Zinc in PDB 5mkp: Non Redox Thiolation in Transfer Rnas Occuring Via Sulfur Activation By A [4FE-4S] Cluster

The structure of Non Redox Thiolation in Transfer Rnas Occuring Via Sulfur Activation By A [4FE-4S] Cluster, PDB code: 5mkp was solved by S.Arragain, O.Bimai, P.Legrand, B.Golinelli-Pimpaneau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.25 / 2.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.120, 70.120, 127.900, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.5

The structure of Non Redox Thiolation in Transfer Rnas Occuring Via Sulfur Activation By A [4FE-4S] Cluster also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Non Redox Thiolation in Transfer Rnas Occuring Via Sulfur Activation By A [4FE-4S] Cluster (pdb code 5mkp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Non Redox Thiolation in Transfer Rnas Occuring Via Sulfur Activation By A [4FE-4S] Cluster, PDB code: 5mkp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Non Redox Thiolation in Transfer Rnas Occuring Via Sulfur Activation By A [4FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Non Redox Thiolation in Transfer Rnas Occuring Via Sulfur Activation By A [4FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:76.2 occ:1.00 ND1 A:HIS25 2.2 75.4 1.0 SG A:CYS6 2.2 80.8 1.0 SG A:CYS3 2.3 86.5 1.0 SG A:CYS22 2.4 74.4 1.0 CE1 A:HIS25 3.1 75.9 1.0 CB A:CYS3 3.1 84.1 1.0 CG A:HIS25 3.2 72.1 1.0 CB A:CYS6 3.3 78.6 1.0 CB A:CYS22 3.3 70.9 1.0 N A:CYS6 3.6 77.9 1.0 CB A:HIS25 3.7 67.5 1.0 CA A:CYS6 4.0 79.3 1.0 N A:CYS22 4.1 71.5 1.0 NE2 A:HIS25 4.2 75.7 1.0 C A:PHE5 4.3 82.2 1.0 CD2 A:HIS25 4.3 74.2 1.0 CA A:CYS22 4.3 69.9 1.0 CA A:CYS3 4.6 84.7 1.0 C A:CYS6 4.6 84.5 1.0 NH1 A:ARG8 4.7 0.4 1.0 CB A:PHE5 4.7 78.2 1.0 N A:HIS25 4.7 66.7 1.0 N A:PHE5 4.7 78.8 1.0 CA A:PHE5 4.7 78.4 1.0 CB A:ARG8 4.8 78.5 1.0 CA A:HIS25 4.8 65.7 1.0 O A:CYS6 4.9 83.9 1.0 CD A:ARG8 5.0 96.8 1.0

Zinc binding site 2 out of 2 in the Non Redox Thiolation in Transfer Rnas Occuring Via Sulfur Activation By A [4FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Non Redox Thiolation in Transfer Rnas Occuring Via Sulfur Activation By A [4FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:77.3 occ:1.00 SG A:CYS287 2.3 73.5 1.0 SG A:CYS275 2.4 74.7 1.0 SG A:CYS272 2.4 82.3 1.0 SG A:CYS284 2.6 75.9 1.0 CB A:CYS272 3.1 78.6 1.0 CB A:CYS287 3.1 70.3 1.0 CB A:CYS275 3.5 71.5 1.0 CB A:CYS284 3.7 73.5 1.0 N A:CYS275 3.8 74.2 1.0 N A:CYS284 4.0 77.5 1.0 CA A:CYS275 4.2 72.9 1.0 CA A:CYS284 4.3 74.8 1.0 N A:CYS287 4.3 67.8 1.0 CA A:CYS287 4.3 69.1 1.0 CB A:ILE274 4.5 79.0 1.0 OH A:TYR137 4.6 72.0 1.0 CA A:CYS272 4.6 80.8 1.0 O A:CYS284 4.7 78.0 1.0 CE2 A:TYR137 4.7 69.5 1.0 O A:HOH532 4.8 77.8 1.0 C A:ILE274 4.8 79.8 1.0 C A:CYS284 4.8 78.2 1.0 C A:CYS275 4.9 77.7 1.0 N A:ARG276 4.9 75.5 1.0 CG2 A:ILE283 4.9 86.0 1.0 N A:ILE274 5.0 78.7 1.0 CA A:ILE274 5.0 77.3 1.0

S.Arragain, O.Bimai, P.Legrand, S.Caillat, J.L.Ravanat, N.Touati, L.Binet, M.Atta, M.Fontecave, B.Golinelli-Pimpaneau. Nonredox Thiolation in Trna Occurring Via Sulfur Activation By A [4FE-4S] Cluster. Proc. Natl. Acad. Sci. V. 114 7355 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28655838
DOI: 10.1073/PNAS.1700902114