Iron in PDB 1vrl: Muty Adenine Glycosylase in Complex with Dna and Soaked Adenine Free Base

The structure of Muty Adenine Glycosylase in Complex with Dna and Soaked Adenine Free Base, PDB code: 1vrl was solved by J.C.Fromme, A.Banerjee, S.J.Huang, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.72 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.977, 85.730, 141.635, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 27.8

The structure of Muty Adenine Glycosylase in Complex with Dna and Soaked Adenine Free Base also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iron atom in the Muty Adenine Glycosylase in Complex with Dna and Soaked Adenine Free Base (pdb code 1vrl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Muty Adenine Glycosylase in Complex with Dna and Soaked Adenine Free Base, PDB code: 1vrl:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Muty Adenine Glycosylase in Complex with Dna and Soaked Adenine Free Base


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Muty Adenine Glycosylase in Complex with Dna and Soaked Adenine Free Base within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:35.4 occ:1.00 FE1 A:SF4400 0.0 35.4 1.0 S2 A:SF4400 2.2 33.9 1.0 S4 A:SF4400 2.2 33.2 1.0 S3 A:SF4400 2.2 34.9 1.0 SG A:CYS208 2.5 43.0 1.0 FE2 A:SF4400 2.7 36.0 1.0 FE3 A:SF4400 2.7 35.6 1.0 FE4 A:SF4400 2.7 36.0 1.0 CB A:CYS208 3.0 43.0 1.0 S1 A:SF4400 3.9 33.2 1.0 CG2 A:VAL210 4.4 42.6 1.0 CA A:GLN211 4.4 53.5 1.0 N A:GLN211 4.5 50.5 1.0 CA A:CYS205 4.5 38.3 1.0 CA A:CYS208 4.5 44.4 1.0 CG1 A:VAL197 4.7 28.4 1.0 CB A:CYS205 4.8 37.4 1.0 C A:VAL210 4.8 47.8 1.0 CB A:CYS198 4.8 29.2 1.0 SG A:CYS198 4.9 34.9 1.0 CB A:CYS214 4.9 50.0 1.0 SG A:CYS205 5.0 34.8 1.0

Iron binding site 2 out of 4 in the Muty Adenine Glycosylase in Complex with Dna and Soaked Adenine Free Base


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Muty Adenine Glycosylase in Complex with Dna and Soaked Adenine Free Base within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:36.0 occ:1.00 FE2 A:SF4400 0.0 36.0 1.0 S3 A:SF4400 2.1 34.9 1.0 S1 A:SF4400 2.3 33.2 1.0 S4 A:SF4400 2.3 33.2 1.0 SG A:CYS198 2.4 34.9 1.0 FE4 A:SF4400 2.6 36.0 1.0 FE1 A:SF4400 2.7 35.4 1.0 FE3 A:SF4400 2.8 35.6 1.0 CB A:CYS198 3.1 29.2 1.0 S2 A:SF4400 3.6 33.9 1.0 CA A:CYS198 3.8 27.5 1.0 CD A:ARG153 4.2 35.0 1.0 NH1 A:ARG153 4.4 27.5 1.0 CB A:ARG153 4.6 35.4 1.0 N A:CYS198 4.7 28.9 1.0 SG A:CYS205 4.9 34.8 1.0 CB A:PRO203 4.9 33.8 1.0 SG A:CYS214 4.9 50.5 1.0 SG A:CYS208 4.9 43.0 1.0 C A:CYS198 5.0 26.4 1.0

Iron binding site 3 out of 4 in the Muty Adenine Glycosylase in Complex with Dna and Soaked Adenine Free Base


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Muty Adenine Glycosylase in Complex with Dna and Soaked Adenine Free Base within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:35.6 occ:1.00 FE3 A:SF4400 0.0 35.6 1.0 S2 A:SF4400 2.0 33.9 1.0 S1 A:SF4400 2.2 33.2 1.0 S4 A:SF4400 2.2 33.2 1.0 SG A:CYS205 2.4 34.8 1.0 FE4 A:SF4400 2.7 36.0 1.0 FE1 A:SF4400 2.7 35.4 1.0 FE2 A:SF4400 2.8 36.0 1.0 CB A:CYS205 2.9 37.4 1.0 CA A:CYS205 3.3 38.3 1.0 S3 A:SF4400 3.8 34.9 1.0 N A:CYS205 3.9 37.8 1.0 CB A:PRO203 4.6 33.8 1.0 C A:CYS205 4.6 38.7 1.0 CB A:CYS208 4.6 43.0 1.0 C A:SER204 4.7 38.2 1.0 SG A:CYS214 4.7 50.5 1.0 CB A:ALA222 4.7 40.2 1.0 SG A:CYS198 4.9 34.9 1.0 CB A:PHE217 4.9 49.3 1.0 CG A:PRO203 5.0 32.8 1.0 O A:CYS205 5.0 36.1 1.0

Iron binding site 4 out of 4 in the Muty Adenine Glycosylase in Complex with Dna and Soaked Adenine Free Base


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Muty Adenine Glycosylase in Complex with Dna and Soaked Adenine Free Base within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:36.0 occ:1.00 FE4 A:SF4400 0.0 36.0 1.0 S2 A:SF4400 2.1 33.9 1.0 S3 A:SF4400 2.2 34.9 1.0 S1 A:SF4400 2.3 33.2 1.0 SG A:CYS214 2.5 50.5 1.0 FE2 A:SF4400 2.6 36.0 1.0 FE3 A:SF4400 2.7 35.6 1.0 FE1 A:SF4400 2.7 35.4 1.0 CB A:CYS214 3.2 50.0 1.0 S4 A:SF4400 3.8 33.2 1.0 CB A:ARG153 4.4 35.4 1.0 CD2 A:LEU154 4.4 41.5 1.0 CA A:CYS214 4.6 50.5 1.0 SG A:CYS198 4.7 34.9 1.0 CB A:PHE217 4.7 49.3 1.0 SG A:CYS205 4.8 34.8 1.0 N A:PHE217 4.9 49.8 1.0 N A:LEU154 4.9 41.4 1.0 CG A:LEU154 5.0 41.8 1.0 C A:ARG153 5.0 39.3 1.0

J.C.Fromme, A.Banerjee, S.J.Huang, G.L.Verdine. Structural Basis For Removal of Adenine Mispaired with 8-Oxoguanine By Muty Adenine Dna Glycosylase Nature V. 427 652 2004.
ISSN: ISSN 0028-0836
PubMed: 14961129
DOI: 10.1038/NATURE02306