Manganese in PDB 7z3d: Xfel Structure of Class Ib Ribonucleotide Reductase Dimanganese(II) Nrdf in Complex with Oxidized Nrdi From Bacillus Cereus

All present enzymatic activity of Xfel Structure of Class Ib Ribonucleotide Reductase Dimanganese(II) Nrdf in Complex with Oxidized Nrdi From Bacillus Cereus:
1.17.4.1;

The structure of Xfel Structure of Class Ib Ribonucleotide Reductase Dimanganese(II) Nrdf in Complex with Oxidized Nrdi From Bacillus Cereus, PDB code: 7z3d was solved by J.John, H.Lebrette, O.Aurelius, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.17 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	61.438, 125.634, 144.997, 90, 90, 90
R / Rfree (%)	15.9 / 19.6

The binding sites of Manganese atom in the Xfel Structure of Class Ib Ribonucleotide Reductase Dimanganese(II) Nrdf in Complex with Oxidized Nrdi From Bacillus Cereus (pdb code 7z3d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Xfel Structure of Class Ib Ribonucleotide Reductase Dimanganese(II) Nrdf in Complex with Oxidized Nrdi From Bacillus Cereus, PDB code: 7z3d:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Xfel Structure of Class Ib Ribonucleotide Reductase Dimanganese(II) Nrdf in Complex with Oxidized Nrdi From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Xfel Structure of Class Ib Ribonucleotide Reductase Dimanganese(II) Nrdf in Complex with Oxidized Nrdi From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:28.9 occ:1.00 OE2 A:GLU93 2.0 34.5 1.0 OE2 A:GLU195 2.1 28.2 0.3 OE2 A:GLU161 2.1 30.7 0.2 ND1 A:HIS198 2.1 25.5 1.0 OE1 A:GLU161 2.1 30.4 0.8 OE2 A:GLU161 2.2 32.1 0.8 OE1 A:GLU195 2.2 28.8 0.7 OE1 A:GLU195 2.3 31.6 0.3 CD A:GLU195 2.4 29.9 0.3 CD A:GLU161 2.5 30.9 0.8 CD A:GLU161 2.7 31.0 0.2 OE1 A:GLU161 2.8 31.6 0.2 CD A:GLU93 2.8 28.7 1.0 OE1 A:GLU93 3.0 33.0 1.0 CE1 A:HIS198 3.0 29.7 1.0 CG A:HIS198 3.1 28.4 1.0 CD A:GLU195 3.4 29.6 0.7 CB A:HIS198 3.5 24.9 1.0 CG A:GLU195 3.9 27.4 0.3 MN A:MN402 3.9 32.7 1.0 CG A:GLU161 4.0 30.3 0.8 CG A:GLU161 4.0 30.2 0.2 NE2 A:HIS198 4.1 27.9 1.0 OE2 A:GLU195 4.2 30.1 0.7 CG A:GLU93 4.2 29.5 1.0 CD2 A:HIS198 4.2 27.1 1.0 CA A:GLU195 4.3 27.5 0.7 CA A:GLU195 4.3 27.5 0.3 CB A:GLU195 4.4 27.6 0.7 CE A:MET70 4.5 40.0 1.0 CG A:GLU195 4.5 26.0 0.7 CG A:GLN65 4.5 34.4 1.0 CB A:GLU161 4.6 30.0 0.2 CB A:GLU195 4.6 27.6 0.3 CE2 A:PHE165 4.6 35.1 1.0 CB A:GLU161 4.7 30.0 0.8 NE2 A:GLN65 4.9 35.7 1.0 CE1 A:HIS96 5.0 25.7 1.0 N A:GLU195 5.0 26.4 1.0

Manganese binding site 2 out of 2 in the Xfel Structure of Class Ib Ribonucleotide Reductase Dimanganese(II) Nrdf in Complex with Oxidized Nrdi From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Xfel Structure of Class Ib Ribonucleotide Reductase Dimanganese(II) Nrdf in Complex with Oxidized Nrdi From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:32.7 occ:1.00 OD1 A:ASP62 2.0 28.5 1.0 OE1 A:GLU93 2.0 33.0 1.0 OE2 A:GLU195 2.0 30.1 0.7 ND1 A:HIS96 2.2 22.6 1.0 OE2 A:GLU195 2.4 28.2 0.3 CD A:GLU195 2.7 29.6 0.7 OE1 A:GLU195 2.8 28.8 0.7 CG A:ASP62 2.9 30.3 1.0 CE1 A:HIS96 3.1 25.7 1.0 OD2 A:ASP62 3.1 36.8 1.0 CD A:GLU93 3.2 28.7 1.0 CG A:HIS96 3.3 24.8 1.0 CD A:GLU195 3.4 29.9 0.3 CB A:HIS96 3.6 23.4 1.0 OE2 A:GLU93 3.8 34.5 1.0 MN A:MN401 3.9 28.9 1.0 CG A:GLU195 4.0 27.4 0.3 CA A:GLU93 4.0 25.1 1.0 CZ A:PHE165 4.1 31.9 1.0 CG A:GLU195 4.2 26.0 0.7 NE2 A:HIS96 4.2 23.0 1.0 CB A:ASP62 4.3 27.1 1.0 CG A:GLU93 4.3 29.5 1.0 CD2 A:HIS96 4.4 25.0 1.0 OE1 A:GLU195 4.4 31.6 0.3 CB A:GLU93 4.4 25.1 1.0 CG2 A:ILE191 4.4 26.1 1.0 CE2 A:PHE165 4.4 35.1 1.0 O A:GLU93 4.6 28.0 1.0 CA A:ASP62 4.8 24.8 1.0 CE1 A:PHE165 4.9 34.7 1.0 C A:GLU93 4.9 24.8 1.0 N A:GLU93 4.9 23.8 1.0 O A:MET92 5.0 27.1 1.0

J.John, O.Aurelius, V.Srinivas, P.Saura, I.S.Kim, A.Bhowmick, P.S.Simon, M.Dasgupta, C.Pham, S.Gul, K.D.Sutherlin, P.Aller, A.Butryn, A.M.Orville, M.H.Cheah, S.Owada, K.Tono, F.D.Fuller, A.Batyuk, A.S.Brewster, N.K.Sauter, V.K.Yachandra, J.Yano, V.R.I.Kaila, J.Kern, H.Lebrette, M.Hogbom. Redox-Controlled Reorganization and Flavin Strain Within the Ribonucleotide Reductase R2B-Nrdi Complex Monitored By Serial Femtosecond Crystallography. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 36083619
DOI: 10.7554/ELIFE.79226