Zinc in PDB 7pr3: Cocrystal Form I of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster

The structure of Cocrystal Form I of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster, PDB code: 7pr3 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)	63.55 / 2.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.135, 79.772, 105.14, 90, 90, 90
R / Rfree (%)	20.7 / 25.3

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

Iron

(Fe)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 37;

Binding sites:

The binding sites of Zinc atom in the Cocrystal Form I of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster (pdb code 7pr3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 37 binding sites of Zinc where determined in the Cocrystal Form I of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster, PDB code: 7pr3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 37 in the Cocrystal Form I 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 I of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:29.8 occ:1.00 O39 A:80M203 1.9 31.0 1.0 O1 D:PO4615 2.1 28.4 1.0 O14 A:80M203 2.1 30.8 1.0 S15 A:80M203 2.5 28.8 1.0 C17 A:80M203 2.9 31.1 1.0 C13 A:80M203 3.0 31.3 1.0 ZN D:ZN602 3.1 30.1 1.0 C16 A:80M203 3.1 31.5 1.0 C12 A:80M203 3.2 32.1 1.0 P D:PO4615 3.2 28.3 1.0 O4 D:PO4615 3.4 32.3 1.0 ZN D:ZN614 3.6 33.6 1.0 O A:HOH305 4.0 31.7 1.0 O3 D:PO4615 4.0 29.8 1.0 C18 A:80M203 4.2 32.2 1.0 O44 A:80M203 4.2 31.2 1.0 O38 A:80M203 4.3 30.8 1.0 O2 D:PO4615 4.3 28.8 1.0 C08 A:80M203 4.4 33.2 1.0 C21 A:80M203 4.5 31.6 1.0 C11 A:80M203 4.6 31.0 1.0 S26 A:80M203 4.9 27.6 1.0 ZN D:ZN601 4.9 31.2 1.0

Zinc binding site 2 out of 37 in the Cocrystal Form I 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 I of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:26.5 occ:1.00 NE2 A:HIS33 2.1 30.2 1.0 O A:GLU103 2.1 28.4 1.0 O A:HOH309 2.4 25.6 1.0 C A:GLU103 2.8 29.1 1.0 OXT A:GLU103 2.8 26.3 1.0 CE1 A:HIS33 3.0 29.3 1.0 CD2 A:HIS33 3.1 29.5 1.0 O A:HOH301 3.2 27.9 1.0 CE A:LYS22 3.5 30.7 1.0 O A:THR102 3.8 29.9 1.0 NZ A:LYS22 4.0 30.3 1.0 ND1 A:HIS33 4.1 29.2 1.0 CG A:HIS33 4.2 30.1 1.0 CA A:GLU103 4.2 28.5 1.0 C A:THR102 4.4 30.5 1.0 N A:GLU103 4.6 27.1 1.0 OE1 A:GLU103 4.7 29.0 1.0 CD A:GLU103 4.8 28.9 1.0 CD A:LYS22 4.8 31.8 1.0 CB A:LYS22 4.9 33.0 1.0 O A:HOH308 5.0 29.4 1.0 OE2 A:GLU103 5.0 28.4 1.0

Zinc binding site 3 out of 37 in the Cocrystal Form I 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 I of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:87.2 occ:1.00 O39 A:80M204 2.4 80.6 0.8 O38 A:80M204 2.6 83.3 0.8 S26 A:80M204 2.8 77.0 0.8 O1 C:PO4617 3.3 76.8 0.5 O2 C:PO4617 3.3 71.2 0.5 C17 A:80M204 3.4 79.2 0.8 C28 A:80M204 3.5 80.0 0.8 O4 C:PO4617 3.5 71.4 0.5 P C:PO4617 3.6 71.7 0.5 C18 A:80M204 3.6 75.6 0.8 C27 A:80M204 3.6 76.5 0.8 ZN C:ZN613 3.9 94.9 1.0 ZN C:ZN612 4.3 92.4 1.0 C16 A:80M204 4.7 77.9 0.8 C29 A:80M204 4.8 78.7 0.8 C19 A:80M204 4.9 71.4 0.8 O44 A:80M204 4.9 81.4 0.8 O14 A:80M204 4.9 80.6 0.8

Zinc binding site 4 out of 37 in the Cocrystal Form I 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 I of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn207 b:106.1 occ:1.00 OE1 A:GLU-3 2.0 71.7 1.0 OE1 A:GLU88 2.3 62.7 1.0 OE2 A:GLU88 2.8 61.4 1.0 CD A:GLU88 2.9 59.5 1.0 CD A:GLU-3 3.2 70.9 1.0 OE2 A:GLU-3 3.9 74.6 1.0 CB A:GLU-3 4.3 61.9 1.0 CG A:GLU88 4.4 53.0 1.0 CG A:GLU-3 4.4 67.0 1.0 CB A:GLU88 4.9 50.5 1.0

