Zinc in PDB 7pr4: Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster

The structure of Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster, PDB code: 7pr4 was solved by R.J.Flood, K.Ramberg, F.Guagnini, P.B.Crowley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.45 / 1.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	35.624, 36.106, 82.898, 90, 90, 90
R / Rfree (%)	18.7 / 22.5

The structure of Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster (pdb code 7pr4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster, PDB code: 7pr4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:14.2 occ:1.00 O3 A:PO4209 2.0 14.4 1.0 O A:HOH370 2.0 15.9 1.0 O38 A:80M202 2.1 12.9 1.0 O44 A:80M202 2.1 11.4 1.0 O A:HOH403 2.2 18.5 1.0 S37 A:80M202 2.5 14.1 1.0 C05 A:80M202 3.0 14.0 1.0 C28 A:80M202 3.1 11.3 1.0 P A:PO4209 3.2 13.6 1.0 C04 A:80M202 3.2 11.4 1.0 C29 A:80M202 3.2 17.0 1.0 O4 A:PO4209 3.5 12.6 1.0 ZN A:ZN204 3.6 13.8 1.0 O2 A:PO4209 3.7 14.0 1.0 O3 A:PO4211 3.7 18.2 1.0 ZN A:ZN206 3.7 13.7 1.0 O4 A:PO4210 3.9 12.2 0.8 O A:HOH343 4.2 19.5 1.0 O4 A:PO4211 4.2 19.1 1.0 O A:HOH372 4.3 21.2 1.0 O39 A:80M202 4.3 12.2 1.0 C06 A:80M202 4.3 15.0 1.0 C27 A:80M202 4.4 14.7 1.0 O1 A:PO4209 4.4 13.7 1.0 O14 A:80M202 4.6 11.5 1.0 C03 A:80M202 4.6 16.5 1.0 C30 A:80M202 4.6 17.8 1.0 P A:PO4211 4.6 18.3 1.0 O A:HOH320 4.7 41.8 1.0 ZN A:ZN205 4.9 12.2 1.0

Zinc binding site 2 out of 6 in the Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:13.8 occ:1.00 O4 A:PO4210 2.0 12.2 0.8 O39 A:80M202 2.0 12.2 1.0 O4 A:PO4209 2.1 12.6 1.0 O38 A:80M202 2.2 12.9 1.0 S26 A:80M202 2.7 14.6 1.0 C17 A:80M202 3.0 13.2 1.0 ZN A:ZN205 3.1 12.2 1.0 C28 A:80M202 3.1 11.3 1.0 C18 A:80M202 3.2 10.7 1.0 P A:PO4210 3.2 12.7 0.8 P A:PO4209 3.3 13.6 1.0 O3 A:PO4209 3.3 14.4 1.0 C27 A:80M202 3.3 14.7 1.0 ZN A:ZN203 3.6 14.2 1.0 O1 A:PO4210 3.7 12.3 0.8 O3 A:PO4210 3.8 13.3 0.8 O A:HOH343 3.9 19.5 1.0 O1 A:PO4209 4.1 13.7 1.0 O14 A:80M202 4.2 11.5 1.0 O A:HOH370 4.2 15.9 1.0 C16 A:80M202 4.2 17.7 1.0 O44 A:80M202 4.3 11.4 1.0 O2 A:PO4209 4.4 14.0 1.0 C29 A:80M202 4.4 17.0 1.0 O2 A:PO4210 4.4 12.9 0.8 C19 A:80M202 4.6 13.2 1.0 ZN A:ZN207 4.7 14.9 1.0 C32 A:80M202 4.7 17.2 1.0 O A:HOH386 4.8 11.6 1.0 ZN A:ZN206 4.9 13.7 1.0 S15 A:80M202 4.9 11.8 1.0 O A:HOH425 5.0 34.0 1.0

