Iron in PDB 2av8: Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli

All present enzymatic activity of Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli:
1.17.4.1;

The structure of Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli, PDB code: 2av8 was solved by S.Han, A.Arvai, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 2.46
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	136.500, 136.500, 109.600, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 23.7

The binding sites of Iron atom in the Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli (pdb code 2av8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli, PDB code: 2av8:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:44.9 occ:1.00 OE2 A:GLU69 2.0 37.1 1.0 O A:HOH1243 2.1 14.8 1.0 O A:HOH1276 2.4 11.0 1.0 O A:HOH1338 2.5 64.2 1.0 CD A:GLU69 3.0 31.6 1.0 NH2 A:ARG221 3.4 28.3 1.0 OE1 A:GLU69 3.5 29.2 1.0 CZ A:ARG221 4.1 28.6 1.0 CG A:GLU69 4.3 25.6 1.0 CB A:MET296 4.4 31.2 1.0 CA A:MET296 4.4 30.2 1.0 NH1 A:ARG221 4.4 30.4 1.0 NE2 A:HIS68 4.6 42.2 1.0 CG A:PRO66 4.7 24.7 1.0 O A:SER295 4.7 34.6 1.0 N A:ILE297 4.7 28.1 1.0 NE A:ARG221 4.9 25.3 1.0 CE1 A:HIS68 5.0 40.9 1.0

Iron binding site 2 out of 5 in the Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:35.4 occ:1.00 FE1 A:FEO401 0.0 35.4 1.0 O A:HOH1202 2.0 50.1 1.0 O A:FEO401 2.0 46.8 1.0 OE1 A:GLU115 2.0 36.7 1.0 ND1 A:HIS118 2.0 26.2 1.0 OD1 A:ASP84 2.1 39.7 1.0 CE1 A:HIS118 2.9 23.6 1.0 CG A:ASP84 2.9 41.6 1.0 OD2 A:ASP84 3.0 42.0 1.0 CD A:GLU115 3.1 37.9 1.0 CG A:HIS118 3.2 27.7 1.0 O A:HOH1201 3.2 33.0 1.0 FE2 A:FEO401 3.4 35.8 1.0 OE2 A:GLU115 3.6 45.3 1.0 CB A:HIS118 3.7 24.8 1.0 OE1 A:GLU238 3.8 57.9 1.0 NE2 A:HIS118 4.1 22.4 1.0 OE2 A:GLU238 4.2 48.1 1.0 CD2 A:HIS118 4.2 25.5 1.0 CB A:ASP84 4.2 33.5 1.0 CE2 A:PHE208 4.3 48.7 1.0 CZ A:PHE208 4.4 46.5 1.0 CG2 A:ILE234 4.4 21.8 1.0 CD A:GLU238 4.4 49.6 1.0 CG A:GLU115 4.4 33.5 1.0 CA A:GLU115 4.4 27.7 1.0 CE1 A:HIS241 4.5 29.6 1.0 ND1 A:HIS241 4.6 26.8 1.0 CB A:GLU115 4.6 30.2 1.0 CA A:ASP84 4.9 33.2 1.0 CD2 A:PHE208 5.0 47.5 1.0 CE1 A:PHE208 5.0 43.9 1.0

Iron binding site 3 out of 5 in the Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:35.8 occ:1.00 FE2 A:FEO401 0.0 35.8 1.0 OE2 A:GLU204 2.0 42.5 1.0 OE2 A:GLU238 2.1 48.1 1.0 O A:FEO401 2.1 46.8 1.0 OE2 A:GLU115 2.1 45.3 1.0 ND1 A:HIS241 2.3 26.8 1.0 O A:HOH1201 2.5 33.0 1.0 CD A:GLU204 3.0 45.6 1.0 CD A:GLU115 3.0 37.9 1.0 CE1 A:HIS241 3.1 29.6 1.0 CD A:GLU238 3.2 49.6 1.0 OE1 A:GLU115 3.2 36.7 1.0 CG A:HIS241 3.4 31.3 1.0 FE1 A:FEO401 3.4 35.4 1.0 OE1 A:GLU238 3.6 57.9 1.0 CG A:GLU204 3.7 41.0 1.0 CB A:HIS241 3.7 29.0 1.0 OE1 A:GLU204 3.9 51.0 1.0 NE1 A:TRP111 4.0 24.8 1.0 NE2 A:HIS241 4.4 27.9 1.0 CG A:GLU115 4.4 33.5 1.0 NE2 A:GLN87 4.4 35.6 1.0 CG A:GLU238 4.5 40.3 1.0 CD2 A:HIS241 4.5 28.9 1.0 CB A:GLU204 4.5 34.0 1.0 OD1 A:ASP84 4.5 39.7 1.0 O A:HOH1202 4.5 50.1 1.0 CD1 A:TRP111 4.6 20.4 1.0 CA A:GLU238 4.7 27.7 1.0 CE1 A:HIS118 4.8 23.6 1.0 ND1 A:HIS118 4.8 26.2 1.0 CG A:GLN87 4.8 32.4 1.0

