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

The structure of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Anaerobic), PDB code: 6cwp 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)	50.00 / 1.92
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	53.455, 53.455, 220.747, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 24.6

The binding sites of Manganese atom in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Ribonucleotide Reductase Beta Subunit (Anaerobic) (pdb code 6cwp). 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 (Anaerobic), PDB code: 6cwp:
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 (Anaerobic)


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 (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:8.7 occ:1.00 OE1 A:GLU97 2.1 9.3 1.0 OE2 A:GLU67 2.2 14.0 1.0 O A:HOH530 2.2 12.5 1.0 OE2 A:GLU195 2.2 14.2 1.0 ND1 A:HIS100 2.3 8.2 1.0 OE1 A:GLU67 2.4 11.3 1.0 CD A:GLU67 2.6 12.1 1.0 CE1 A:HIS100 3.1 8.3 1.0 CD A:GLU195 3.2 13.0 1.0 CD A:GLU97 3.2 9.4 1.0 CG A:HIS100 3.3 8.1 1.0 OE2 A:GLU97 3.7 10.9 1.0 CB A:HIS100 3.7 8.2 1.0 MN A:MN402 3.7 9.4 1.0 CG A:GLU195 4.0 12.4 1.0 OE1 A:GLU195 4.0 15.2 1.0 CG A:GLU67 4.1 12.0 1.0 NZ A:LYS71 4.1 13.6 1.0 NE2 A:HIS100 4.3 8.5 1.0 CD2 A:HIS100 4.4 8.4 1.0 O A:HOH528 4.4 22.0 1.0 CG A:GLU97 4.5 8.9 1.0 CG2 A:THR191 4.6 9.3 1.0 O A:HOH533 4.7 25.3 1.0 CA A:GLU97 4.7 8.2 1.0 CD A:LYS71 4.8 14.1 1.0 CB A:GLU97 4.9 8.4 1.0 CE1 A:HIS198 4.9 8.9 1.0 ND1 A:HIS198 5.0 9.1 1.0 CB A:GLU67 5.0 11.4 1.0 CD1 A:LEU164 5.0 11.8 1.0

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


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 (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:9.4 occ:1.00 OE2 A:GLU97 1.9 10.9 1.0 OE1 A:GLU195 1.9 15.2 1.0 OE1 A:GLU160 2.1 11.3 1.0 ND1 A:HIS198 2.3 9.1 1.0 OE2 A:GLU195 2.5 14.2 1.0 CD A:GLU195 2.5 13.0 1.0 CD A:GLU160 2.9 12.2 1.0 CD A:GLU97 2.9 9.4 1.0 OE2 A:GLU160 3.1 12.3 1.0 CE1 A:HIS198 3.2 8.9 1.0 CG A:HIS198 3.3 9.0 1.0 OE1 A:GLU97 3.3 9.3 1.0 O A:HOH530 3.4 12.5 1.0 CB A:HIS198 3.7 9.1 1.0 MN A:MN401 3.7 8.7 1.0 O A:HOH533 4.0 25.3 1.0 CG A:GLU195 4.0 12.4 1.0 NE1 A:TRP74 4.1 11.0 1.0 CG A:GLU97 4.2 8.9 1.0 CG A:GLU160 4.2 12.5 1.0 NE2 A:HIS198 4.3 9.0 1.0 O A:HOH528 4.3 22.0 1.0 CD2 A:HIS198 4.4 8.7 1.0 CD1 A:TRP74 4.5 11.2 1.0 CA A:GLU195 4.6 10.5 1.0 CB A:GLU195 4.7 11.2 1.0 CB A:GLU160 4.8 12.7 1.0

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


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 (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:12.8 occ:1.00 OE2 B:GLU195 2.0 21.5 1.0 OE2 B:GLU67 2.1 14.4 1.0 OE1 B:GLU97 2.2 13.4 1.0 O B:HOH525 2.3 19.4 1.0 ND1 B:HIS100 2.3 9.0 1.0 OE1 B:GLU67 2.3 13.4 1.0 CD B:GLU67 2.6 13.1 1.0 CD B:GLU195 3.1 19.4 1.0 CE1 B:HIS100 3.2 8.9 1.0 CD B:GLU97 3.2 13.6 1.0 CG B:HIS100 3.3 8.8 1.0 OE2 B:GLU97 3.6 16.6 1.0 CB B:HIS100 3.6 8.8 1.0 MN B:MN402 3.7 13.5 1.0 OE1 B:GLU195 3.9 21.9 1.0 CG B:GLU195 4.0 18.0 1.0 CG B:GLU67 4.1 12.6 1.0 NZ B:LYS71 4.2 13.7 1.0 NE2 B:HIS100 4.3 8.8 1.0 CD2 B:HIS100 4.4 8.8 1.0 CG B:GLU97 4.5 12.3 1.0 O B:HOH519 4.5 26.8 1.0 CA B:GLU97 4.6 10.6 1.0 CG2 B:THR191 4.6 14.6 1.0 O B:HOH529 4.8 23.0 1.0 CB B:GLU97 4.8 11.2 1.0 CD B:LYS71 4.8 14.3 1.0 CE1 B:HIS198 4.9 13.9 1.0 CD2 B:LEU164 5.0 19.0 1.0 ND1 B:HIS198 5.0 14.2 1.0

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


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 (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:13.5 occ:1.00 OE2 B:GLU97 1.8 16.6 1.0 OE1 B:GLU195 2.0 21.9 1.0 ND1 B:HIS198 2.2 14.2 1.0 OE1 B:GLU160 2.3 19.3 1.0 CD B:GLU195 2.6 19.4 1.0 OE2 B:GLU195 2.6 21.5 1.0 CD B:GLU97 2.9 13.6 1.0 CD B:GLU160 3.0 20.5 1.0 CE1 B:HIS198 3.1 13.9 1.0 OE2 B:GLU160 3.1 20.7 1.0 CG B:HIS198 3.3 14.3 1.0 OE1 B:GLU97 3.4 13.4 1.0 O B:HOH525 3.4 19.4 1.0 CB B:HIS198 3.7 15.1 1.0 MN B:MN401 3.7 12.8 1.0 CG B:GLU195 4.1 18.0 1.0 NE1 B:TRP74 4.1 16.6 1.0 CG B:GLU97 4.2 12.3 1.0 O B:HOH529 4.2 23.0 1.0 NE2 B:HIS198 4.3 14.4 1.0 O B:HOH519 4.3 26.8 1.0 CG B:GLU160 4.4 20.5 1.0 CD2 B:HIS198 4.4 14.2 1.0 CD1 B:TRP74 4.6 16.1 1.0 CA B:GLU195 4.6 16.6 1.0 CB B:GLU195 4.7 17.2 1.0 CB B:GLU160 4.8 20.2 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