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Manganese in PDB 6qo9: Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Soaked with Manganese Ions

Enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Soaked with Manganese Ions

All present enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Soaked with Manganese Ions:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Soaked with Manganese Ions, PDB code: 6qo9 was solved by K.Grave, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.76 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.529, 61.231, 95.836, 90.00, 106.48, 90.00
R / Rfree (%) 13.6 / 15.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Soaked with Manganese Ions (pdb code 6qo9). 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 Ribonucleotide Reductase Nrdf From Bacillus Anthracis Soaked with Manganese Ions, PDB code: 6qo9:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6qo9

Go back to Manganese Binding Sites List in 6qo9
Manganese binding site 1 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Soaked with Manganese Ions


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 Ribonucleotide Reductase Nrdf From Bacillus Anthracis Soaked with Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:6.2
occ:1.00
 OD1 A:ASP62 1.9 9.8 1.0
OE2 A:GLU195 1.9 10.1 1.0
ND1 A:HIS96 2.0 9.2 1.0
OE2 A:GLU93 2.1 9.6 1.0
CG A:ASP62 2.8 9.3 1.0
CD A:GLU195 2.8 9.6 1.0
CE1 A:HIS96 2.9 10.5 1.0
HA A:GLU93 2.9 9.8 1.0
OD2 A:ASP62 3.0 10.5 1.0
CD A:GLU93 3.0 8.9 1.0
HE1 A:HIS96 3.0 12.6 1.0
OE1 A:GLU195 3.0 9.4 1.0
CG A:HIS96 3.1 9.3 1.0
HB2 A:HIS96 3.2 10.6 1.0
HZ A:PHE165 3.5 12.1 1.0
HG23 A:ILE191 3.5 12.9 1.0
CB A:HIS96 3.5 8.8 1.0
HB3 A:HIS96 3.6 10.6 1.0
OE1 A:GLU93 3.6 10.2 1.0
CA A:GLU93 3.8 8.2 1.0
HB3 A:GLU93 3.9 10.3 1.0
MN A:MN406 3.9 6.1 1.0
CZ A:PHE165 4.0 10.1 1.0
CG A:GLU93 4.1 8.8 1.0
NE2 A:HIS96 4.1 9.5 1.0
CB A:GLU93 4.1 8.6 1.0
CB A:ASP62 4.2 9.3 1.0
CG A:GLU195 4.2 9.7 1.0
CD2 A:HIS96 4.2 9.2 1.0
HA A:ASP62 4.2 10.0 1.0
HE1 A:HIS198 4.3 11.2 1.0
CG2 A:ILE191 4.3 10.8 1.0
HB3 A:ASP62 4.4 11.1 1.0
HG2 A:GLU195 4.4 11.6 1.0
HG21 A:ILE191 4.4 12.9 1.0
HE2 A:PHE165 4.4 12.0 1.0
HG3 A:GLU195 4.4 11.6 1.0
HG22 A:ILE191 4.5 12.9 1.0
CE2 A:PHE165 4.5 10.0 1.0
O A:GLU93 4.6 7.9 1.0
HH A:TYR100 4.6 12.3 0.6
HG2 A:GLU93 4.7 10.6 1.0
HG3 A:GLU93 4.7 10.6 1.0
N A:GLU93 4.7 8.0 1.0
CE1 A:PHE165 4.7 10.9 1.0
O A:MET92 4.8 8.4 1.0
C A:GLU93 4.8 8.1 1.0
CA A:ASP62 4.8 8.4 1.0
HB2 A:ASP62 4.8 11.1 1.0
HE1 A:PHE165 4.8 13.1 1.0
HE2 A:HIS96 4.8 11.4 1.0
CE1 A:HIS198 4.9 9.3 1.0

Manganese binding site 2 out of 4 in 6qo9

Go back to Manganese Binding Sites List in 6qo9
Manganese binding site 2 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Soaked with Manganese Ions


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 Ribonucleotide Reductase Nrdf From Bacillus Anthracis Soaked with Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn406

