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Iron in PDB 1rsr: Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase

Enzymatic activity of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase

All present enzymatic activity of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase:
1.17.4.1;

Protein crystallography data

The structure of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase, PDB code: 1rsr was solved by M.E.Andersson, M.Hogbom, A.Rinaldo-Matthis, K.K.Andersson, 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.800, 84.200, 113.500, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1rsr:

The structure of Azide Complex of the Diferrous F208A 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 F208A Mutant R2 Subunit of Ribonucleotide Reductase (pdb code 1rsr). 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 F208A Mutant R2 Subunit of Ribonucleotide Reductase, PDB code: 1rsr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1rsr

Go back to Iron Binding Sites List in 1rsr
Iron binding site 1 out of 4 in the Azide Complex of the Diferrous F208A 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 F208A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1003

b:31.2
occ:1.00
 OD1 A:ASP84 1.8 32.3 1.0
OE1 A:GLU115 2.2 30.3 1.0
ND1 A:HIS118 2.2 16.7 1.0
OE2 A:GLU238 2.5 34.8 1.0
CG A:ASP84 2.8 31.5 1.0
OD2 A:ASP84 3.1 30.8 1.0
CE1 A:HIS118 3.1 15.0 1.0
CG A:HIS118 3.2 16.1 1.0
CD A:GLU115 3.3 28.0 1.0
CD A:GLU238 3.4 37.0 1.0
CB A:HIS118 3.6 17.2 1.0
OE1 A:GLU238 3.7 36.8 1.0
OE2 A:GLU115 3.8 29.3 1.0
FE A:FE21004 3.8 29.5 1.0
CB A:ASP84 4.1 27.2 1.0
NE2 A:HIS118 4.3 14.2 1.0
CD2 A:HIS118 4.3 17.6 1.0
CA A:GLU115 4.4 17.9 1.0
CG2 A:ILE234 4.5 21.1 1.0
CG A:GLU115 4.5 25.2 1.0
CB A:GLU115 4.6 19.3 1.0
CG A:GLU238 4.7 34.0 1.0
CA A:ASP84 4.7 25.4 1.0
O A:GLU115 4.9 18.4 1.0
CE1 A:HIS241 4.9 20.8 1.0
ND1 A:HIS241 5.0 18.7 1.0

Iron binding site 2 out of 4 in 1rsr

Go back to Iron Binding Sites List in 1rsr
Iron binding site 2 out of 4 in the Azide Complex of the Diferrous F208A 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 F208A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1004

b:29.5
occ:1.00
 OE1 A:GLU204 1.8 55.6 1.0
OE2 A:GLU115 2.1 29.3 1.0
ND1 A:HIS241 2.2 18.7 1.0
OE1 A:GLU238 2.2 36.8 1.0
CD A:GLU204 2.9 52.6 1.0
CD A:GLU115 3.0 28.0 1.0
CE1 A:HIS241 3.1 20.8 1.0
OE1 A:GLU115 3.2 30.3 1.0
CD A:GLU238 3.3 37.0 1.0
CG A:HIS241 3.3 21.1 1.0
OE2 A:GLU204 3.4 53.2 1.0
CB A:HIS241 3.6 21.0 1.0
OE2 A:GLU238 3.7 34.8 1.0
FE A:FE21003 3.8 31.2 1.0
NE1 A:TRP111 3.8 20.9 1.0
CG A:GLU204 4.1 49.1 1.0
NE2 A:HIS241 4.3 20.9 1.0
CD2 A:HIS241 4.4 20.1 1.0
CD1 A:TRP111 4.4 21.0 1.0
CG A:GLU115 4.4 25.2 1.0
CA A:GLU238 4.5 26.3 1.0
CG A:GLU238 4.5 34.0 1.0
CB A:GLU204 4.6 40.8 1.0
CB A:GLU238 4.7 27.4 1.0
CE1 A:HIS118 4.9 15.0 1.0
CE2 A:TRP111 5.0 19.9 1.0

