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Iron in PDB 1biq: Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A

Enzymatic activity of Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A

All present enzymatic activity of Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A:
1.17.4.1;

Protein crystallography data

The structure of Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A, PDB code: 1biq was solved by D.T.Logan, F.Demare, B.O.Persson, A.Slaby, B.M.Sjoberg, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.053, 83.780, 113.953, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 26.6

Other elements in 1biq:

The structure of Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A also contains other interesting chemical elements:

Mercury (Hg) 16 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A (pdb code 1biq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A, PDB code: 1biq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1biq

Go back to Iron Binding Sites List in 1biq
Iron binding site 1 out of 4 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe376

b:27.3
occ:1.00
OE1 A:GLU115 2.0 15.8 1.0
OD1 A:ASP84 2.0 27.5 1.0
O A:OH379 2.2 28.8 1.0
O A:OH378 2.2 15.6 1.0
ND1 A:HIS118 2.2 13.2 1.0
CG A:ASP84 2.8 27.6 1.0
OD2 A:ASP84 2.9 32.6 1.0
CD A:GLU115 3.2 23.1 1.0
CE1 A:HIS118 3.2 12.3 1.0
CG A:HIS118 3.2 12.6 1.0
FE A:FE377 3.4 20.6 1.0
OH A:MTY208 3.4 46.4 1.0
CB A:HIS118 3.6 11.2 1.0
CZ A:MTY208 3.6 58.9 1.0
CE2 A:MTY208 3.7 0.0 1.0
OE2 A:GLU115 3.7 27.8 1.0
CB A:ASP84 4.2 17.3 1.0
NE2 A:HIS118 4.3 12.6 1.0
CG A:GLU115 4.4 16.6 1.0
CD2 A:HIS118 4.4 13.2 1.0
CA A:GLU115 4.4 10.5 1.0
CB A:GLU115 4.4 11.0 1.0
CG2 A:ILE234 4.5 15.7 1.0
CE1 A:MTY208 4.5 36.6 1.0
CE1 A:HIS241 4.6 19.8 1.0
CD2 A:MTY208 4.7 40.2 1.0
ND1 A:HIS241 4.8 20.9 1.0
CA A:ASP84 4.8 17.0 1.0

Iron binding site 2 out of 4 in 1biq

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Iron binding site 2 out of 4 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe377

b:20.6
occ:1.00
OE2 A:GLU115 2.0 27.8 1.0
O A:OH378 2.1 15.6 1.0
ND1 A:HIS241 2.2 20.9 1.0
OE1 A:GLU204 2.2 21.9 1.0
OE2 A:GLU204 2.6 20.8 1.0
CD A:GLU204 2.8 37.0 1.0
OH A:MTY208 2.8 46.4 1.0
CD A:GLU115 2.8 23.1 1.0
OE1 A:GLU115 2.9 15.8 1.0
CE1 A:HIS241 3.0 19.8 1.0
CG A:HIS241 3.3 18.9 1.0
FE A:FE2376 3.4 27.3 1.0
CB A:HIS241 3.8 14.5 1.0
CE2 A:MTY208 3.8 0.0 1.0
NE1 A:TRP111 4.0 18.6 1.0
NE2 A:HIS241 4.2 20.0 1.0
CG A:GLU115 4.3 16.6 1.0
CG A:GLU204 4.3 20.9 1.0
CD2 A:HIS241 4.3 20.3 1.0
CD2 A:MTY208 4.4 40.2 1.0
CA A:ALA238 4.4 18.0 1.0
O A:OH379 4.5 28.8 1.0
CD1 A:TRP111 4.5 18.9 1.0
CB A:ALA238 4.6 19.4 1.0
OD1 A:ASP84 4.7 27.5 1.0
ND1 A:HIS118 4.7 13.2 1.0
CZ A:MTY208 4.7 58.9 1.0
CE1 A:HIS118 4.8 12.3 1.0

Iron binding site 3 out of 4 in 1biq

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Iron binding site 3 out of 4 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe376

b:28.5
occ:1.00
ND1 B:HIS118 2.0 12.7 1.0
OD1 B:ASP84 2.2 30.7 1.0
OD2 B:ASP84 2.2 28.4 1.0
OE1 B:GLU115 2.3 19.0 1.0
CG B:ASP84 2.4 28.4 1.0
O B:OH378 2.5 17.2 1.0
CE1 B:HIS118 2.9 12.3 1.0
CG B:HIS118 3.1 11.8 1.0
CD B:GLU115 3.4 24.7 1.0
CB B:HIS118 3.6 9.5 1.0
FE B:FE2377 3.7 25.0 1.0
CE2 B:PHE208 3.8 37.1 1.0
CZ B:PHE208 3.8 35.2 1.0
OE2 B:GLU115 3.9 28.8 1.0
CB B:ASP84 3.9 15.7 1.0
NE2 B:HIS118 4.0 12.5 1.0
CD2 B:HIS118 4.2 12.5 1.0
CG2 B:ILE234 4.4 13.4 1.0
CB B:GLU115 4.5 12.5 1.0
CA B:GLU115 4.5 11.4 1.0
CG B:GLU115 4.6 16.2 1.0
CD2 B:PHE208 4.6 33.8 1.0
CE1 B:PHE208 4.7 36.1 1.0
CA B:ASP84 4.8 13.9 1.0
O B:GLU115 4.9 16.9 1.0
CE1 B:HIS241 5.0 13.5 1.0

Iron binding site 4 out of 4 in 1biq

Go back to Iron Binding Sites List in 1biq
Iron binding site 4 out of 4 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe377

b:25.0
occ:1.00
ND1 B:HIS241 2.2 14.0 1.0
O B:OH378 2.2 17.2 1.0
OE2 B:GLU115 2.2 28.8 1.0
OE1 B:GLU204 2.4 26.9 1.0
OE2 B:GLU204 2.6 22.1 1.0
CD B:GLU204 2.9 36.7 1.0
OE1 B:GLU115 2.9 19.0 1.0
CD B:GLU115 2.9 24.7 1.0
CE1 B:HIS241 3.0 13.5 1.0
CG B:HIS241 3.3 12.9 1.0
FE B:FE2376 3.7 28.5 1.0
CB B:HIS241 3.7 11.1 1.0
NE1 B:TRP111 3.9 11.8 1.0
NE2 B:HIS241 4.2 13.6 1.0
CG B:GLU115 4.3 16.2 1.0
CD2 B:HIS241 4.3 13.2 1.0
CG B:GLU204 4.4 24.8 1.0
CA B:ALA238 4.5 13.3 1.0
CD1 B:TRP111 4.5 12.6 1.0
OD1 B:ASP84 4.6 30.7 1.0
CE1 B:HIS118 4.6 12.3 1.0
CB B:ALA238 4.7 13.8 1.0
ND1 B:HIS118 4.8 12.7 1.0
NE2 B:GLN87 4.9 21.8 1.0

Reference:

D.T.Logan, F.Demare, B.O.Persson, A.Slaby, B.M.Sjoberg, P.Nordlund. Crystal Structures of Two Self-Hydroxylating Ribonucleotide Reductase Protein R2 Mutants: Structural Basis For the Oxygen-Insertion Step of Hydroxylation Reactions Catalyzed By Diiron Proteins. Biochemistry V. 37 10798 1998.
ISSN: ISSN 0006-2960
PubMed: 9692970
DOI: 10.1021/BI9806403
Page generated: Sun Dec 13 14:07:56 2020

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