Iron binding site 4 out of 5 in the Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:41.6 occ:1.00 FE1 B:FEO403 0.0 41.6 1.0 O B:HOH1204 1.9 59.3 1.0 OE1 B:GLU115 2.0 45.2 1.0 ND1 B:HIS118 2.1 30.0 1.0 OD1 B:ASP84 2.2 41.4 1.0 O B:FEO403 2.5 44.8 1.0 OD2 B:ASP84 2.7 42.5 1.0 CG B:ASP84 2.7 43.5 1.0 CE1 B:HIS118 3.0 26.4 1.0 CD B:GLU115 3.1 44.5 1.0 O B:HOH1203 3.2 53.7 1.0 CG B:HIS118 3.2 32.2 1.0 FE2 B:FEO403 3.5 43.2 1.0 OE2 B:GLU115 3.6 52.0 1.0 CB B:HIS118 3.7 32.3 1.0 CB B:ASP84 4.1 38.3 1.0 NE2 B:HIS118 4.2 27.4 1.0 OE2 B:GLU238 4.2 59.0 1.0 CA B:GLU115 4.3 29.4 1.0 CD2 B:HIS118 4.3 28.8 1.0 CG B:GLU115 4.3 39.7 1.0 CE2 B:PHE208 4.3 54.9 1.0 CZ B:PHE208 4.3 54.2 1.0 OE1 B:GLU238 4.4 54.4 1.0 CB B:GLU115 4.4 31.1 1.0 CE1 B:HIS241 4.6 32.7 1.0 CG2 B:ILE234 4.6 18.8 1.0 CD B:GLU238 4.6 54.2 1.0 ND1 B:HIS241 4.6 34.6 1.0 CA B:ASP84 4.8 35.4 1.0

Iron binding site 5 out of 5 in the Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:43.2 occ:1.00 FE2 B:FEO403 0.0 43.2 1.0 OE1 B:GLU238 2.1 54.4 1.0 O B:FEO403 2.2 44.8 1.0 OE2 B:GLU115 2.2 52.0 1.0 OE2 B:GLU204 2.3 46.5 1.0 ND1 B:HIS241 2.3 34.6 1.0 O B:HOH1203 2.7 53.7 1.0 CD B:GLU115 3.0 44.5 1.0 CD B:GLU238 3.0 54.2 1.0 CD B:GLU204 3.1 48.2 1.0 OE1 B:GLU115 3.1 45.2 1.0 OE2 B:GLU238 3.2 59.0 1.0 CE1 B:HIS241 3.3 32.7 1.0 CG B:HIS241 3.4 35.7 1.0 FE1 B:FEO403 3.5 41.6 1.0 CB B:HIS241 3.7 33.9 1.0 CG B:GLU204 3.7 45.8 1.0 NE1 B:TRP111 3.9 31.2 1.0 OE1 B:GLU204 4.0 52.3 1.0 NE2 B:HIS241 4.4 32.6 1.0 O B:HOH1204 4.4 59.3 1.0 CG B:GLU238 4.5 45.6 1.0 CG B:GLU115 4.5 39.7 1.0 CB B:GLU204 4.5 38.3 1.0 CD2 B:HIS241 4.5 31.9 1.0 OD1 B:ASP84 4.5 41.4 1.0 CD1 B:TRP111 4.5 32.4 1.0 NE2 B:GLN87 4.6 31.1 1.0 CA B:GLU238 4.7 30.8 1.0 ND1 B:HIS118 4.8 30.0 1.0 CE1 B:HIS118 4.9 26.4 1.0 CG B:GLN87 4.9 31.2 1.0 CE2 B:TRP111 5.0 31.6 1.0

W.Tong, D.Burdi, P.Riggs-Gelasco, S.Chen, D.Edmondson, B.H.Huynh, J.Stubbe, S.Han, A.Arvai, J.A.Tainer. Characterization of Y122F R2 of Escherichia Coli Ribonucleotide Reductase By Time-Resolved Physical Biochemical Methods and X-Ray Crystallography. Biochemistry V. 37 5840 1998.
ISSN: ISSN 0006-2960
PubMed: 9558317
DOI: 10.1021/BI9728811