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Manganese in PDB 1pm2: Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)

Enzymatic activity of Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)

All present enzymatic activity of Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase):
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase), PDB code: 1pm2 was solved by W.C.Voegtli, M.Sommerhalter, J.Baldwin, L.Saleh, J.M.Bollingerjr., A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.950, 83.940, 114.340, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.5

Other elements in 1pm2:

The structure of Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) also contains other interesting chemical elements:

Mercury (Hg) 14 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) (pdb code 1pm2). 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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase), PDB code: 1pm2:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1pm2

Go back to Manganese Binding Sites List in 1pm2
Manganese binding site 1 out of 4 in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)


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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:27.1
occ:0.91
 OE1 A:GLU238 1.9 22.4 1.0
ND1 A:HIS118 2.0 11.2 1.0
OE1 A:GLU115 2.1 17.0 1.0
OE2 A:GLU84 2.2 18.0 1.0
OE1 A:GLU84 2.3 17.8 1.0
CD A:GLU84 2.5 15.4 1.0
CE1 A:HIS118 2.9 11.7 1.0
CD A:GLU238 3.1 21.5 1.0
CG A:HIS118 3.2 13.3 1.0
CD A:GLU115 3.2 16.8 1.0
CB A:HIS118 3.6 13.1 1.0
OE2 A:GLU238 3.7 21.9 1.0
CZ A:PHE208 3.7 24.4 1.0
OE2 A:GLU115 3.8 16.8 1.0
MN A:MN502 3.8 22.1 1.0
CE2 A:PHE208 4.1 23.9 1.0
NE2 A:HIS118 4.1 12.7 1.0
CG A:GLU84 4.1 14.7 1.0
CG2 A:ILE234 4.1 14.0 1.0
CD2 A:HIS118 4.2 13.2 1.0
CG A:GLU238 4.3 17.8 1.0
CE1 A:PHE208 4.3 22.4 1.0
CA A:GLU115 4.4 13.2 1.0
CG A:GLU115 4.4 12.9 1.0
O A:HOH682 4.5 26.3 1.0
CB A:GLU115 4.5 12.5 1.0
CE1 A:HIS241 4.7 11.1 1.0
ND1 A:HIS241 4.8 10.3 1.0
CD2 A:PHE208 4.9 21.6 1.0
CB A:GLU84 4.9 12.1 1.0
O A:GLU115 5.0 13.8 1.0

Manganese binding site 2 out of 4 in 1pm2

Go back to Manganese Binding Sites List in 1pm2
Manganese binding site 2 out of 4 in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)


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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:22.1
occ:0.98
 OE2 A:GLU238 2.0 21.9 1.0
ND1 A:HIS241 2.0 10.3 1.0
OE2 A:GLU115 2.1 16.8 1.0
OE1 A:GLU204 2.1 26.9 1.0
CD A:GLU204 2.8 24.1 1.0
CD A:GLU115 2.9 16.8 1.0
OE2 A:GLU204 2.9 25.1 1.0
CE1 A:HIS241 2.9 11.1 1.0
CD A:GLU238 3.0 21.5 1.0
CG A:HIS241 3.1 11.5 1.0
OE1 A:GLU115 3.1 17.0 1.0
OE1 A:GLU238 3.3 22.4 1.0
CB A:HIS241 3.4 11.4 1.0
NE1 A:TRP111 3.6 14.7 1.0
MN A:MN501 3.8 27.1 0.9
CE2 A:PHE208 3.9 23.9 1.0
NE2 A:HIS241 4.1 10.8 1.0
CD2 A:HIS241 4.2 12.3 1.0
CD1 A:TRP111 4.2 13.7 1.0
CG A:GLU115 4.2 12.9 1.0
CG A:GLU204 4.3 22.8 1.0
CG A:GLU238 4.3 17.8 1.0
CA A:GLU238 4.3 15.2 1.0
CD2 A:PHE208 4.5 21.6 1.0
CB A:GLU238 4.6 16.5 1.0
CZ A:PHE208 4.8 24.4 1.0
CE2 A:TRP111 4.8 15.1 1.0
CB A:GLU204 4.9 19.8 1.0
CE1 A:HIS118 4.9 11.7 1.0
CA A:HIS241 5.0 12.2 1.0