b:6.1
occ:1.00
 OE1 A:GLU93 2.0 10.2 1.0
OE2 A:GLU161 2.0 9.3 1.0
ND1 A:HIS198 2.0 8.4 1.0
OE1 A:GLU195 2.0 9.4 1.0
OE1 A:GLU161 2.5 10.1 1.0
CD A:GLU161 2.5 8.1 1.0
CD A:GLU93 2.8 8.9 1.0
CE1 A:HIS198 3.0 9.3 1.0
OE2 A:GLU93 3.0 9.6 1.0
CG A:HIS198 3.1 7.5 1.0
HE1 A:HIS198 3.1 11.2 1.0
HA A:GLU195 3.1 10.3 1.0
CD A:GLU195 3.1 9.6 1.0
HB2 A:HIS198 3.2 10.6 1.0
HB3 A:HIS198 3.4 10.6 1.0
CB A:HIS198 3.5 8.9 1.0
HG2 A:GLN65 3.7 11.6 1.0
HE2 A:PHE165 3.7 12.0 1.0
OE2 A:GLU195 3.8 10.1 1.0
MN A:MN405 3.9 6.2 1.0
HB3 A:GLU195 3.9 10.2 1.0
CA A:GLU195 4.0 8.6 1.0
CG A:GLU161 4.0 9.4 1.0
NE2 A:HIS198 4.1 9.2 1.0
CG A:GLU93 4.1 8.8 1.0
CD2 A:HIS198 4.2 9.0 1.0
HE3 A:MET70 4.2 14.8 1.0
CG A:GLU195 4.2 9.7 1.0
HE1 A:HIS96 4.2 12.6 1.0
CB A:GLU195 4.2 8.5 1.0
HE21 A:GLN65 4.3 13.3 1.0
HG3 A:GLU93 4.3 10.6 1.0
HG2 A:GLU93 4.3 10.6 1.0
HB3 A:GLU161 4.4 11.0 1.0
HE2 A:MET70 4.4 14.8 1.0
HG3 A:GLU161 4.4 11.3 1.0
HA A:GLU161 4.5 9.8 1.0
CE2 A:PHE165 4.5 10.0 1.0
HG2 A:GLU161 4.5 11.3 1.0
HZ A:PHE165 4.5 12.1 1.0
CG A:GLN65 4.6 9.6 1.0
N A:GLU195 4.7 10.1 1.0
CB A:GLU161 4.7 9.2 1.0
HG3 A:GLN65 4.7 11.6 1.0
CE A:MET70 4.7 12.3 1.0
HG3 A:GLU195 4.8 11.6 1.0
HG2 A:GLU195 4.8 11.6 1.0
HE2 A:HIS198 4.9 11.1 1.0
CE1 A:HIS96 4.9 10.5 1.0
O A:GLU195 4.9 8.9 1.0
CZ A:PHE165 4.9 10.1 1.0
OD1 A:ASP62 4.9 9.8 1.0
O A:ASP194 4.9 9.4 1.0
HB3 A:MET89 5.0 9.1 1.0
CA A:HIS198 5.0 8.4 1.0
C A:GLU195 5.0 8.8 1.0

Manganese binding site 3 out of 4 in 6qo9

Go back to Manganese Binding Sites List in 6qo9
Manganese binding site 3 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Soaked with Manganese Ions


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 Ribonucleotide Reductase Nrdf From Bacillus Anthracis Soaked with Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn404

b:5.7
occ:1.00
 OE2 B:GLU195 1.9 9.2 1.0
OD1 B:ASP62 2.0 9.3 1.0
ND1 B:HIS96 2.0 8.0 1.0
OE2 B:GLU93 2.0 8.8 1.0
CG B:ASP62 2.8 8.0 1.0
CD B:GLU195 2.8 7.9 1.0
CE1 B:HIS96 2.9 8.5 1.0
OD2 B:ASP62 2.9 10.0 1.0
HA B:GLU93 2.9 8.3 1.0
CD B:GLU93 2.9 8.3 1.0
HE1 B:HIS96 3.0 10.2 1.0
OE1 B:GLU195 3.0 9.6 1.0
CG B:HIS96 3.1 7.6 1.0
HB2 B:HIS96 3.3 9.8 1.0
HZ B:PHE165 3.5 11.4 1.0
OE1 B:GLU93 3.5 9.8 1.0
HG23 B:ILE191 3.5 12.3 1.0
CB B:HIS96 3.6 8.2 1.0
HB3 B:HIS96 3.6 9.8 1.0
CA B:GLU93 3.8 6.9 1.0
HB3 B:GLU93 3.9 9.5 1.0
MN B:MN405 3.9 5.9 1.0
CZ B:PHE165 4.0 9.5 1.0
NE2 B:HIS96 4.0 8.1 1.0
CG B:GLU93 4.1 8.3 1.0
CB B:GLU93 4.1 7.9 1.0
CB B:ASP62 4.2 8.5 1.0
CG B:GLU195 4.2 8.6 1.0
CD2 B:HIS96 4.2 8.6 1.0
HA B:ASP62 4.2 9.2 1.0
HE1 B:HIS198 4.2 10.9 1.0
O B:HOH501 4.3 11.4 0.5
CG2 B:ILE191 4.3 10.3 1.0
HG2 B:GLU195 4.4 10.3 1.0
HB3 B:ASP62 4.4 10.2 1.0
HE2 B:PHE165 4.4 12.0 1.0
HG3 B:GLU195 4.4 10.3 1.0
HG21 B:ILE191 4.4 12.3 1.0
HG22 B:ILE191 4.5 12.3 1.0
CE2 B:PHE165 4.5 10.0 1.0
HH B:TYR100 4.6 12.2 0.5
O B:GLU93 4.6 8.3 1.0
HG2 B:GLU93 4.6 9.9 1.0
HG3 B:GLU93 4.7 9.9 1.0
N B:GLU93 4.7 7.0 1.0
O B:MET92 4.7 7.6 1.0
CE1 B:PHE165 4.7 10.2 1.0
C B:GLU93 4.7 7.5 1.0
HE1 B:PHE165 4.8 12.3 1.0
CA B:ASP62 4.8 7.6 1.0
HB2 B:ASP62 4.8 10.2 1.0
HE2 B:HIS96 4.8 9.7 1.0
CE1 B:HIS198 4.9 9.1 1.0
ND1 B:HIS198 5.0 7.6 1.0

