Iron in PDB 4yoq: Crystal Structure of Muty Bound to Its Anti-Substrate

The structure of Crystal Structure of Muty Bound to Its Anti-Substrate, PDB code: 4yoq was solved by L.Wang, S.Lee, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.41 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.697, 84.594, 142.457, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 25

The structure of Crystal Structure of Muty Bound to Its Anti-Substrate also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Iron atom in the Crystal Structure of Muty Bound to Its Anti-Substrate (pdb code 4yoq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Muty Bound to Its Anti-Substrate, PDB code: 4yoq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Muty Bound to Its Anti-Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Muty Bound to Its Anti-Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:58.5 occ:1.00 FE1 A:SF4401 0.0 58.5 1.0 S2 A:SF4401 2.1 54.7 1.0 S4 A:SF4401 2.2 44.0 1.0 S3 A:SF4401 2.2 39.6 1.0 SG A:CYS205 2.5 53.1 1.0 FE3 A:SF4401 2.9 48.4 1.0 CB A:CYS205 2.9 49.5 1.0 FE4 A:SF4401 2.9 44.2 1.0 FE2 A:SF4401 3.0 43.2 1.0 CA A:CYS205 3.2 48.1 1.0 S1 A:SF4401 3.8 39.4 1.0 N A:CYS205 3.9 51.5 1.0 C A:CYS205 4.5 63.3 1.0 CB A:CYS208 4.5 46.5 1.0 CB A:ALA222 4.6 61.6 1.0 CB A:PRO203 4.7 40.4 1.0 CB A:PHE217 4.7 67.4 1.0 O A:CYS205 4.8 69.5 1.0 C A:SER204 4.8 56.8 1.0 CD1 A:PHE217 5.0 83.5 1.0 CG A:PRO203 5.0 44.4 1.0 SG A:CYS214 5.0 68.4 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Muty Bound to Its Anti-Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Muty Bound to Its Anti-Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:43.2 occ:1.00 FE2 A:SF4401 0.0 43.2 1.0 S1 A:SF4401 2.2 39.4 1.0 S3 A:SF4401 2.2 39.6 1.0 S4 A:SF4401 2.2 44.0 1.0 SG A:CYS198 2.5 41.0 1.0 FE4 A:SF4401 2.8 44.2 1.0 FE3 A:SF4401 2.9 48.4 1.0 FE1 A:SF4401 3.0 58.5 1.0 CB A:CYS198 3.3 36.7 1.0 S2 A:SF4401 3.7 54.7 1.0 CD A:ARG153 3.9 41.7 1.0 CA A:CYS198 4.0 36.1 1.0 CB A:ARG153 4.3 58.5 1.0 NH1 A:ARG153 4.5 37.9 1.0 CG A:ARG153 4.8 52.9 1.0 SG A:CYS205 4.9 53.1 1.0 CB A:PRO203 4.9 40.4 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Muty Bound to Its Anti-Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Muty Bound to Its Anti-Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:48.4 occ:1.00 FE3 A:SF4401 0.0 48.4 1.0 S4 A:SF4401 2.1 44.0 1.0 S2 A:SF4401 2.2 54.7 1.0 S1 A:SF4401 2.2 39.4 1.0 SG A:CYS208 2.4 58.6 1.0 FE1 A:SF4401 2.9 58.5 1.0 FE2 A:SF4401 2.9 43.2 1.0 CB A:CYS208 2.9 46.5 1.0 FE4 A:SF4401 3.0 44.2 1.0 S3 A:SF4401 3.8 39.6 1.0 CG2 A:VAL210 4.3 48.2 1.0 CA A:CYS208 4.4 47.5 1.0 N A:GLN211 4.5 70.4 1.0 CA A:GLN211 4.6 70.3 1.0 CA A:CYS205 4.7 48.1 1.0 CG1 A:VAL197 4.7 40.0 1.0 C A:VAL210 4.8 58.8 1.0 CB A:CYS198 4.8 36.7 1.0 CD2 A:LEU193 4.9 40.3 1.0 SG A:CYS198 5.0 41.0 1.0 C A:CYS208 5.0 50.0 1.0 CB A:CYS214 5.0 65.5 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Muty Bound to Its Anti-Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Muty Bound to Its Anti-Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:44.2 occ:1.00 FE4 A:SF4401 0.0 44.2 1.0 S3 A:SF4401 2.1 39.6 1.0 S1 A:SF4401 2.2 39.4 1.0 S2 A:SF4401 2.2 54.7 1.0 SG A:CYS214 2.5 68.4 1.0 FE2 A:SF4401 2.8 43.2 1.0 FE1 A:SF4401 2.9 58.5 1.0 FE3 A:SF4401 3.0 48.4 1.0 CB A:CYS214 3.0 65.5 1.0 S4 A:SF4401 3.7 44.0 1.0 CB A:ARG153 4.4 58.5 1.0 CD2 A:LEU154 4.4 50.8 1.0 CA A:CYS214 4.4 66.7 1.0 CB A:PHE217 4.6 67.4 1.0 CG A:LEU154 4.8 48.4 1.0 N A:PHE217 4.9 65.6 1.0 C A:ARG153 4.9 56.4 1.0 N A:LEU154 4.9 48.5 1.0

L.Wang, S.-J.Lee, G.Verdine. Structural Basis For Avoidance of Promutagenic Dna Repair By Muty Adenine Dna Glycosylase. J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M115.657866