Iron in PDB 4ypr: Crystal Structure of D144N Muty Bound to Its Anti-Substrate

The structure of Crystal Structure of D144N Muty Bound to Its Anti-Substrate, PDB code: 4ypr 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)	85.01 / 2.59
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	105.272, 105.272, 235.374, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 22.8

The binding sites of Iron atom in the Crystal Structure of D144N Muty Bound to Its Anti-Substrate (pdb code 4ypr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of D144N Muty Bound to Its Anti-Substrate, PDB code: 4ypr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of D144N 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 D144N Muty Bound to Its Anti-Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:37.5 occ:1.00 FE1 A:SF4400 0.0 37.5 1.0 S2 A:SF4400 2.1 35.4 1.0 S3 A:SF4400 2.2 36.9 1.0 S4 A:SF4400 2.2 40.6 1.0 SG A:CYS208 2.4 48.7 1.0 CB A:CYS208 2.9 34.5 1.0 FE3 A:SF4400 2.9 42.8 1.0 FE4 A:SF4400 2.9 41.8 1.0 FE2 A:SF4400 2.9 43.2 1.0 S1 A:SF4400 3.8 42.3 1.0 CG2 A:VAL210 4.3 29.7 1.0 CA A:CYS208 4.4 38.5 1.0 N A:GLN211 4.5 32.9 1.0 CA A:CYS205 4.5 36.1 1.0 CA A:GLN211 4.6 40.4 1.0 C A:VAL210 4.8 35.0 1.0 CB A:CYS198 4.8 28.5 1.0 CB A:CYS205 4.9 37.3 1.0 CG1 A:VAL197 4.9 35.4 1.0 C A:CYS208 5.0 36.6 1.0 SG A:CYS198 5.0 39.7 1.0

Iron binding site 2 out of 8 in the Crystal Structure of D144N 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 D144N Muty Bound to Its Anti-Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:43.2 occ:1.00 FE2 A:SF4400 0.0 43.2 1.0 S4 A:SF4400 2.2 40.6 1.0 S3 A:SF4400 2.2 36.9 1.0 S1 A:SF4400 2.2 42.3 1.0 SG A:CYS205 2.5 44.1 1.0 FE3 A:SF4400 2.9 42.8 1.0 FE4 A:SF4400 2.9 41.8 1.0 FE1 A:SF4400 2.9 37.5 1.0 CB A:CYS205 3.0 37.3 1.0 CA A:CYS205 3.4 36.1 1.0 S2 A:SF4400 3.7 35.4 1.0 N A:CYS205 4.0 43.1 1.0 CB A:PRO203 4.2 43.5 1.0 CG A:PRO203 4.3 35.9 1.0 CD1 A:PHE217 4.7 43.5 1.0 CB A:CYS208 4.7 34.5 1.0 C A:CYS205 4.8 39.5 1.0 CB A:PHE217 4.8 34.1 1.0 CB A:ALA222 4.9 37.5 1.0 C A:SER204 5.0 39.7 1.0 SG A:CYS198 5.0 39.7 1.0

Iron binding site 3 out of 8 in the Crystal Structure of D144N 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 D144N Muty Bound to Its Anti-Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:42.8 occ:1.00 FE3 A:SF4400 0.0 42.8 1.0 S1 A:SF4400 2.2 42.3 1.0 S4 A:SF4400 2.2 40.6 1.0 S2 A:SF4400 2.2 35.4 1.0 SG A:CYS198 2.4 39.7 1.0 FE2 A:SF4400 2.9 43.2 1.0 FE4 A:SF4400 2.9 41.8 1.0 FE1 A:SF4400 2.9 37.5 1.0 CB A:CYS198 3.1 28.5 1.0 S3 A:SF4400 3.7 36.9 1.0 CA A:CYS198 3.8 31.2 1.0 CD A:ARG153 4.2 45.4 1.0 NH1 A:ARG153 4.4 45.6 1.0 CB A:PRO203 4.5 43.5 1.0 CB A:ARG153 4.6 36.2 1.0 N A:CYS198 4.8 39.0 1.0 C A:CYS198 4.8 34.0 1.0 CG A:ARG153 4.9 36.3 1.0 CG A:PRO203 5.0 35.9 1.0 SG A:CYS208 5.0 48.7 1.0

Iron binding site 4 out of 8 in the Crystal Structure of D144N 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 D144N Muty Bound to Its Anti-Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:41.8 occ:1.00 FE4 A:SF4400 0.0 41.8 1.0 S2 A:SF4400 2.2 35.4 1.0 S3 A:SF4400 2.2 36.9 1.0 S1 A:SF4400 2.2 42.3 1.0 SG A:CYS214 2.5 51.4 1.0 FE3 A:SF4400 2.9 42.8 1.0 FE1 A:SF4400 2.9 37.5 1.0 FE2 A:SF4400 2.9 43.2 1.0 CB A:CYS214 3.0 33.2 1.0 S4 A:SF4400 3.7 40.6 1.0 CB A:PHE217 4.2 34.1 1.0 CD2 A:LEU154 4.3 31.4 1.0 CA A:CYS214 4.5 44.7 1.0 CB A:ARG153 4.5 36.2 1.0 N A:PHE217 4.7 38.1 1.0 SG A:CYS198 5.0 39.7 1.0 CA A:PHE217 5.0 39.5 1.0

