 ND1 C:HIS359 4.0 0.7 1.0 CA C:CYS364 4.2 0.1 1.0 CD2 C:HIS391 4.3 0.5 1.0 NE2 C:HIS391 4.3 0.6 1.0 CG C:HIS359 4.3 0.9 1.0 N C:HIS391 4.3 0.2 1.0 CA C:CYS388 4.3 0.6 1.0 CA C:HIS391 4.5 0.6 1.0 CD1 C:LEU379 4.8 0.3 1.0 C C:CYS388 4.9 0.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Gsuk Rck Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Gsuk Rck Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:0.9 occ:1.00 ND1 D:HIS391 2.0 0.2 1.0 SG D:CYS364 2.1 0.5 1.0 NE2 D:HIS359 2.2 0.7 1.0 SG D:CYS388 2.2 0.0 1.0 CE1 D:HIS391 2.9 0.2 1.0 CE1 D:HIS359 3.0 0.6 1.0 CB D:CYS388 3.0 0.7 1.0 CG D:HIS391 3.1 0.5 1.0 CB D:CYS364 3.3 98.7 1.0 CD2 D:HIS359 3.3 99.9 1.0 CB D:HIS391 3.5 0.7 1.0 CA D:CYS364 3.9 95.6 1.0 NE2 D:HIS391 4.0 0.1 1.0 CD2 D:HIS391 4.1 0.1 1.0 ND1 D:HIS359 4.2 0.4 1.0 CG D:HIS359 4.3 0.1 1.0 CA D:CYS388 4.4 0.8 1.0 O D:CYS364 4.5 98.8 1.0 C D:CYS364 4.6 97.2 1.0 N D:HIS391 4.6 0.5 1.0 CA D:HIS391 4.7 0.3 1.0 CD1 D:LEU379 4.9 0.5 1.0

C.Kong, W.Zeng, S.Ye, L.Chen, D.B.Sauer, Y.Lam, M.G.Derebe, Y.Jiang. Distinct Gating Mechanisms Revealed By the Structures of A Multi-Ligand Gated K(+) Channel. Elife V. 1 00184 2012.
PubMed: 23240087
DOI: 10.7554/ELIFE.00184