Atomistry » Manganese » PDB 1pj4-1r1o » 1pm2
Atomistry »
  Manganese »
    PDB 1pj4-1r1o »
      1pm2 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy