Manganese in PDB 4dr0: Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf

All present enzymatic activity of Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf:
1.17.4.1;

The structure of Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf, PDB code: 4dr0 was solved by A.K.Boal, J.A.Cotruvo Jr., J.Stubbe, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.29 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	110.525, 112.912, 51.286, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.4

The binding sites of Manganese atom in the Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf (pdb code 4dr0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf, PDB code: 4dr0:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:25.1 occ:0.85 OE2 A:GLU97 2.0 29.2 1.0 OE2 A:GLU164 2.0 28.6 1.0 OE1 A:GLU164 2.1 28.8 1.0 OE1 A:GLU198 2.2 27.6 1.0 CD A:GLU164 2.3 29.2 1.0 ND1 A:HIS201 2.4 20.7 1.0 CD A:GLU97 2.8 26.3 1.0 OE1 A:GLU97 3.0 29.9 1.0 CG A:HIS201 3.3 21.8 1.0 CD A:GLU198 3.4 26.3 1.0 CE1 A:HIS201 3.4 22.3 1.0 CB A:HIS201 3.5 21.8 1.0 MN A:MN402 3.7 26.4 0.8 CG A:GLU164 3.9 27.1 1.0 OE2 A:GLU198 4.1 26.9 1.0 CA A:GLU198 4.2 24.2 1.0 CG A:GLU97 4.2 24.4 1.0 CB A:GLU198 4.4 24.1 1.0 CG A:GLN69 4.4 24.3 1.0 CG A:GLU198 4.4 25.0 1.0 NE2 A:HIS201 4.5 22.5 1.0 CD2 A:HIS201 4.5 22.1 1.0 CE2 A:PHE168 4.6 30.2 1.0 NE2 A:GLN69 4.8 27.7 1.0 CB A:GLU164 4.8 26.2 1.0 OD1 A:ASP66 4.9 27.5 1.0 CE1 A:HIS101 5.0 22.6 1.0 N A:GLU198 5.0 23.9 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:26.4 occ:0.85 OD1 A:ASP66 2.0 27.5 1.0 OE2 A:GLU198 2.1 26.9 1.0 OE1 A:GLU97 2.1 29.9 1.0 ND1 A:HIS101 2.2 22.8 1.0 OE1 A:GLU198 2.7 27.6 1.0 CD A:GLU198 2.7 26.3 1.0 CG A:ASP66 2.9 24.6 1.0 CE1 A:HIS101 3.1 22.6 1.0 OD2 A:ASP66 3.1 28.0 1.0 CD A:GLU97 3.2 26.3 1.0 CG A:HIS101 3.2 23.0 1.0 CB A:HIS101 3.6 23.3 1.0 OE2 A:GLU97 3.7 29.2 1.0 MN A:MN401 3.7 25.1 0.8 CZ A:PHE168 3.9 29.8 1.0 CA A:GLU97 4.2 22.0 1.0 CG A:GLU198 4.2 25.0 1.0 CE2 A:PHE168 4.2 30.2 1.0 NE2 A:HIS101 4.2 21.8 1.0 CB A:ASP66 4.3 22.2 1.0 CD2 A:HIS101 4.3 23.2 1.0 CG2 A:ILE194 4.4 21.9 1.0 CG A:GLU97 4.4 24.4 1.0 CB A:GLU97 4.5 22.0 1.0 CE1 A:PHE168 4.8 28.5 1.0 O A:GLU97 4.8 22.2 1.0 N A:GLU97 4.9 21.2 1.0 CA A:ASP66 4.9 22.0 1.0 OE1 A:GLU164 4.9 28.8 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:22.5 occ:1.00 OE2 B:GLU97 1.9 27.5 1.0 OE1 B:GLU198 2.1 25.1 1.0 OE1 B:GLU164 2.3 28.0 1.0 OE2 B:GLU164 2.3 25.5 1.0 ND1 B:HIS201 2.3 18.4 1.0 O B:HOH501 2.4 25.4 1.0 CD B:GLU164 2.7 24.2 1.0 CD B:GLU97 2.9 24.1 1.0 CD B:GLU198 3.1 24.0 1.0 OE1 B:GLU97 3.2 26.4 1.0 CE1 B:HIS201 3.2 18.3 1.0 CG B:HIS201 3.4 19.2 1.0 OE2 B:GLU198 3.7 24.5 1.0 CB B:HIS201 3.7 19.8 1.0 MN B:MN402 3.9 24.7 1.0 CA B:GLU198 4.2 20.7 1.0 CG B:GLU164 4.2 22.2 1.0 CG B:GLU97 4.3 23.1 1.0 CG B:GLN69 4.3 27.8 1.0 CG B:GLU198 4.3 22.0 1.0 NE2 B:HIS201 4.4 20.0 1.0 CB B:GLU198 4.4 20.6 1.0 CE B:MET74 4.5 28.9 1.0 OD1 B:ASP66 4.5 26.9 1.0 CD2 B:HIS201 4.5 17.6 1.0 N B:GLU198 4.8 20.6 1.0 CE2 B:PHE168 4.8 22.1 1.0 CE1 B:HIS101 4.9 19.9 1.0 NE2 B:GLN69 4.9 28.2 1.0 ND1 B:HIS101 5.0 20.5 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Bacillus Subtilis Dimanganese(II) Nrdf within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:24.7 occ:1.00 OE1 B:GLU97 2.0 26.4 1.0 OE2 B:GLU198 2.1 24.5 1.0 ND1 B:HIS101 2.1 20.5 1.0 OD2 B:ASP66 2.2 23.1 1.0 OD1 B:ASP66 2.3 26.9 1.0 CG B:ASP66 2.5 25.8 1.0 CD B:GLU198 3.0 24.0 1.0 CE1 B:HIS101 3.1 19.9 1.0 CG B:HIS101 3.2 22.8 1.0 CD B:GLU97 3.2 24.1 1.0 OE1 B:GLU198 3.2 25.1 1.0 O B:HOH501 3.4 25.4 1.0 CB B:HIS101 3.5 23.2 1.0 OE2 B:GLU97 3.8 27.5 1.0 MN B:MN401 3.9 22.5 1.0 O B:HOH502 3.9 19.5 1.0 CB B:ASP66 4.0 25.5 1.0 CA B:GLU97 4.2 23.5 1.0 NE2 B:HIS101 4.2 21.6 1.0 CD2 B:HIS101 4.3 21.0 1.0 CG B:GLU97 4.3 23.1 1.0 CB B:GLU97 4.3 23.1 1.0 CG B:GLU198 4.4 22.0 1.0 O B:HOH591 4.5 33.0 1.0 CG2 B:ILE194 4.5 20.2 1.0 CA B:ASP66 4.9 25.8 1.0 N B:GLU97 4.9 22.7 1.0 CZ B:PHE168 5.0 22.6 1.0

A.K.Boal, J.A.Cotruvo, J.Stubbe, A.C.Rosenzweig. The Dimanganese(II) Site of Bacillus Subtilis Class Ib Ribonucleotide Reductase. Biochemistry V. 51 3861 2012.
ISSN: ISSN 0006-2960
PubMed: 22443445
DOI: 10.1021/BI201925T