Zinc binding site 5 out of 37 in the Cocrystal Form I 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 I of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:28.7 occ:1.00 O38 B:80M203 2.0 29.0 1.0 O4 C:PO4615 2.1 27.1 1.0 O44 B:80M203 2.2 30.1 1.0 O B:HOH313 2.2 28.9 1.0 S37 B:80M203 2.6 27.4 1.0 C28 B:80M203 2.9 29.8 1.0 ZN C:ZN603 3.1 29.1 1.0 C05 B:80M203 3.1 29.9 1.0 C29 B:80M203 3.2 30.2 1.0 C04 B:80M203 3.3 29.4 1.0 P C:PO4615 3.3 27.7 1.0 O3 C:PO4615 3.5 29.9 1.0 ZN C:ZN601 3.6 29.2 1.0 O1 C:PO4615 4.0 30.3 1.0 C27 B:80M203 4.2 29.8 1.0 O14 B:80M203 4.3 28.4 1.0 O39 B:80M203 4.3 29.6 1.0 C06 B:80M203 4.4 30.0 1.0 O2 C:PO4615 4.4 27.0 1.0 O B:HOH312 4.5 31.5 1.0 C30 B:80M203 4.5 28.8 1.0 C03 B:80M203 4.7 29.3 1.0 O C:HOH702 4.8 29.9 1.0 S26 B:80M203 4.9 26.6 1.0 ZN C:ZN602 5.0 29.5 1.0

Zinc binding site 6 out of 37 in the Cocrystal Form I 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 I of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn205 b:28.0 occ:1.00 OXT B:GLU103 2.1 27.9 1.0 NE2 B:HIS33 2.2 29.2 1.0 O B:HOH311 2.5 24.3 1.0 C B:GLU103 2.8 27.8 1.0 O B:GLU103 2.9 25.9 1.0 CE1 B:HIS33 3.1 29.4 1.0 CD2 B:HIS33 3.2 29.2 1.0 CE B:LYS22 3.4 29.4 1.0 O B:HOH302 3.8 26.6 1.0 O B:HOH303 3.9 28.7 1.0 O B:THR102 3.9 30.4 1.0 NZ B:LYS22 4.2 29.2 1.0 ND1 B:HIS33 4.2 29.6 1.0 CA B:GLU103 4.2 29.5 1.0 CG B:HIS33 4.3 30.4 1.0 C B:THR102 4.4 29.8 1.0 N B:GLU103 4.5 29.4 1.0 CD B:LYS22 4.7 30.8 1.0 CG B:LYS22 4.7 31.2 1.0 OE1 B:GLU103 4.8 26.5 1.0 CB B:LYS22 4.8 30.8 1.0 CD B:GLU103 4.8 28.4 1.0 O B:HOH304 4.9 27.0 1.0 OE2 B:GLU103 5.0 26.8 1.0

Zinc binding site 7 out of 37 in the Cocrystal Form I 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 7 of Cocrystal Form I of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn206 b:81.7 occ:1.00 CG B:GLU-3 2.5 59.0 1.0 OE1 B:GLU88 2.6 53.2 1.0 O2 D:PO4617 2.7 61.4 0.5 OE2 B:GLU88 3.1 53.6 1.0 CD B:GLU-3 3.1 64.3 1.0 O B:HOH314 3.2 53.0 1.0 CD B:GLU88 3.2 51.2 1.0 O1 D:PO4617 3.2 58.9 0.5 OE1 B:GLU-3 3.3 63.9 1.0 P D:PO4617 3.3 59.2 0.5 O3 D:PO4617 3.6 59.5 0.5 CB B:GLU-3 3.9 55.5 1.0 OE2 B:GLU-3 4.0 62.8 1.0 O B:GLU-3 4.5 49.9 1.0 CG B:GLU88 4.7 46.6 1.0 O4 D:PO4617 4.8 57.9 0.5 C B:GLU-3 5.0 48.5 1.0 NH2 B:ARG91 5.0 45.5 1.0 CA B:GLU-3 5.0 51.5 1.0

