Manganese in PDB 3mjo: Small Subunit (R2F) of Native Ribonucleotide Reductase From Corynebacterium Ammoniagenes

The structure of Small Subunit (R2F) of Native Ribonucleotide Reductase From Corynebacterium Ammoniagenes, PDB code: 3mjo was solved by H.Ogata, P.Stolle, M.Stehr, G.Auling, W.Lubitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.36
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.210, 87.683, 83.249, 90.00, 99.29, 90.00
R / Rfree (%)	15 / 21

The binding sites of Manganese atom in the Small Subunit (R2F) of Native Ribonucleotide Reductase From Corynebacterium Ammoniagenes (pdb code 3mjo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Small Subunit (R2F) of Native Ribonucleotide Reductase From Corynebacterium Ammoniagenes, PDB code: 3mjo:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Small Subunit (R2F) of Native Ribonucleotide Reductase From Corynebacterium Ammoniagenes


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Small Subunit (R2F) of Native Ribonucleotide Reductase From Corynebacterium Ammoniagenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:13.6 occ:1.00 OD2 A:ASP77 2.0 18.3 1.0 OE1 A:GLU108 2.0 21.1 1.0 O A:HOH1003 2.0 19.2 1.0 O A:HOH1005 2.1 20.2 1.0 ND1 A:HIS111 2.2 11.1 1.0 O A:HOH1004 2.7 21.9 1.0 CG A:ASP77 2.8 18.6 1.0 OD1 A:ASP77 2.9 24.4 1.0 CE1 A:HIS111 3.0 10.6 1.0 CD A:GLU108 3.1 13.7 1.0 MN A:MN31002 3.3 12.5 1.0 CG A:HIS111 3.3 9.9 1.0 OE2 A:GLU108 3.6 16.0 1.0 CB A:HIS111 3.8 8.6 1.0 OE2 A:GLU202 3.9 21.5 1.0 CB A:ASP77 4.2 14.6 1.0 NE2 A:HIS111 4.2 10.1 1.0 OE1 A:GLU202 4.3 17.0 1.0 CD A:GLU202 4.3 18.4 1.0 CE1 A:PHE172 4.3 17.8 1.0 CG A:GLU108 4.4 10.8 1.0 CD2 A:HIS111 4.4 8.8 1.0 CA A:GLU108 4.4 8.2 1.0 CZ A:PHE172 4.4 20.8 1.0 CG2 A:ILE198 4.6 9.7 1.0 CB A:GLU108 4.6 8.8 1.0 CD1 A:PHE172 4.7 14.9 1.0 ND1 A:HIS205 4.8 11.3 1.0 CE1 A:HIS205 4.8 10.5 1.0 CE2 A:PHE172 4.9 23.1 1.0

Manganese binding site 2 out of 4 in the Small Subunit (R2F) of Native Ribonucleotide Reductase From Corynebacterium Ammoniagenes


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Small Subunit (R2F) of Native Ribonucleotide Reductase From Corynebacterium Ammoniagenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:12.5 occ:1.00 O A:HOH1005 2.0 20.2 1.0 OE1 A:GLU168 2.0 18.1 1.0 OE1 A:GLU202 2.1 17.0 1.0 OE2 A:GLU108 2.2 16.0 1.0 ND1 A:HIS205 2.3 11.3 1.0 O A:HOH1004 2.3 21.9 1.0 CD A:GLU108 3.0 13.7 1.0 CD A:GLU202 3.1 18.4 1.0 CD A:GLU168 3.1 20.8 1.0 CE1 A:HIS205 3.2 10.5 1.0 OE1 A:GLU108 3.2 21.1 1.0 MN A:MN31001 3.3 13.6 1.0 CG A:HIS205 3.3 11.5 1.0 OE2 A:GLU202 3.5 21.5 1.0 CB A:HIS205 3.7 9.4 1.0 CG A:GLU168 3.8 22.9 1.0 O A:HOH2169 3.9 48.9 1.0 OE2 A:GLU168 4.0 45.8 1.0 O A:HOH1003 4.2 19.2 1.0 NE2 A:HIS205 4.3 9.3 1.0 CG A:GLU202 4.4 14.4 1.0 CA A:GLU202 4.4 11.2 1.0 CG A:GLU108 4.4 10.8 1.0 CD2 A:HIS205 4.4 9.6 1.0 CG A:GLN80 4.6 13.5 1.0 OD1 A:ASP77 4.6 24.4 1.0 CB A:GLU202 4.7 12.7 1.0 CB A:GLU168 4.7 14.1 1.0 CE1 A:HIS111 4.7 10.6 1.0 CG2 A:ILE104 4.8 9.7 1.0 ND1 A:HIS111 4.8 11.1 1.0

