Atomistry » Iron » PDB 1b2o-1biy » 1biq
Atomistry »
  Iron »
    PDB 1b2o-1biy »
      1biq »

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

Go back to Iron Binding Sites List in 1biq
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

Go back to Iron Binding Sites List in 1biq
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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy