Iron in PDB 4yph: Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced

The structure of Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced, PDB code: 4yph 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)	41.37 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.636, 83.757, 142.735, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 25.9

The structure of Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced 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 with the Disulfide Cross-Linker Reduced (pdb code 4yph). 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 with the Disulfide Cross-Linker Reduced, PDB code: 4yph:
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 with the Disulfide Cross-Linker Reduced


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 with the Disulfide Cross-Linker Reduced within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:44.0 occ:1.00 FE1 A:SF4401 0.0 44.0 1.0 S4 A:SF4401 2.2 40.6 1.0 S3 A:SF4401 2.2 43.1 1.0 S2 A:SF4401 2.2 47.5 1.0 SG A:CYS205 2.5 50.1 1.0 FE3 A:SF4401 2.9 43.1 1.0 FE2 A:SF4401 2.9 48.3 1.0 FE4 A:SF4401 2.9 48.3 1.0 CB A:CYS205 3.2 46.8 1.0 CA A:CYS205 3.4 46.9 1.0 S1 A:SF4401 3.8 40.8 1.0 N A:CYS205 4.0 45.0 1.0 CB A:PRO203 4.2 40.0 1.0 CB A:ALA222 4.5 46.2 1.0 CG A:PRO203 4.5 40.9 1.0 CB A:CYS208 4.6 39.5 1.0 CB A:PHE217 4.7 47.4 1.0 C A:CYS205 4.7 50.8 1.0 CD1 A:PHE217 4.8 46.9 1.0 C A:SER204 4.9 45.4 1.0 SG A:CYS214 4.9 53.8 1.0 O A:CYS205 5.0 53.3 1.0 SG A:CYS198 5.0 36.7 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced


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 with the Disulfide Cross-Linker Reduced within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:48.3 occ:1.00 FE2 A:SF4401 0.0 48.3 1.0 S3 A:SF4401 2.1 43.1 1.0 S1 A:SF4401 2.2 40.8 1.0 S4 A:SF4401 2.2 40.6 1.0 SG A:CYS198 2.4 36.7 1.0 FE3 A:SF4401 2.9 43.1 1.0 FE4 A:SF4401 2.9 48.3 1.0 FE1 A:SF4401 2.9 44.0 1.0 CB A:CYS198 3.1 32.9 1.0 S2 A:SF4401 3.8 47.5 1.0 CA A:CYS198 3.8 31.4 1.0 CD A:ARG153 4.1 42.9 1.0 CB A:ARG153 4.3 46.3 1.0 NH1 A:ARG153 4.4 33.5 1.0 CB A:PRO203 4.6 40.0 1.0 CG A:ARG153 4.7 46.3 1.0 N A:CYS198 4.8 39.0 1.0 C A:CYS198 4.9 34.4 1.0 SG A:CYS208 5.0 51.3 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced


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 with the Disulfide Cross-Linker Reduced within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:43.1 occ:1.00 FE3 A:SF4401 0.0 43.1 1.0 S2 A:SF4401 2.2 47.5 1.0 S4 A:SF4401 2.2 40.6 1.0 S1 A:SF4401 2.2 40.8 1.0 SG A:CYS208 2.4 51.3 1.0 CB A:CYS208 2.8 39.5 1.0 FE1 A:SF4401 2.9 44.0 1.0 FE2 A:SF4401 2.9 48.3 1.0 FE4 A:SF4401 2.9 48.3 1.0 S3 A:SF4401 3.7 43.1 1.0 CA A:CYS208 4.3 48.0 1.0 CG2 A:VAL210 4.5 42.2 1.0 CA A:CYS205 4.6 46.9 1.0 N A:GLN211 4.6 46.5 1.0 CA A:GLN211 4.6 49.2 1.0 CB A:CYS198 4.8 32.9 1.0 CG1 A:VAL197 4.8 34.1 1.0 SG A:CYS198 4.9 36.7 1.0 C A:VAL210 4.9 49.6 1.0 C A:CYS208 5.0 42.2 1.0 CB A:CYS214 5.0 46.8 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Muty Bound to Its Anti-Substrate with the Disulfide Cross-Linker Reduced


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 with the Disulfide Cross-Linker Reduced within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:48.3 occ:1.00 FE4 A:SF4401 0.0 48.3 1.0 S3 A:SF4401 2.2 43.1 1.0 S1 A:SF4401 2.2 40.8 1.0 S2 A:SF4401 2.2 47.5 1.0 SG A:CYS214 2.4 53.8 1.0 FE3 A:SF4401 2.9 43.1 1.0 FE2 A:SF4401 2.9 48.3 1.0 FE1 A:SF4401 2.9 44.0 1.0 CB A:CYS214 2.9 46.8 1.0 S4 A:SF4401 3.8 40.6 1.0 CB A:PHE217 4.3 47.4 1.0 CB A:ARG153 4.4 46.3 1.0 CA A:CYS214 4.4 56.4 1.0 CD2 A:LEU154 4.4 44.7 1.0 N A:PHE217 4.8 53.9 1.0 C A:ARG153 4.9 44.1 1.0 CG A:LEU154 5.0 43.2 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