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

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

Resolution Low / High (Å)	72.63 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	48.356, 50.816, 79.285, 106.15, 105.03, 95.75
R / Rfree (%)	19.2 / 21.2

The structure of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (As-Isolated) 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 (As-Isolated) (pdb code 6cwq). 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 (As-Isolated), PDB code: 6cwq:
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 (As-Isolated)


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 (As-Isolated) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:19.0 occ:0.93 OE2 A:GLU195 1.9 21.9 1.0 OE1 A:GLU67 2.3 22.4 1.0 ND1 A:HIS100 2.3 13.5 1.0 OE2 A:GLU67 2.4 23.0 1.0 OE1 A:GLU97 2.4 26.2 1.0 CD A:GLU67 2.7 19.6 1.0 O A:HOH580 2.9 32.6 1.0 OE2 A:GLU97 3.0 27.0 1.0 CD A:GLU97 3.1 24.0 1.0 CD A:GLU195 3.1 19.7 1.0 CE1 A:HIS100 3.2 13.5 1.0 CG A:HIS100 3.4 13.4 1.0 OE1 A:GLU195 3.6 20.8 1.0 MN A:MN402 3.6 20.8 0.9 CB A:HIS100 3.7 13.0 1.0 NZ A:LYS71 4.1 21.0 1.0 CG A:GLU67 4.2 17.8 1.0 CG A:GLU195 4.2 18.3 1.0 NE2 A:HIS100 4.3 13.7 1.0 CD2 A:HIS100 4.5 13.4 1.0 CG A:GLU97 4.6 21.5 1.0 O A:HOH523 4.6 30.1 1.0 CG2 A:THR191 4.6 13.7 1.0 CA A:GLU97 4.9 17.2 1.0 CE1 A:HIS198 4.9 15.7 1.0 CD1 A:LEU164 4.9 21.8 1.0 ND1 A:HIS198 5.0 15.9 1.0

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


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 (As-Isolated) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:20.8 occ:0.94 OE1 A:GLU195 2.1 20.8 1.0 OE2 A:GLU97 2.3 27.0 1.0 ND1 A:HIS198 2.3 15.9 1.0 O A:HOH523 2.4 30.1 1.0 OE1 A:GLU160 2.5 24.6 1.0 O A:HOH580 2.8 32.6 1.0 OE2 A:GLU160 2.9 26.8 1.0 CD A:GLU160 3.0 24.5 1.0 CD A:GLU195 3.0 19.7 1.0 CE1 A:HIS198 3.2 15.7 1.0 OE2 A:GLU195 3.2 21.9 1.0 CD A:GLU97 3.4 24.0 1.0 CG A:HIS198 3.4 15.2 1.0 MN A:MN401 3.6 19.0 0.9 CB A:HIS198 3.8 14.4 1.0 OE1 A:GLU97 4.0 26.2 1.0 NE2 A:HIS198 4.4 15.7 1.0 CG A:GLU160 4.4 23.7 1.0 CG A:GLU195 4.4 18.3 1.0 CG A:GLU97 4.5 21.5 1.0 NE1 A:TRP74 4.5 16.8 1.0 CD2 A:HIS198 4.5 15.4 1.0 CA A:GLU195 4.6 16.2 1.0 CB A:GLU160 4.8 23.1 1.0 CB A:GLU195 4.8 17.1 1.0 CD1 A:TRP74 4.9 16.6 1.0

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


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 (As-Isolated) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:20.7 occ:0.88 OE2 B:GLU195 1.9 24.6 1.0 OE1 B:GLU67 2.3 22.7 1.0 ND1 B:HIS100 2.3 18.3 1.0 OE2 B:GLU67 2.3 23.9 1.0 OE1 B:GLU97 2.5 31.4 1.0 CD B:GLU67 2.6 20.7 1.0 O B:HOH555 2.9 34.9 1.0 OE2 B:GLU97 3.0 32.6 1.0 CD B:GLU195 3.0 21.5 1.0 CD B:GLU97 3.1 28.0 1.0 CE1 B:HIS100 3.2 18.4 1.0 CG B:HIS100 3.4 17.7 1.0 OE1 B:GLU195 3.6 21.9 1.0 MN B:MN402 3.6 24.0 0.9 CB B:HIS100 3.7 17.1 1.0 NZ B:LYS71 4.1 24.5 1.0 CG B:GLU67 4.1 19.6 1.0 CG B:GLU195 4.3 20.1 1.0 NE2 B:HIS100 4.4 18.2 1.0 CD2 B:HIS100 4.5 18.0 1.0 O B:HOH505 4.5 32.9 1.0 CG B:GLU97 4.6 25.1 1.0 CG2 B:THR191 4.6 17.7 1.0 CD2 B:LEU164 4.9 23.1 1.0 CA B:GLU97 4.9 20.0 1.0 CB B:GLU67 5.0 18.5 1.0 ND1 B:HIS198 5.0 17.4 1.0 CE1 B:HIS198 5.0 17.5 1.0

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


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 (As-Isolated) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:24.0 occ:0.94 OE1 B:GLU195 2.1 21.9 1.0 O B:HOH505 2.1 32.9 1.0 OE2 B:GLU97 2.4 32.6 1.0 ND1 B:HIS198 2.5 17.4 1.0 OE2 B:GLU160 2.6 31.8 1.0 O B:HOH555 2.7 34.9 1.0 OE1 B:GLU160 2.9 28.7 1.0 CD B:GLU195 3.0 21.5 1.0 CD B:GLU160 3.0 28.2 1.0 OE2 B:GLU195 3.3 24.6 1.0 CE1 B:HIS198 3.4 17.5 1.0 CD B:GLU97 3.4 28.0 1.0 CG B:HIS198 3.5 16.8 1.0 MN B:MN401 3.6 20.7 0.9 CB B:HIS198 3.8 15.9 1.0 OE1 B:GLU97 3.9 31.4 1.0 CG B:GLU160 4.4 27.1 1.0 CG B:GLU195 4.4 20.1 1.0 CG B:GLU97 4.5 25.1 1.0 NE2 B:HIS198 4.5 17.6 1.0 CA B:GLU195 4.6 17.6 1.0 CD2 B:HIS198 4.6 17.1 1.0 NE1 B:TRP74 4.6 17.2 1.0 CB B:GLU160 4.8 26.4 1.0 CB B:GLU195 4.8 18.6 1.0 CA B:GLU160 4.9 26.2 1.0 CD1 B:TRP74 5.0 17.2 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