Zinc binding site 3 out of 6 in the Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:12.2 occ:1.00 O A:HOH386 2.0 11.6 1.0 O39 A:80M202 2.0 12.2 1.0 O14 A:80M202 2.0 11.5 1.0 O4 A:PO4209 2.0 12.6 1.0 S15 A:80M202 2.6 11.8 1.0 C17 A:80M202 2.9 13.2 1.0 C13 A:80M202 3.0 11.1 1.0 ZN A:ZN204 3.1 13.8 1.0 C16 A:80M202 3.2 17.7 1.0 P A:PO4209 3.2 13.6 1.0 C12 A:80M202 3.3 12.8 1.0 O2 A:PO4209 3.4 14.0 1.0 ZN A:ZN206 3.6 13.7 1.0 O A:HOH453 4.0 12.5 1.0 O A:HOH364 4.1 18.6 1.0 O1 A:PO4209 4.1 13.7 1.0 C18 A:80M202 4.2 10.7 1.0 O A:HOH452 4.2 15.1 1.0 O38 A:80M202 4.3 12.9 1.0 O3 A:PO4209 4.3 14.4 1.0 O44 A:80M202 4.3 11.4 1.0 C08 A:80M202 4.3 12.4 1.0 C21 A:80M202 4.5 17.8 1.0 C11 A:80M202 4.7 15.2 1.0 O4 A:PO4210 4.8 12.2 0.8 S26 A:80M202 4.8 14.6 1.0 ZN A:ZN203 4.9 14.2 1.0

Zinc binding site 4 out of 6 in the Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:13.7 occ:1.00 O2 A:PO4209 1.9 14.0 1.0 O A:HOH372 2.1 21.2 1.0 O44 A:80M202 2.2 11.4 1.0 O14 A:80M202 2.2 11.5 1.0 O A:HOH364 2.2 18.6 1.0 S07 A:80M202 2.4 14.9 1.0 C13 A:80M202 3.1 11.1 1.0 P A:PO4209 3.1 13.6 1.0 C05 A:80M202 3.1 14.0 1.0 C08 A:80M202 3.2 12.4 1.0 C06 A:80M202 3.2 15.0 1.0 O4 A:PO4209 3.4 12.6 1.0 O3 A:PO4209 3.5 14.4 1.0 ZN A:ZN205 3.6 12.2 1.0 ZN A:ZN203 3.7 14.2 1.0 O A:HOH406 3.8 23.4 1.0 O A:HOH386 3.9 11.6 1.0 O A:HOH403 4.2 18.5 1.0 O1 A:PO4209 4.3 13.7 1.0 O39 A:80M202 4.4 12.2 1.0 C12 A:80M202 4.4 12.8 1.0 C04 A:80M202 4.4 11.4 1.0 C09 A:80M202 4.6 15.8 1.0 C01 A:80M202 4.6 15.4 1.0 O38 A:80M202 4.6 12.9 1.0 ZN A:ZN204 4.9 13.8 1.0

Zinc binding site 5 out of 6 in the Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn207 b:14.9 occ:1.00 O1 A:PO4209 1.9 13.7 1.0 O1 A:PO4210 1.9 12.3 0.8 O2 A:PO4211 2.0 17.9 1.0 P A:PO4209 3.1 13.6 1.0 P A:PO4211 3.2 18.3 1.0 P A:PO4210 3.2 12.7 0.8 O3 A:PO4209 3.4 14.4 1.0 O A:HOH315 3.5 32.1 1.0 O3 A:PO4211 3.5 18.2 1.0 O4 A:PO4211 3.7 19.1 1.0 O2 A:PO4210 3.7 12.9 0.8 O4 A:PO4209 3.7 12.6 1.0 O4 A:PO4210 3.9 12.2 0.8 O2 A:PO4209 4.3 14.0 1.0 O3 A:PO4210 4.3 13.3 0.8 ZN A:ZN208 4.4 89.4 1.0 O1 A:PO4211 4.4 19.2 1.0 ZN A:ZN204 4.7 13.8 1.0

Zinc binding site 6 out of 6 in the Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cocrystal Form II of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn208 b:89.4 occ:1.00 O4 A:PO4211 1.9 19.1 1.0 O2 A:PO4210 2.0 12.9 0.8 O A:HOH417 2.2 31.4 1.0 P A:PO4211 3.0 18.3 1.0 O A:HOH348 3.1 25.0 1.0 O2 A:PO4211 3.3 17.9 1.0 P A:PO4210 3.4 12.7 0.8 O1 A:PO4211 3.5 19.2 1.0 O1 A:PO4210 3.9 12.3 0.8 O4 A:PO4210 4.2 12.2 0.8 O3 A:PO4211 4.3 18.2 1.0 O A:HOH370 4.3 15.9 1.0 O A:HOH343 4.3 19.5 1.0 O3 A:PO4210 4.4 13.3 0.8 ZN A:ZN207 4.4 14.9 1.0

R.J.Flood, K.O.Ramberg, D.B.Mengel, F.Guagnini, P.B.Crowley. Protein Frameworks with Thiacalixarene and Zinc. Cryst.Growth Des. V. 22 3271 2022.
ISSN: ISSN 1528-7483
PubMed: 35529063
DOI: 10.1021/ACS.CGD.2C00108