Manganese in PDB 6cwo: X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Aerobic)

The structure of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Aerobic), PDB code: 6cwo was solved by A.O.Maggiolo, H.R.Rose, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.95 / 1.87
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	53.690, 53.690, 221.845, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 23.3

The structure of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Aerobic) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Aerobic) (pdb code 6cwo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Aerobic), PDB code: 6cwo:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Aerobic)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Aerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:11.7 occ:1.00 OE1 A:GLU97 2.1 14.5 1.0 OE2 A:GLU195 2.3 15.9 1.0 OE2 A:GLU67 2.3 11.4 1.0 O A:HOH551 2.3 17.6 1.0 OE1 A:GLU67 2.4 11.4 1.0 ND1 A:HIS100 2.4 9.0 1.0 CD A:GLU67 2.7 11.0 1.0 CD A:GLU195 3.1 12.7 1.0 CD A:GLU97 3.2 13.7 1.0 CE1 A:HIS100 3.3 8.9 1.0 OE2 A:GLU97 3.5 16.3 1.0 CG A:HIS100 3.5 8.9 1.0 MN A:MN402 3.7 13.7 1.0 OE1 A:GLU195 3.7 14.3 1.0 CB A:HIS100 3.8 9.0 1.0 O A:HOH502 4.0 23.9 1.0 CG A:GLU195 4.0 11.8 1.0 NZ A:LYS71 4.1 13.2 1.0 CG A:GLU67 4.2 10.8 1.0 NE2 A:HIS100 4.5 9.2 1.0 O A:HOH516 4.5 24.0 1.0 CD2 A:HIS100 4.6 9.1 1.0 CG A:GLU97 4.6 12.4 1.0 CG2 A:THR191 4.8 9.4 1.0 CA A:GLU97 4.8 10.2 1.0 CE1 A:HIS198 4.9 9.2 1.0 ND1 A:HIS198 5.0 9.0 1.0 CB A:GLU67 5.0 10.5 1.0 CD A:LYS71 5.0 14.3 1.0

Manganese binding site 2 out of 4 in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Aerobic)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Aerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:13.7 occ:1.00 OE1 A:GLU195 1.9 14.3 1.0 OE2 A:GLU97 2.0 16.3 1.0 OE1 A:GLU160 2.3 12.6 1.0 ND1 A:HIS198 2.3 9.0 1.0 O A:HOH502 2.3 23.9 1.0 CD A:GLU195 2.7 12.7 1.0 OE2 A:GLU195 2.7 15.9 1.0 CD A:GLU160 3.0 13.4 1.0 CD A:GLU97 3.1 13.7 1.0 OE2 A:GLU160 3.1 14.4 1.0 CE1 A:HIS198 3.2 9.2 1.0 O A:HOH551 3.3 17.6 1.0 CG A:HIS198 3.4 8.6 1.0 OE1 A:GLU97 3.5 14.5 1.0 MN A:MN401 3.7 11.7 1.0 CB A:HIS198 3.7 8.4 1.0 NE1 A:TRP74 4.1 12.0 1.0 CG A:GLU195 4.2 11.8 1.0 O A:HOH516 4.3 24.0 1.0 NE2 A:HIS198 4.3 8.9 1.0 CG A:GLU97 4.3 12.4 1.0 CG A:GLU160 4.4 13.1 1.0 CD2 A:HIS198 4.4 8.9 1.0 CD1 A:TRP74 4.5 12.0 1.0 CA A:GLU195 4.7 10.1 1.0 CB A:GLU195 4.8 10.9 1.0 CB A:GLU160 4.9 13.1 1.0

Manganese binding site 3 out of 4 in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Aerobic)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Aerobic) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:14.4 occ:1.00 OE2 B:GLU195 2.1 24.8 1.0 OE1 B:GLU97 2.2 17.2 1.0 OE1 B:GLU67 2.2 13.6 1.0 OE2 B:GLU67 2.3 14.7 1.0 ND1 B:HIS100 2.3 9.5 1.0 O B:HOH529 2.4 19.3 1.0 CD B:GLU67 2.6 13.1 1.0 CD B:GLU195 3.1 19.9 1.0 CE1 B:HIS100 3.2 9.5 1.0 CD B:GLU97 3.2 16.0 1.0 CG B:HIS100 3.4 9.1 1.0 OE2 B:GLU97 3.5 18.4 1.0 MN B:MN402 3.6 20.1 1.0 CB B:HIS100 3.7 8.9 1.0 OE1 B:GLU195 3.9 22.6 1.0 NZ B:LYS71 4.0 16.8 1.0 CG B:GLU195 4.0 19.3 1.0 CG B:GLU67 4.1 12.5 1.0 NE2 B:HIS100 4.3 9.7 1.0 O B:HOH524 4.3 45.5 1.0 O B:HOH515 4.4 32.8 1.0 CD2 B:HIS100 4.4 9.1 1.0 CG B:GLU97 4.6 14.5 1.0 CG2 B:THR191 4.7 14.6 1.0 CA B:GLU97 4.8 11.4 1.0 CB B:GLU67 4.9 12.2 1.0 CD B:LYS71 4.9 17.4 1.0 CE1 B:HIS198 5.0 16.2 1.0 CB B:GLU97 5.0 12.8 1.0 CD2 B:LEU164 5.0 24.5 1.0 ND1 B:HIS198 5.0 17.3 1.0

Manganese binding site 4 out of 4 in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Aerobic)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Aerobic) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:20.1 occ:1.00 OE2 B:GLU97 2.1 18.4 1.0 OE1 B:GLU195 2.2 22.6 1.0 ND1 B:HIS198 2.4 17.3 1.0 OE1 B:GLU160 2.5 21.0 1.0 OE2 B:GLU195 2.6 24.8 1.0 CD B:GLU195 2.7 19.9 1.0 O B:HOH524 2.8 45.5 1.0 CD B:GLU160 3.0 22.5 1.0 OE2 B:GLU160 3.0 23.3 1.0 O B:HOH529 3.0 19.3 1.0 CD B:GLU97 3.1 16.0 1.0 CE1 B:HIS198 3.3 16.2 1.0 CG B:HIS198 3.5 16.1 1.0 OE1 B:GLU97 3.5 17.2 1.0 MN B:MN401 3.6 14.4 1.0 CB B:HIS198 3.8 16.9 1.0 O B:HOH515 4.1 32.8 1.0 NE1 B:TRP74 4.2 16.3 1.0 CG B:GLU195 4.2 19.3 1.0 CG B:GLU97 4.4 14.5 1.0 CG B:GLU160 4.4 22.1 1.0 NE2 B:HIS198 4.4 16.1 1.0 CD2 B:HIS198 4.6 15.9 1.0 CD1 B:TRP74 4.6 15.5 1.0 CA B:GLU195 4.8 17.6 1.0 CB B:GLU160 4.9 21.9 1.0 CB B:GLU195 4.9 18.1 1.0

H.R.Rose, M.K.Ghosh, A.O.Maggiolo, C.J.Pollock, E.J.Blaesi, V.Hajj, Y.Wei, L.J.Rajakovich, W.C.Chang, Y.Han, M.Hajj, C.Krebs, A.Silakov, M.E.Pandelia, J.M.Bollinger, A.K.Boal. Structural Basis For Superoxide Activation of Flavobacterium Johnsoniae Class I Ribonucleotide Reductase and For Radical Initiation By Its Dimanganese Cofactor. Biochemistry V. 57 2679 2018.
ISSN: ISSN 1520-4995
PubMed: 29609464
DOI: 10.1021/ACS.BIOCHEM.8B00247