Iron binding site 5 out of 8 in the Crystal Structure of D144N 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 5 of Crystal Structure of D144N Muty Bound to Its Anti-Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:37.6 occ:1.00 FE1 B:SF4400 0.0 37.6 1.0 S3 B:SF4400 2.2 35.1 1.0 S4 B:SF4400 2.2 35.8 1.0 S2 B:SF4400 2.2 34.8 1.0 SG B:CYS198 2.4 40.5 1.0 FE3 B:SF4400 2.9 38.7 1.0 FE4 B:SF4400 2.9 40.3 1.0 FE2 B:SF4400 2.9 35.4 1.0 CB B:CYS198 3.1 25.3 1.0 S1 B:SF4400 3.7 33.1 1.0 CA B:CYS198 3.8 34.4 1.0 CD B:ARG153 4.1 30.7 1.0 NH1 B:ARG153 4.3 29.6 1.0 CB B:PRO203 4.6 30.8 1.0 CB B:ARG153 4.6 27.6 1.0 N B:CYS198 4.7 32.8 1.0 C B:CYS198 4.9 33.2 1.0 SG B:CYS214 4.9 37.8 1.0 SG B:CYS208 5.0 37.3 1.0

Iron binding site 6 out of 8 in the Crystal Structure of D144N 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 6 of Crystal Structure of D144N Muty Bound to Its Anti-Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:35.4 occ:1.00 FE2 B:SF4400 0.0 35.4 1.0 S1 B:SF4400 2.2 33.1 1.0 S4 B:SF4400 2.2 35.8 1.0 S3 B:SF4400 2.2 35.1 1.0 SG B:CYS214 2.3 37.8 1.0 FE1 B:SF4400 2.9 37.6 1.0 CB B:CYS214 2.9 27.2 1.0 FE4 B:SF4400 2.9 40.3 1.0 FE3 B:SF4400 2.9 38.7 1.0 S2 B:SF4400 3.8 34.8 1.0 CB B:PHE217 4.1 43.8 1.0 CA B:CYS214 4.3 34.9 1.0 CD2 B:LEU154 4.4 34.8 1.0 CB B:ARG153 4.5 27.6 1.0 N B:PHE217 4.6 30.9 1.0 CA B:PHE217 5.0 36.6 1.0 SG B:CYS198 5.0 40.5 1.0 C B:CYS214 5.0 38.7 1.0

Iron binding site 7 out of 8 in the Crystal Structure of D144N 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 7 of Crystal Structure of D144N Muty Bound to Its Anti-Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:38.7 occ:1.00 FE3 B:SF4400 0.0 38.7 1.0 S4 B:SF4400 2.1 35.8 1.0 S1 B:SF4400 2.1 33.1 1.0 S2 B:SF4400 2.2 34.8 1.0 SG B:CYS208 2.4 37.3 1.0 FE1 B:SF4400 2.9 37.6 1.0 FE4 B:SF4400 2.9 40.3 1.0 FE2 B:SF4400 2.9 35.4 1.0 CB B:CYS208 3.0 27.8 1.0 S3 B:SF4400 3.8 35.1 1.0 CG2 B:VAL210 4.2 26.1 1.0 N B:GLN211 4.4 39.6 1.0 CA B:CYS208 4.5 31.4 1.0 CA B:GLN211 4.6 36.7 1.0 CA B:CYS205 4.7 33.8 1.0 C B:VAL210 4.8 38.1 1.0 CB B:CYS198 4.8 25.3 1.0 CG1 B:VAL197 4.8 30.6 1.0 CB B:CYS214 4.9 27.2 1.0 SG B:CYS198 4.9 40.5 1.0

Iron binding site 8 out of 8 in the Crystal Structure of D144N 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 8 of Crystal Structure of D144N Muty Bound to Its Anti-Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:40.3 occ:1.00 FE4 B:SF4400 0.0 40.3 1.0 S1 B:SF4400 2.2 33.1 1.0 S2 B:SF4400 2.2 34.8 1.0 S3 B:SF4400 2.2 35.1 1.0 SG B:CYS205 2.4 39.5 1.0 FE1 B:SF4400 2.9 37.6 1.0 FE2 B:SF4400 2.9 35.4 1.0 FE3 B:SF4400 2.9 38.7 1.0 CB B:CYS205 3.1 35.3 1.0 CA B:CYS205 3.5 33.8 1.0 S4 B:SF4400 3.7 35.8 1.0 N B:CYS205 3.9 30.8 1.0 CB B:PRO203 4.3 30.8 1.0 CG B:PRO203 4.5 30.8 1.0 CB B:PHE217 4.7 43.8 1.0 CD1 B:PHE217 4.7 50.5 1.0 CB B:CYS208 4.7 27.8 1.0 C B:CYS205 4.8 34.8 1.0 C B:SER204 4.9 37.8 1.0 SG B:CYS214 4.9 37.8 1.0 CB B:ALA222 5.0 35.3 1.0 SG B:CYS208 5.0 37.3 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