Manganese binding site 3 out of 4 in 1pm2

Go back to Manganese Binding Sites List in 1pm2
Manganese binding site 3 out of 4 in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)


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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:28.9
occ:0.91
 OE2 B:GLU238 2.1 25.6 1.0
OE2 B:GLU84 2.1 14.3 1.0
OE1 B:GLU115 2.1 18.1 1.0
ND1 B:HIS118 2.2 12.3 1.0
OE1 B:GLU84 2.3 18.3 1.0
CD B:GLU84 2.5 16.3 1.0
CE1 B:HIS118 3.0 14.3 1.0
CD B:GLU238 3.2 21.0 1.0
CD B:GLU115 3.2 16.1 1.0
CG B:HIS118 3.3 11.3 1.0
CB B:HIS118 3.7 11.8 1.0
OE2 B:GLU115 3.7 16.2 1.0
CZ B:PHE208 3.7 24.1 1.0
OE1 B:GLU238 3.8 20.7 1.0
MN B:MN504 3.8 20.4 1.0
CE2 B:PHE208 4.0 25.0 1.0
CG B:GLU84 4.0 16.5 1.0
NE2 B:HIS118 4.2 13.9 1.0
CG2 B:ILE234 4.2 13.6 1.0
CG B:GLU238 4.3 17.6 1.0
CD2 B:HIS118 4.3 14.6 1.0
CE1 B:PHE208 4.3 22.0 1.0
CA B:GLU115 4.4 12.3 1.0
CG B:GLU115 4.4 12.6 1.0
CB B:GLU115 4.6 12.9 1.0
O B:HOH668 4.7 21.4 1.0
CE1 B:HIS241 4.7 12.4 1.0
ND1 B:HIS241 4.8 10.8 1.0
CD2 B:PHE208 4.8 22.2 1.0
CB B:GLU84 4.9 13.9 1.0
O B:GLU115 5.0 11.2 1.0

Manganese binding site 4 out of 4 in 1pm2

Go back to Manganese Binding Sites List in 1pm2
Manganese binding site 4 out of 4 in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)


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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn504

b:20.4
occ:0.99
 OE1 B:GLU238 1.9 20.7 1.0
OE2 B:GLU115 2.0 16.2 1.0
OE1 B:GLU204 2.1 26.9 1.0
ND1 B:HIS241 2.1 10.8 1.0
CD B:GLU238 2.8 21.0 1.0
CD B:GLU204 2.8 21.8 1.0
OE2 B:GLU204 2.8 25.3 1.0
CD B:GLU115 2.9 16.1 1.0
OE2 B:GLU238 3.0 25.6 1.0
CE1 B:HIS241 3.1 12.4 1.0
CG B:HIS241 3.1 10.3 1.0
OE1 B:GLU115 3.1 18.1 1.0
CB B:HIS241 3.4 12.7 1.0
NE1 B:TRP111 3.7 13.2 1.0
MN B:MN503 3.8 28.9 0.9
CE2 B:PHE208 3.9 25.0 1.0
CG B:GLU238 4.2 17.6 1.0
CG B:GLU115 4.2 12.6 1.0
NE2 B:HIS241 4.2 10.0 1.0
CD1 B:TRP111 4.2 13.6 1.0
CD2 B:HIS241 4.2 11.4 1.0
CG B:GLU204 4.3 22.1 1.0
CA B:GLU238 4.3 15.0 1.0
CD2 B:PHE208 4.4 22.2 1.0
CB B:GLU238 4.6 16.3 1.0
CZ B:PHE208 4.8 24.1 1.0
CB B:GLU204 4.8 18.0 1.0
CE2 B:TRP111 4.9 13.3 1.0
NE2 B:GLN87 4.9 18.2 1.0
CA B:HIS241 4.9 12.4 1.0

Reference:

W.C.Voegtli, M.Sommerhalter, L.Saleh, J.Baldwin, J.M.Bollinger Jr., A.C.Rosenzweig. Variable Coordination Geometries at the Diiron(II) Active Site of Ribonucleotide Reductase R2. J.Am.Chem.Soc. V. 125 15822 2003.
ISSN: ISSN 0002-7863
PubMed: 14677973
DOI: 10.1021/JA0370387
Page generated: Sat Oct 5 12:07:35 2024

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