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Manganese in PDB 4bmu: Crystal Structure of Ribonucleotide Reductase Di-Manganese(II) Nrdf From Bacillus Cereus

Enzymatic activity of Crystal Structure of Ribonucleotide Reductase Di-Manganese(II) Nrdf From Bacillus Cereus

All present enzymatic activity of Crystal Structure of Ribonucleotide Reductase Di-Manganese(II) Nrdf From Bacillus Cereus:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Ribonucleotide Reductase Di-Manganese(II) Nrdf From Bacillus Cereus, PDB code: 4bmu was solved by H.-P.Hersleth, A.B.Tomter, M.Hammerstad, A.K.Rohr, K.K.Andersson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.10 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.880, 49.210, 98.520, 90.00, 107.19, 90.00
R / Rfree (%) 18.4 / 23.313

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Ribonucleotide Reductase Di-Manganese(II) Nrdf From Bacillus Cereus (pdb code 4bmu). 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 Di-Manganese(II) Nrdf From Bacillus Cereus, PDB code: 4bmu:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4bmu

Go back to Manganese Binding Sites List in 4bmu
Manganese binding site 1 out of 4 in the Crystal Structure of Ribonucleotide Reductase Di-Manganese(II) Nrdf 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 Crystal Structure of Ribonucleotide Reductase Di-Manganese(II) Nrdf From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1323

b:19.0
occ:1.00
 OE1 A:GLU93 2.0 19.1 1.0
OD1 A:ASP62 2.1 15.7 1.0
O A:HOH2034 2.3 20.8 1.0
OE2 A:GLU195 2.4 14.6 1.0
ND1 A:HIS96 2.4 14.0 1.0
OE2 A:GLU161 2.7 17.9 0.7
CG A:ASP62 3.0 15.6 1.0
CE1 A:HIS96 3.2 13.2 1.0
CD A:GLU195 3.2 15.8 1.0
CD A:GLU93 3.2 14.0 1.0
OD2 A:ASP62 3.2 18.1 1.0
CG A:HIS96 3.5 11.8 1.0
CD A:GLU161 3.5 18.4 0.7
MN A:MN1324 3.6 14.8 0.9
OE1 A:GLU161 3.7 18.7 0.7
CG A:GLU195 3.7 15.6 1.0
OE2 A:GLU93 3.8 13.6 1.0
CB A:HIS96 3.9 12.0 1.0
CZ A:PHE165 4.0 10.3 0.3
CA A:GLU93 4.1 10.8 1.0
CE2 A:PHE165 4.2 10.8 0.3
OE1 A:GLU195 4.3 14.2 1.0
CB A:ASP62 4.3 13.4 1.0
CB A:GLU93 4.4 11.3 1.0
CG A:GLU93 4.4 12.5 1.0
NE2 A:HIS96 4.4 13.6 1.0
CE2 A:PHE165 4.5 15.2 0.7
CD2 A:HIS96 4.6 12.7 1.0
CZ A:PHE165 4.6 14.4 0.7
CG2 A:ILE191 4.6 13.7 1.0
OE1 A:GLU161 4.8 11.6 0.3
CE1 A:PHE165 4.9 10.4 0.3
CA A:ASP62 4.9 13.2 1.0
O A:GLU93 4.9 11.5 1.0
CG A:GLU161 4.9 18.6 0.7
ND1 A:HIS198 5.0 10.2 1.0
N A:GLU93 5.0 9.7 1.0
OE2 A:GLU161 5.0 13.4 0.3
CE1 A:HIS198 5.0 9.4 1.0

Manganese binding site 2 out of 4 in 4bmu

Go back to Manganese Binding Sites List in 4bmu
Manganese binding site 2 out of 4 in the Crystal Structure of Ribonucleotide Reductase Di-Manganese(II) Nrdf 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 Crystal Structure of Ribonucleotide Reductase Di-Manganese(II) Nrdf From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1324

b:14.8
occ:0.90
 OE2 A:GLU195 1.8 14.6 1.0
OE2 A:GLU161 1.9 13.4 0.3
OE1 A:GLU161 2.0 18.7 0.7
OE2 A:GLU93 2.1 13.6 1.0
OE1 A:GLU195 2.2 14.2 1.0
O A:HOH2038 2.2 19.0 0.7
ND1 A:HIS198 2.3 10.2 1.0
OE1 A:GLU161 2.3 11.6 0.3
CD A:GLU195 2.3 15.8 1.0
CD A:GLU161 2.4 13.3 0.3
CD A:GLU161 2.8 18.4 0.7
CD A:GLU93 2.9 14.0 1.0
OE1 A:GLU93 3.0 19.1 1.0
CE1 A:HIS198 3.2 9.4 1.0
CG A:HIS198 3.3 10.0 1.0
OE2 A:GLU161 3.3 17.9 0.7
MN A:MN1323 3.6 19.0 1.0
CB A:HIS198 3.6 11.1 1.0
CG A:GLU161 3.8 18.6 0.7
CG A:GLU195 3.8 15.6 1.0
CG A:GLU161 3.9 14.2 0.3
CB A:GLU161 4.0 18.9 0.7
CE A:MET70 4.1 21.6 0.5
NE2 A:HIS198 4.3 9.5 1.0
CG A:GLU93 4.3 12.5 1.0
CD2 A:HIS198 4.4 8.9 1.0
CG A:GLN65 4.5 17.5 1.0
CA A:GLU195 4.6 12.9 1.0
NE2 A:GLN65 4.6 18.7 1.0
CB A:GLU195 4.6 13.2 1.0
O A:HOH2063 4.6 27.6 0.7
CB A:GLU161 4.8 14.2 0.3
CE1 A:HIS96 4.9 13.2 1.0
O A:HOH2034 4.9 20.8 1.0
CE2 A:PHE165 5.0 10.8 0.3
ND1 A:HIS96 5.0 14.0 1.0