Manganese binding site 3 out of 4 in the Small Subunit (R2F) of Native Ribonucleotide Reductase From Corynebacterium Ammoniagenes


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Small Subunit (R2F) of Native Ribonucleotide Reductase From Corynebacterium Ammoniagenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1006 b:12.3 occ:1.00 O B:HOH1009 2.0 16.3 1.0 OE2 B:GLU108 2.1 15.7 1.0 OE2 B:GLU168 2.1 17.6 1.0 OE2 B:GLU202 2.2 17.2 1.0 ND1 B:HIS205 2.2 11.9 1.0 O B:HOH1008 2.4 18.9 1.0 CD B:GLU108 3.0 12.6 1.0 CD B:GLU168 3.0 18.5 1.0 CD B:GLU202 3.1 18.9 1.0 CE1 B:HIS205 3.1 10.7 1.0 OE1 B:GLU108 3.2 17.1 1.0 MN B:MN31007 3.3 12.9 1.0 CG B:HIS205 3.3 9.2 1.0 OE1 B:GLU202 3.5 19.7 1.0 CG B:GLU168 3.5 26.3 1.0 CB B:HIS205 3.6 8.6 1.0 O B:HOH2562 3.7 33.0 1.0 OE1 B:GLU168 4.1 30.4 1.0 O B:HOH1010 4.3 16.4 1.0 NE2 B:HIS205 4.3 9.3 1.0 CG B:GLU108 4.4 8.0 1.0 CA B:GLU202 4.4 9.3 1.0 CD2 B:HIS205 4.4 9.6 1.0 CG B:GLU202 4.4 14.7 1.0 CG B:GLN80 4.6 12.8 1.0 CB B:GLU168 4.6 19.0 1.0 OD2 B:ASP77 4.7 21.5 1.0 CB B:GLU202 4.7 11.6 1.0 CE1 B:HIS111 4.8 11.1 1.0 ND1 B:HIS111 4.8 10.5 1.0 NE2 B:GLN80 4.9 33.8 1.0 CG2 B:ILE104 4.9 10.1 1.0 OD1 B:ASP77 5.0 14.9 1.0

Manganese binding site 4 out of 4 in the Small Subunit (R2F) of Native Ribonucleotide Reductase From Corynebacterium Ammoniagenes


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Small Subunit (R2F) of Native Ribonucleotide Reductase From Corynebacterium Ammoniagenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1007 b:12.9 occ:1.00 OE1 B:GLU108 1.9 17.1 1.0 OD1 B:ASP77 1.9 14.9 1.0 O B:HOH1009 2.0 16.3 1.0 O B:HOH1010 2.1 16.4 1.0 ND1 B:HIS111 2.3 10.5 1.0 O B:HOH1008 2.7 18.9 1.0 CG B:ASP77 2.8 14.7 1.0 OD2 B:ASP77 2.9 21.5 1.0 CD B:GLU108 3.0 12.6 1.0 CE1 B:HIS111 3.1 11.1 1.0 MN B:MN31006 3.3 12.3 1.0 CG B:HIS111 3.4 9.0 1.0 OE2 B:GLU108 3.5 15.7 1.0 CB B:HIS111 3.9 7.8 1.0 OE1 B:GLU202 3.9 19.7 1.0 CB B:ASP77 4.2 13.3 1.0 OE2 B:GLU202 4.3 17.2 1.0 NE2 B:HIS111 4.3 10.0 1.0 CD B:GLU202 4.3 18.9 1.0 CG B:GLU108 4.3 8.0 1.0 CE1 B:PHE172 4.4 19.2 1.0 CA B:GLU108 4.4 6.2 1.0 CD2 B:HIS111 4.4 8.2 1.0 CZ B:PHE172 4.5 23.4 1.0 CB B:GLU108 4.6 7.4 1.0 CG2 B:ILE198 4.7 8.6 1.0 ND1 B:HIS205 4.7 11.9 1.0 CD1 B:PHE172 4.7 17.2 1.0 CE1 B:HIS205 4.8 10.7 1.0 CE2 B:PHE172 4.9 23.1 1.0

N.Cox, H.Ogata, P.Stolle, E.Reijerse, G.Auling, W.Lubitz. A Tyrosyl-Dimanganese Coupled Spin System Is the Native Metalloradical Cofactor of the R2F Subunit of the Ribonucleotide Reductase of Corynebacterium Ammoniagenes. J.Am.Chem.Soc. V. 132 11197 2010.
ISSN: ISSN 0002-7863
PubMed: 20698687
DOI: 10.1021/JA1036995