Iron 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:

Zinc

(Zn)

2 atoms

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Non Redox Thiolation in Transfer Rnas Occuring Via Sulfur Activation By A [4FE-4S] Cluster, PDB code: 5mkp:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 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 Iron with other atoms in the Fe 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:Fe403 b:0.2 occ:0.95 FE1 A:Q46403 0.0 0.2 1.0 S2 A:Q46403 2.3 1.0 0.7 S3 A:Q46403 2.3 0.8 1.0 S4 A:Q46403 2.3 0.5 0.7 SG A:CYS128 2.4 96.6 1.0 FE4 A:Q46403 2.7 0.9 1.0 CB A:CYS128 2.7 92.0 1.0 FE3 A:Q46403 2.8 0.1 0.7 FE2 A:Q46403 2.8 0.2 1.0 CA A:CYS128 2.9 90.6 1.0 N A:CYS128 3.8 90.4 1.0 S1 A:Q46403 3.9 0.4 0.7 C A:CYS128 4.0 93.0 1.0 O A:CYS128 4.0 92.3 1.0 SG A:CYS220 4.1 0.8 1.0 CB A:CYS131 4.5 79.1 1.0 C A:PRO127 4.7 92.2 1.0 SG A:CYS131 4.7 82.8 1.0 O A:PRO127 4.9 91.2 1.0

Iron binding site 2 out of 4 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 Iron with other atoms in the Fe 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:Fe403 b:0.1 occ:0.70 FE3 A:Q46403 0.0 0.1 0.7 S4 A:Q46403 2.3 0.5 0.7 S2 A:Q46403 2.3 1.0 0.7 S1 A:Q46403 2.3 0.4 0.7 S5 A:Q46403 2.4 0.3 0.7 FE2 A:Q46403 2.7 0.2 1.0 FE4 A:Q46403 2.8 0.9 1.0 FE1 A:Q46403 2.8 0.2 1.0 NZ A:LYS135 3.2 0.3 1.0 S3 A:Q46403 3.9 0.8 1.0 CE A:LYS135 4.4 0.4 1.0 SG A:CYS131 4.7 82.8 1.0 SG A:CYS220 4.8 0.8 1.0 SG A:CYS128 5.0 96.6 1.0

Iron binding site 3 out of 4 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 Iron with other atoms in the Fe binding site number 3 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:Fe403 b:0.2 occ:0.95 FE2 A:Q46403 0.0 0.2 1.0 SG A:CYS131 2.3 82.8 1.0 S1 A:Q46403 2.3 0.4 0.7 S3 A:Q46403 2.3 0.8 1.0 S4 A:Q46403 2.3 0.5 0.7 FE4 A:Q46403 2.7 0.9 1.0 FE3 A:Q46403 2.7 0.1 0.7 FE1 A:Q46403 2.8 0.2 1.0 CB A:CYS131 3.0 79.1 1.0 NZ A:LYS135 3.8 0.3 1.0 S2 A:Q46403 3.9 1.0 0.7 CE A:LYS135 4.1 0.4 1.0 CD1 A:LEU81 4.2 66.6 1.0 CA A:CYS131 4.4 78.0 1.0 CA A:CYS128 4.5 90.6 1.0 CG2 A:ILE118 4.6 66.7 1.0 C A:CYS131 4.7 78.5 1.0 CD A:LYS135 4.7 87.9 1.0 SG A:CYS220 4.7 0.8 1.0 S5 A:Q46403 4.8 0.3 0.7 O A:CYS128 4.8 92.3 1.0 CB A:CYS220 4.9 0.2 1.0 N A:GLY132 4.9 72.9 1.0 O A:PRO127 5.0 91.2 1.0

Iron binding site 4 out of 4 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 Iron with other atoms in the Fe binding site number 4 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:Fe403 b:0.9 occ:0.95 FE4 A:Q46403 0.0 0.9 1.0 SG A:CYS220 2.2 0.8 1.0 S3 A:Q46403 2.3 0.8 1.0 S2 A:Q46403 2.3 1.0 0.7 S1 A:Q46403 2.3 0.4 0.7 FE1 A:Q46403 2.7 0.2 1.0 FE2 A:Q46403 2.7 0.2 1.0 FE3 A:Q46403 2.8 0.1 0.7 CB A:CYS220 2.8 0.2 1.0 S4 A:Q46403 3.9 0.5 0.7 CA A:CYS220 4.0 0.3 1.0 N A:CYS220 4.1 0.4 1.0 SG A:CYS128 4.3 96.6 1.0 C A:GLU219 4.6 0.6 1.0 S5 A:Q46403 4.6 0.3 0.7 N A:ALA223 4.7 92.9 1.0 CB A:ALA223 4.8 0.3 1.0 CB A:GLU219 4.8 98.0 1.0 C A:CYS220 4.8 0.4 1.0 SG A:CYS131 4.9 82.8 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