Manganese binding site 3 out of 4 in 4bmu

Go back to Manganese Binding Sites List in 4bmu
Manganese binding site 3 out of 4 in the Crystal Structure of Ribonucleotide Reductase Di-Manganese(II) Nrdf From Bacillus Cereus


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 Di-Manganese(II) Nrdf From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1323

b:22.7
occ:1.00
 O B:HOH2029 2.1 29.9 1.0
OD1 B:ASP62 2.1 12.7 1.0
ND1 B:HIS96 2.2 14.1 1.0
OE1 B:GLU93 2.2 18.8 1.0
OE2 B:GLU195 2.4 19.4 1.0
CG B:ASP62 2.9 12.7 1.0
OD2 B:ASP62 3.0 14.7 1.0
CE1 B:HIS96 3.0 15.6 1.0
O B:HOH2030 3.0 10.6 0.7
CD B:GLU195 3.2 21.8 1.0
CG B:HIS96 3.3 13.1 1.0
CD B:GLU93 3.4 18.1 1.0
CG B:GLU195 3.7 17.9 1.0
MN B:MN1324 3.7 21.2 1.0
CB B:HIS96 3.7 12.7 1.0
OE2 B:GLU161 4.0 12.0 0.3
CA B:GLU93 4.0 15.6 1.0
OE2 B:GLU93 4.1 21.6 1.0
CZ B:PHE165 4.1 31.0 1.0
NE2 B:HIS96 4.2 14.7 1.0
CB B:ASP62 4.2 12.2 1.0
OE1 B:GLU195 4.3 23.6 1.0
CD2 B:HIS96 4.3 13.5 1.0
CB B:GLU93 4.4 15.6 1.0
CG2 B:ILE191 4.4 14.6 1.0
CG B:GLU93 4.5 17.7 1.0
CE2 B:PHE165 4.5 29.5 1.0
CE1 B:PHE165 4.7 25.6 1.0
O B:GLU93 4.8 15.4 1.0
OE2 B:GLU161 4.8 13.1 0.3
N B:GLU93 4.9 14.9 1.0
CA B:ASP62 4.9 11.0 1.0
C B:GLU93 4.9 15.9 1.0
CD B:GLU161 4.9 13.2 0.3
O B:MET92 5.0 12.8 1.0

Manganese binding site 4 out of 4 in 4bmu

Go back to Manganese Binding Sites List in 4bmu
Manganese binding site 4 out of 4 in the Crystal Structure of Ribonucleotide Reductase Di-Manganese(II) Nrdf From Bacillus Cereus


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 Di-Manganese(II) Nrdf From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1324

b:21.2
occ:1.00
 OE1 B:GLU161 1.7 12.4 0.3
OE2 B:GLU195 1.8 19.4 1.0
OE2 B:GLU161 2.1 13.1 0.3
OE1 B:GLU161 2.1 11.9 0.3
OE1 B:GLU195 2.1 23.6 1.0
OE2 B:GLU93 2.1 21.6 1.0
CD B:GLU161 2.2 13.2 0.3
CD B:GLU195 2.3 21.8 1.0
ND1 B:HIS198 2.3 14.1 1.0
OE2 B:GLU161 2.3 12.0 0.3
OE2 B:GLU161 2.5 12.4 0.3
CD B:GLU161 2.6 12.8 0.3
CD B:GLU161 2.7 13.8 0.3
OE1 B:GLU161 2.8 12.8 0.3
OE1 B:GLU93 2.8 18.8 1.0
CD B:GLU93 2.8 18.1 1.0
O B:HOH2030 2.9 10.6 0.7
CE1 B:HIS198 3.2 13.5 1.0
CG B:HIS198 3.4 12.1 1.0
CG B:GLU161 3.6 14.2 0.3
CB B:HIS198 3.6 11.8 1.0
MN B:MN1323 3.7 22.7 1.0
CG B:GLU195 3.8 17.9 1.0
CB B:GLU161 4.1 14.7 0.3
CG B:GLU161 4.1 12.9 0.3
CG B:GLU161 4.1 14.5 0.3
CE B:MET70 4.2 22.7 1.0
CG B:GLU93 4.3 17.7 1.0
NE2 B:HIS198 4.4 12.0 1.0
CD2 B:HIS198 4.4 12.4 1.0
CA B:GLU195 4.5 16.9 1.0
CG B:GLN65 4.5 17.2 1.0
CB B:GLU195 4.5 17.7 1.0
O B:HOH2029 4.6 29.9 1.0
NE2 B:GLN65 4.7 20.3 1.0
CB B:GLU161 4.8 13.7 0.3
CE1 B:HIS96 4.8 15.6 1.0
OD1 B:ASP62 4.9 12.7 1.0
CE2 B:PHE165 5.0 29.5 1.0

Reference:

M.Hammerstad, H.Hersleth, A.B.Tomter, A.K.Rohr, K.K.Andersson. Crystal Structure of Bacillus Cereus Class Ib Ribonucleotide Reductase Di-Iron Nrdf in Complex with Nrdi. Acs Chem.Biol. V. 9 526 2014.
ISSN: ISSN 1554-8929
PubMed: 24295378
DOI: 10.1021/CB400757H
Page generated: Sat Oct 5 18:50:31 2024

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