Zinc binding site 8 out of 37 in the Cocrystal Form I 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 8 of Cocrystal Form I of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn207 b:58.1 occ:0.46 O44 B:80M204 2.0 56.0 0.3 O38 B:80M204 2.1 57.3 0.3 O4 D:PO4617 2.4 57.9 0.5 S37 B:80M204 2.7 55.7 0.3 C05 B:80M204 2.9 54.9 0.3 O48 B:80M204 3.1 54.8 0.3 C28 B:80M204 3.1 56.8 0.3 C04 B:80M204 3.2 55.0 0.3 O2 D:PO4617 3.3 61.4 0.5 C29 B:80M204 3.4 56.1 0.3 P D:PO4617 3.4 59.2 0.5 ZN B:ZN208 3.7 56.0 0.6 C03 B:80M204 3.7 56.3 0.3 ZN D:ZN612 3.8 64.8 0.6 C02 B:80M204 4.1 56.1 0.3 S45 B:80M204 4.2 55.2 0.3 C06 B:80M204 4.2 54.3 0.3 O1 D:PO4617 4.3 58.9 0.5 C27 B:80M204 4.4 56.5 0.3 C04 B:80M204 4.4 56.6 0.3 O14 B:80M204 4.4 56.1 0.3 O3 D:PO4617 4.5 59.5 0.5 O39 B:80M204 4.6 57.2 0.3 C03 B:80M204 4.6 54.3 0.3 C30 B:80M204 4.7 55.8 0.3 CG B:GLU66 4.8 48.0 1.0 S37 B:80M204 4.9 56.9 0.3 S07 B:80M204 4.9 53.0 0.3 O47 B:80M204 4.9 53.7 0.3

Zinc binding site 9 out of 37 in the Cocrystal Form I 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 9 of Cocrystal Form I of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn207 b:59.7 occ:0.54 S15 B:80M204 2.4 56.5 0.3 C16 B:80M204 2.5 56.9 0.3 O2 D:PO4617 2.5 59.5 0.5 O14 B:80M204 2.6 56.2 0.3 C21 B:80M204 2.6 56.4 0.3 O44 B:80M204 2.8 56.9 0.3 O1 D:PO4617 3.1 58.9 0.5 P D:PO4617 3.3 60.9 0.5 S07 B:80M204 3.4 55.8 0.3 C17 B:80M204 3.5 57.0 0.3 C20 B:80M204 3.7 56.2 0.3 C13 B:80M204 3.7 55.5 0.3 O4 D:PO4617 3.8 56.8 0.5 C05 B:80M204 3.9 56.8 0.3 ZN D:ZN613 4.0 58.8 0.5 C08 B:80M204 4.0 55.2 0.3 C12 B:80M204 4.1 55.6 0.3 O39 B:80M204 4.1 57.2 0.3 C06 B:80M204 4.2 56.2 0.3 ZN B:ZN208 4.2 56.2 0.4 ZN D:ZN613 4.3 57.5 0.5 C18 B:80M204 4.3 56.9 0.3 O24 B:80M204 4.4 55.1 0.3 C19 B:80M204 4.4 56.3 0.3 O3 D:PO4617 4.6 58.0 0.5 C11 B:80M204 4.7 54.9 0.3 S22 B:80M204 4.7 54.9 0.3 C12 B:80M204 4.9 54.8 0.3 ZN D:ZN610 4.9 89.0 1.0

Zinc binding site 10 out of 37 in the Cocrystal Form I 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 10 of Cocrystal Form I of A Cytochrome C, Sulfonato-Thiacalix[4]Arene - Zinc Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn208 b:56.0 occ:0.64 O14 B:80M204 2.2 56.1 0.3 O4 D:PO4617 2.4 57.9 0.5 O44 B:80M204 2.6 56.0 0.3 S07 B:80M204 2.6 53.0 0.3 O1 D:PO4617 2.7 58.9 0.5 C13 B:80M204 3.1 55.5 0.3 P D:PO4617 3.1 59.2 0.5 C08 B:80M204 3.3 54.7 0.3 C01 B:80M204 3.4 55.7 0.3 C05 B:80M204 3.4 54.9 0.3 O47 B:80M204 3.5 53.7 0.3 C02 B:80M204 3.5 56.1 0.3 C06 B:80M204 3.5 54.3 0.3 ZN D:ZN613 3.5 58.8 0.5 ZN B:ZN207 3.7 58.1 0.5 O48 B:80M204 3.8 54.8 0.3 OG1 B:THR69 3.8 41.4 1.0 S45 B:80M204 3.8 55.2 0.3 C06 B:80M204 4.0 56.2 0.3 O2 D:PO4617 4.2 61.4 0.5 C03 B:80M204 4.2 56.3 0.3 O3 D:PO4617 4.2 59.5 0.5 O39 B:80M204 4.2 57.2 0.3 CG2 B:THR69 4.2 45.7 1.0 CG B:GLU66 4.3 48.0 1.0 CB B:THR69 4.3 42.1 1.0 C12 B:80M204 4.4 55.6 0.3 CA B:GLU66 4.5 39.5 1.0 NH2 B:ARG91 4.6 45.5 1.0 C09 B:80M204 4.6 53.8 0.3 O38 B:80M204 4.7 57.3 0.3 C05 B:80M204 4.7 56.8 0.3 C04 B:80M204 4.7 56.6 0.3 C04 B:80M204 4.8 55.0 0.3 S07 B:80M204 4.8 55.8 0.3 C01 B:80M204 4.8 53.8 0.3 CB B:GLU66 4.9 41.9 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