Iron binding site 3 out of 4 in 1rsr

Go back to Iron Binding Sites List in 1rsr
Iron binding site 3 out of 4 in the Azide Complex of the Diferrous F208A 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 F208A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:29.5
occ:1.00
 OD1 B:ASP84 1.9 31.5 1.0
OE1 B:GLU115 2.1 20.4 1.0
ND1 B:HIS118 2.2 16.1 1.0
OE2 B:GLU238 2.4 21.2 1.0
N1 B:AZI900 2.7 22.9 0.7
CG B:ASP84 2.9 26.5 1.0
CE1 B:HIS118 2.9 17.0 1.0
CD B:GLU115 3.1 20.3 1.0
N2 B:AZI900 3.2 29.1 0.7
OD2 B:ASP84 3.2 26.6 1.0
FE B:FE21002 3.3 24.8 1.0
CG B:HIS118 3.3 17.2 1.0
CD B:GLU238 3.5 28.2 1.0
OE2 B:GLU115 3.6 25.0 1.0
CB B:HIS118 3.8 16.2 1.0
N3 B:AZI900 3.9 31.6 0.7
NE2 B:HIS118 4.1 18.5 1.0
CB B:ASP84 4.2 21.8 1.0
OE1 B:GLU238 4.2 29.6 1.0
CD2 B:HIS118 4.3 19.5 1.0
CG B:GLU115 4.4 17.4 1.0
CG B:GLU238 4.4 26.4 1.0
CG2 B:ILE234 4.4 16.2 1.0
CA B:GLU115 4.4 15.3 1.0
CE1 B:HIS241 4.5 18.5 1.0
CB B:GLU115 4.5 14.8 1.0
ND1 B:HIS241 4.6 13.4 1.0
CA B:ASP84 4.8 20.0 1.0

Iron binding site 4 out of 4 in 1rsr

Go back to Iron Binding Sites List in 1rsr
Iron binding site 4 out of 4 in the Azide Complex of the Diferrous F208A 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 F208A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:24.8
occ:1.00
 OE2 B:GLU115 2.1 25.0 1.0
OE2 B:GLU204 2.2 26.1 1.0
OE2 B:GLU238 2.2 21.2 1.0
OE1 B:GLU238 2.2 29.6 1.0
ND1 B:HIS241 2.2 13.4 1.0
N1 B:AZI900 2.3 22.9 0.7
CD B:GLU238 2.5 28.2 1.0
CD B:GLU115 2.8 20.3 1.0
OE1 B:GLU115 2.9 20.4 1.0
CE1 B:HIS241 3.1 18.5 1.0
N2 B:AZI900 3.2 29.1 0.7
CD B:GLU204 3.2 33.2 1.0
FE B:FE21001 3.3 29.5 1.0
CG B:HIS241 3.3 16.0 1.0
CB B:HIS241 3.7 15.6 1.0
NE1 B:TRP111 3.9 16.2 1.0
CG B:GLU204 3.9 32.4 1.0
CG B:GLU238 4.0 26.4 1.0
OE1 B:GLU204 4.1 32.2 1.0
N3 B:AZI900 4.2 31.6 0.7
CG B:GLU115 4.2 17.4 1.0
NE2 B:HIS241 4.2 15.8 1.0
CD2 B:HIS241 4.4 13.4 1.0
CD1 B:TRP111 4.4 12.5 1.0
OD1 B:ASP84 4.6 31.5 1.0
CA B:GLU238 4.7 21.8 1.0
OE1 B:GLN87 4.7 25.4 1.0
CE1 B:HIS118 4.7 17.0 1.0
CB B:GLU204 4.7 29.1 1.0
ND1 B:HIS118 4.8 16.1 1.0
CB B:GLU238 4.8 22.6 1.0
CG B:GLN87 5.0 21.1 1.0
CB B:GLN87 5.0 20.2 1.0

Reference:

M.E.Andersson, M.Hogbom, A.Rinaldo-Matthis, K.K.Andersson, B.M.Sjoberg, P.Nordlund. The Crystal Structure of An Azide Complex of the Diferrous R2 Subunit of Ribonucleotide Reductase Displays A Novel Carboxylate Shift with Important Mechanistic Implications For Diiron-Catalyzed Oxygen Activation J.Am.Chem.Soc. V. 121 2346 1999.
ISSN: ISSN 0002-7863
DOI: 10.1021/JA982280C
Page generated: Sun Dec 13 14:30:51 2020

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