Manganese binding site 4 out of 4 in 6qo9

Go back to Manganese Binding Sites List in 6qo9
Manganese binding site 4 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Soaked with Manganese Ions


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 Ribonucleotide Reductase Nrdf From Bacillus Anthracis Soaked with Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn405

b:5.9
occ:1.00
 OE2 B:GLU161 2.0 10.2 1.0
OE1 B:GLU93 2.0 9.8 1.0
OE1 B:GLU195 2.1 9.6 1.0
ND1 B:HIS198 2.1 7.6 1.0
OE1 B:GLU161 2.4 10.2 1.0
CD B:GLU161 2.5 8.7 1.0
CD B:GLU93 2.8 8.3 1.0
CE1 B:HIS198 3.0 9.1 1.0
OE2 B:GLU93 3.0 8.8 1.0
CG B:HIS198 3.1 7.3 1.0
HA B:GLU195 3.2 9.5 1.0
CD B:GLU195 3.2 7.9 1.0
HB2 B:HIS198 3.2 9.3 1.0
HE1 B:HIS198 3.2 10.9 1.0
HB3 B:HIS198 3.3 9.3 1.0
CB B:HIS198 3.4 7.8 1.0
HG2 B:GLN65 3.6 12.1 1.0
HE2 B:PHE165 3.7 12.0 1.0
OE2 B:GLU195 3.8 9.2 1.0
MN B:MN404 3.9 5.7 1.0
HB3 B:GLU195 4.0 10.2 1.0
CG B:GLU161 4.0 8.9 1.0
CA B:GLU195 4.0 8.0 1.0
CG B:GLU93 4.1 8.3 1.0
NE2 B:HIS198 4.1 9.0 1.0
CD2 B:HIS198 4.2 9.0 1.0
HE1 B:HIS96 4.2 10.2 1.0
HE3 B:MET70 4.2 14.6 1.0
CG B:GLU195 4.3 8.6 1.0
CB B:GLU195 4.3 8.5 1.0
HE21 B:GLN65 4.3 13.5 1.0
HG3 B:GLU93 4.3 9.9 1.0
HG2 B:GLU93 4.3 9.9 1.0
HE2 B:MET70 4.4 14.6 1.0
HG3 B:GLU161 4.4 10.6 1.0
HZ B:PHE165 4.4 11.4 1.0
CE2 B:PHE165 4.5 10.0 1.0
HB3 B:GLU161 4.5 9.7 1.0
HA B:GLU161 4.5 9.3 1.0
HG2 B:GLU161 4.5 10.6 1.0
CG B:GLN65 4.6 10.1 1.0
HG3 B:GLN65 4.7 12.1 1.0
CB B:GLU161 4.7 8.0 1.0
CE B:MET70 4.8 12.2 1.0
N B:GLU195 4.8 8.8 1.0
HG3 B:GLU195 4.8 10.3 1.0
CZ B:PHE165 4.9 9.5 1.0
HG2 B:GLU195 4.9 10.3 1.0
O B:GLU195 4.9 8.5 1.0
OD1 B:ASP62 4.9 9.3 1.0
HE2 B:HIS198 4.9 10.8 1.0
CE1 B:HIS96 4.9 8.5 1.0
O B:ASP194 4.9 8.8 1.0
CA B:HIS198 5.0 8.0 1.0
HB3 B:MET89 5.0 8.9 1.0

Reference:

K.Grave, W.Lambert, G.Berggren, J.J.Griese, M.D.Bennett, D.T.Logan, M.Hogbom. Redox-Induced Structural Changes in the Di-Iron and Di-Manganese Forms of Bacillus Anthracis Ribonucleotide Reductase Subunit Nrdf Suggest A Mechanism For Gating of Radical Access. J.Biol.Inorg.Chem. V. 24 849 2019.
ISSN: ESSN 1432-1327
PubMed: 31410573
DOI: 10.1007/S00775-019-01703-Z
Page generated: Sun Oct 6 06:01:11 2024

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