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Iron in PDB 1rsv: Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase

Enzymatic activity of Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase

All present enzymatic activity of Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase:
1.17.4.1;

Protein crystallography data

The structure of Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase, PDB code: 1rsv was solved by M.Assarsson, M.E.Andersson, M.Hogbom, B.O.Persson, M.Sahlin, A.L.Barra, B.M.Sjoberg, P.Nordlund, A.Graslund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.893, 84.501, 113.963, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1rsv:

The structure of Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase also contains other interesting chemical elements:

Mercury (Hg) 12 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase (pdb code 1rsv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase, PDB code: 1rsv:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1rsv

Go back to Iron Binding Sites List in 1rsv
Iron binding site 1 out of 4 in the Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1003

b:22.7
occ:0.70
 OD1 A:ASP84 1.9 24.0 1.0
OE1 A:GLU115 2.0 20.0 1.0
ND1 A:HIS118 2.1 16.4 1.0
N1 A:AZI901 2.3 22.5 0.7
N2 A:AZI901 2.5 30.6 0.7
CG A:ASP84 2.7 23.8 1.0
OD2 A:ASP84 3.0 31.2 1.0
CG A:HIS118 3.1 14.7 1.0
CE1 A:HIS118 3.1 15.5 1.0
N3 A:AZI901 3.1 39.4 0.7
CD A:GLU115 3.2 28.9 1.0
CB A:HIS118 3.4 11.7 1.0
CZ A:PHE208 3.7 20.8 1.0
OE2 A:GLU115 3.7 20.9 1.0
FE A:FE1004 3.8 17.8 1.0
CE2 A:PHE208 3.9 22.7 1.0
CB A:ASP84 4.1 15.8 1.0
NE2 A:HIS118 4.2 15.7 1.0
CD2 A:HIS118 4.2 15.9 1.0
CG A:GLU115 4.4 16.1 1.0
CE1 A:PHE208 4.4 22.6 1.0
CG2 A:ILE234 4.4 17.9 1.0
CA A:GLU115 4.4 11.3 1.0
CB A:GLU115 4.5 12.2 1.0
CA A:ASP84 4.8 14.4 1.0
CE1 A:HIS241 4.8 18.9 1.0
CD2 A:PHE208 4.8 20.2 1.0
CA A:HIS118 5.0 11.6 1.0
O A:GLU115 5.0 16.1 1.0
ND1 A:HIS241 5.0 19.9 1.0

Iron binding site 2 out of 4 in 1rsv

Go back to Iron Binding Sites List in 1rsv
Iron binding site 2 out of 4 in the Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1004

b:17.8
occ:1.00
 OE2 A:GLU115 2.0 20.9 1.0
ND1 A:HIS241 2.0 19.9 1.0
N1 A:AZI901 2.0 22.5 0.7
OE2 A:GLU204 2.3 17.9 1.0
OE1 A:GLU204 2.3 18.6 1.0
N2 A:AZI901 2.6 30.6 0.7
CD A:GLU204 2.6 27.6 1.0
CE1 A:HIS241 2.9 18.9 1.0
CD A:GLU115 2.9 28.9 1.0
OE1 A:GLU115 3.1 20.0 1.0
CG A:HIS241 3.2 18.4 1.0
N3 A:AZI901 3.4 39.4 0.7
CB A:HIS241 3.7 15.2 1.0
FE A:FE1003 3.8 22.7 0.7
NE1 A:TRP111 3.9 16.0 1.0
NE2 A:HIS241 4.1 19.1 1.0
CG A:GLU204 4.1 20.2 1.0
CD2 A:HIS241 4.2 19.3 1.0
CG A:GLU115 4.3 16.1 1.0
CE2 A:PHE208 4.3 22.7 1.0
CD1 A:TRP111 4.5 16.5 1.0
CA A:ALA238 4.5 16.5 1.0
CE1 A:HIS118 4.5 15.5 1.0
CD2 A:PHE208 4.6 20.2 1.0
ND1 A:HIS118 4.6 16.4 1.0
CB A:ALA238 4.9 17.4 1.0
OE1 A:GLN87 4.9 26.3 1.0
CB A:GLU204 4.9 16.3 1.0
OD1 A:ASP84 4.9 24.0 1.0

