Zinc in PDB 4pht: Atpase Gspe in Complex with the Cytoplasmic Domain of Gspl From the Vibrio Vulnificus Type II Secretion System

The structure of Atpase Gspe in Complex with the Cytoplasmic Domain of Gspl From the Vibrio Vulnificus Type II Secretion System, PDB code: 4pht was solved by C.Lu, K.Korotkov, W.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.22 / 2.83
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	226.430, 133.900, 93.490, 90.00, 91.41, 90.00
R / Rfree (%)	24.8 / 28

The structure of Atpase Gspe in Complex with the Cytoplasmic Domain of Gspl From the Vibrio Vulnificus Type II Secretion System also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the Atpase Gspe in Complex with the Cytoplasmic Domain of Gspl From the Vibrio Vulnificus Type II Secretion System (pdb code 4pht). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Atpase Gspe in Complex with the Cytoplasmic Domain of Gspl From the Vibrio Vulnificus Type II Secretion System, PDB code: 4pht:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Atpase Gspe in Complex with the Cytoplasmic Domain of Gspl From the Vibrio Vulnificus Type II Secretion System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Atpase Gspe in Complex with the Cytoplasmic Domain of Gspl From the Vibrio Vulnificus Type II Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:50.6 occ:1.00 SG A:CYS426 2.2 56.6 1.0 SG A:CYS396 2.2 52.6 1.0 SG A:CYS393 2.4 53.4 1.0 SG A:CYS429 2.9 72.1 1.0 CB A:CYS396 3.1 53.6 1.0 CB A:CYS393 3.2 50.7 1.0 CB A:CYS426 3.4 57.1 1.0 N A:CYS426 3.6 58.6 1.0 CB A:CYS429 3.8 71.2 1.0 N A:CYS429 3.8 73.1 1.0 N A:CYS396 3.9 58.7 1.0 CA A:CYS426 3.9 59.5 1.0 CA A:CYS396 4.1 56.5 1.0 C A:GLY425 4.2 55.0 1.0 CB A:LYS428 4.3 85.0 1.0 C A:CYS426 4.4 64.1 1.0 CA A:CYS429 4.4 71.4 1.0 O A:CYS426 4.5 71.3 1.0 CA A:GLY425 4.5 52.4 1.0 CB A:ASP395 4.6 71.8 1.0 CA A:CYS393 4.6 49.3 1.0 N A:LYS428 4.7 78.4 1.0 C A:LYS428 4.7 78.6 1.0 C A:ASP395 4.7 64.9 1.0 CA A:LYS428 4.8 81.1 1.0 O A:GLY425 4.9 57.7 1.0 CA A:GLY433 4.9 57.7 1.0 C A:CYS393 4.9 52.7 1.0 O A:CYS393 4.9 54.5 1.0 C A:CYS396 5.0 58.5 1.0

Zinc binding site 2 out of 3 in the Atpase Gspe in Complex with the Cytoplasmic Domain of Gspl From the Vibrio Vulnificus Type II Secretion System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Atpase Gspe in Complex with the Cytoplasmic Domain of Gspl From the Vibrio Vulnificus Type II Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:54.0 occ:1.00 SG B:CYS396 2.0 55.3 1.0 SG B:CYS429 2.2 54.2 1.0 SG B:CYS426 2.3 56.0 1.0 SG B:CYS393 2.5 50.7 1.0 CB B:CYS396 3.1 57.0 1.0 CB B:CYS393 3.2 57.4 1.0 N B:CYS426 3.4 65.0 1.0 CB B:CYS426 3.4 58.8 1.0 CB B:CYS429 3.6 61.4 1.0 CA B:CYS426 3.8 63.0 1.0 N B:CYS429 3.9 71.6 1.0 C B:GLY425 3.9 65.2 1.0 N B:CYS396 4.0 60.9 1.0 CA B:CYS396 4.1 57.0 1.0 CA B:GLY425 4.2 63.1 1.0 C B:CYS426 4.3 66.9 1.0 O B:CYS426 4.3 73.3 1.0 CA B:CYS429 4.4 67.8 1.0 O B:LYS432 4.5 72.9 1.0 CB B:LYS428 4.5 79.2 1.0 CA B:CYS393 4.6 57.2 1.0 O B:GLY425 4.7 66.9 1.0 N B:LYS428 4.8 70.9 1.0 C B:LYS428 4.9 73.5 1.0 CB B:ASP395 4.9 71.4 1.0 C B:ASP395 4.9 65.2 1.0 C B:CYS396 4.9 52.9 1.0 O B:CYS393 4.9 69.4 1.0 C B:CYS393 5.0 64.8 1.0 N B:GLY425 5.0 62.8 1.0 CA B:LYS428 5.0 75.2 1.0

Zinc binding site 3 out of 3 in the Atpase Gspe in Complex with the Cytoplasmic Domain of Gspl From the Vibrio Vulnificus Type II Secretion System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Atpase Gspe in Complex with the Cytoplasmic Domain of Gspl From the Vibrio Vulnificus Type II Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:64.2 occ:1.00 SG C:CYS396 2.1 68.0 1.0 SG C:CYS429 2.1 67.8 1.0 SG C:CYS393 2.4 64.7 1.0 SG C:CYS426 2.4 70.3 1.0 CB C:CYS393 3.1 67.6 1.0 CB C:CYS396 3.2 67.0 1.0 N C:CYS426 3.4 74.8 1.0 CB C:CYS429 3.5 72.1 1.0 CB C:CYS426 3.5 67.0 1.0 N C:CYS429 3.8 76.8 1.0 CA C:CYS426 3.9 71.7 1.0 N C:CYS396 4.0 65.1 1.0 C C:GLY425 4.0 76.8 1.0 CA C:CYS396 4.2 64.5 1.0 CA C:GLY425 4.3 76.6 1.0 CA C:CYS429 4.3 75.0 1.0 C C:CYS426 4.3 75.3 1.0 O C:CYS426 4.4 84.6 1.0 O C:LYS432 4.4 72.7 1.0 CB C:LYS428 4.5 84.6 1.0 CA C:CYS393 4.5 63.7 1.0 C C:LYS428 4.8 80.9 1.0 O C:GLY425 4.8 82.8 1.0 N C:LYS428 4.9 76.8 1.0 O C:CYS393 4.9 70.6 1.0 CB C:ASP395 4.9 68.2 1.0 C C:CYS393 4.9 65.9 1.0 C C:ASP395 4.9 66.2 1.0 C C:CYS396 5.0 65.3 1.0 CA C:LYS428 5.0 81.0 1.0 N C:GLY425 5.0 77.1 1.0

C.Lu, K.V.Korotkov, W.G.Hol. Crystal Structure of the Full-Length Atpase Gspe From the Vibrio Vulnificus Type II Secretion System in Complex with the Cytoplasmic Domain of Gspl. J.Struct.Biol. V. 187 223 2014.
ISSN: ESSN 1095-8657
PubMed: 25092625
DOI: 10.1016/J.JSB.2014.07.006