Iron binding site 3 out of 4 in 1rsv

Go back to Iron Binding Sites List in 1rsv
Iron binding site 3 out of 4 in the Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:41.5
occ:0.70
 ND1 B:HIS118 2.0 20.5 1.0
OE1 B:GLU115 2.2 17.9 1.0
OD1 B:ASP84 2.2 30.9 1.0
OD2 B:ASP84 2.6 31.7 1.0
O B:HOH2180 2.6 27.3 1.0
CG B:ASP84 2.6 29.1 1.0
CE1 B:HIS118 3.0 20.3 1.0
CG B:HIS118 3.1 18.7 1.0
CD B:GLU115 3.3 31.0 1.0
CB B:HIS118 3.5 15.2 1.0
FE B:FE1002 3.8 24.1 1.0
OE2 B:GLU115 3.9 29.5 1.0
CZ B:PHE208 4.0 32.8 1.0
CB B:ASP84 4.1 18.5 1.0
NE2 B:HIS118 4.1 20.8 1.0
CE2 B:PHE208 4.2 34.4 1.0
CD2 B:HIS118 4.2 20.8 1.0
CA B:GLU115 4.3 12.7 1.0
CB B:GLU115 4.4 13.4 1.0
CG B:GLU115 4.5 19.3 1.0
CG2 B:ILE234 4.6 15.7 1.0
CE1 B:PHE208 4.6 33.2 1.0
CA B:ASP84 4.8 17.2 1.0
CE1 B:HIS241 4.8 17.0 1.0
O B:GLU115 4.9 19.1 1.0
ND1 B:HIS241 5.0 17.7 1.0
CA B:HIS118 5.0 14.9 1.0

Iron binding site 4 out of 4 in 1rsv

Go back to Iron Binding Sites List in 1rsv
Iron binding site 4 out of 4 in the Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:24.1
occ:1.00
 ND1 B:HIS241 2.0 17.7 1.0
OE1 B:GLU204 2.2 22.3 1.0
OE2 B:GLU115 2.2 29.5 1.0
O B:HOH2180 2.4 27.3 1.0
OE2 B:GLU204 2.6 26.1 1.0
CD B:GLU204 2.7 33.9 1.0
CE1 B:HIS241 2.8 17.0 1.0
CD B:GLU115 2.9 31.0 1.0
OE1 B:GLU115 3.0 17.9 1.0
CG B:HIS241 3.1 16.6 1.0
CB B:HIS241 3.6 13.8 1.0
NE1 B:TRP111 3.7 15.2 1.0
FE B:FE1001 3.8 41.5 0.7
NE2 B:HIS241 4.0 17.4 1.0
CD2 B:HIS241 4.2 17.7 1.0
CG B:GLU204 4.2 25.8 1.0
CG B:GLU115 4.3 19.3 1.0
CD1 B:TRP111 4.3 15.9 1.0
CA B:ALA238 4.6 18.4 1.0
CE1 B:HIS118 4.7 20.3 1.0
CB B:ALA238 4.7 19.3 1.0
CE2 B:PHE208 4.8 34.4 1.0
OD1 B:ASP84 4.8 30.9 1.0
ND1 B:HIS118 4.8 20.5 1.0
CE2 B:TRP111 4.9 16.7 1.0
OE1 B:GLN87 4.9 29.8 1.0
CB B:GLU204 5.0 21.2 1.0
CD2 B:PHE208 5.0 31.0 1.0

Reference:

M.Assarsson, M.E.Andersson, M.Hogbom, B.O.Persson, M.Sahlin, A.L.Barra, B.M.Sjoberg, P.Nordlund, A.Graslund. Restoring Proper Radical Generation By Azide Binding to the Iron Site of the E238A Mutant R2 Protein of Ribonucleotide Reductase From Escherichia Coli. J.Biol.Chem. V. 276 26852 2001.
ISSN: ISSN 0021-9258
PubMed: 11328804
DOI: 10.1074/JBC.M008190200
Page generated: Sat Aug 3 14:24:14 2024

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