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Iron in PDB 1rnr: Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein

Enzymatic activity of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein

All present enzymatic activity of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein:
1.17.4.1;

Protein crystallography data

The structure of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein, PDB code: 1rnr was solved by A.Aberg, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.100, 85.300, 115.700, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / n/a

Other elements in 1rnr:

The structure of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein also contains other interesting chemical elements:

Mercury (Hg) 14 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein (pdb code 1rnr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein, PDB code: 1rnr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1rnr

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Iron binding site 1 out of 4 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:23.6
occ:0.70
 OE1 A:GLU115 1.9 15.7 1.0
OD1 A:ASP84 1.9 22.8 1.0
OE2 A:DAH208 2.0 51.6 1.0
OZ A:DAH208 2.2 53.0 1.0
ND1 A:HIS118 2.4 9.4 1.0
OE2 A:GLU238 2.8 28.8 1.0
CE2 A:DAH208 2.9 51.8 1.0
CZ A:DAH208 2.9 52.4 1.0
CG A:ASP84 3.0 23.6 1.0
CD A:GLU115 3.0 12.4 1.0
CG A:HIS118 3.3 9.6 1.0
OD2 A:ASP84 3.4 28.5 1.0
CE1 A:HIS118 3.5 8.7 1.0
OE2 A:GLU115 3.5 15.5 1.0
FE A:FE402 3.6 15.8 1.0
CB A:HIS118 3.7 12.6 1.0
CD A:GLU238 3.9 27.6 1.0
CD2 A:DAH208 4.2 48.8 1.0
CG A:GLU115 4.2 11.5 1.0
CE1 A:DAH208 4.3 51.0 1.0
CB A:ASP84 4.3 20.6 1.0
CA A:GLU115 4.4 11.1 1.0
CD2 A:HIS118 4.5 10.6 1.0
CB A:GLU115 4.5 8.1 1.0
NE2 A:HIS118 4.5 8.0 1.0
CG2 A:ILE234 4.6 11.6 1.0
OE1 A:GLU238 4.7 32.5 1.0
CG A:GLU238 4.7 24.5 1.0
CA A:ASP84 4.8 18.7 1.0
O A:GLU115 4.9 13.9 1.0

Iron binding site 2 out of 4 in 1rnr

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Iron binding site 2 out of 4 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:15.8
occ:1.00
 OE2 A:GLU238 1.9 28.8 1.0
OE2 A:GLU204 2.0 26.2 1.0
OE2 A:GLU115 2.0 15.5 1.0
OE1 A:GLU238 2.3 32.5 1.0
ND1 A:HIS241 2.4 14.0 1.0
CD A:GLU238 2.4 27.6 1.0
CD A:GLU115 3.0 12.4 1.0
CD A:GLU204 3.1 26.2 1.0
OE1 A:GLU115 3.2 15.7 1.0
OZ A:DAH208 3.3 53.0 1.0
CE1 A:HIS241 3.3 11.3 1.0
CG A:HIS241 3.4 15.1 1.0
CZ A:DAH208 3.6 52.4 1.0
FE A:FE401 3.6 23.6 0.7
CB A:HIS241 3.7 14.6 1.0
OE1 A:GLU204 3.8 30.2 1.0
CG A:GLU238 3.9 24.5 1.0
CE1 A:DAH208 4.0 51.0 1.0
CG A:GLU204 4.0 27.0 1.0
CE2 A:DAH208 4.1 51.8 1.0
NE1 A:TRP111 4.2 8.8 1.0
OE2 A:DAH208 4.3 51.6 1.0
CG A:GLU115 4.4 11.5 1.0
NE2 A:HIS241 4.4 13.1 1.0
CD2 A:HIS241 4.5 13.3 1.0
CD1 A:TRP111 4.6 9.8 1.0
CA A:GLU238 4.7 14.5 1.0
CB A:GLU238 4.8 17.3 1.0
CB A:GLU204 4.8 24.6 1.0
CD1 A:DAH208 4.8 48.2 1.0
ND1 A:HIS118 4.9 9.4 1.0
CE1 A:HIS118 5.0 8.7 1.0
CD2 A:DAH208 5.0 48.8 1.0

Iron binding site 3 out of 4 in 1rnr

Go back to Iron Binding Sites List in 1rnr
Iron binding site 3 out of 4 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:17.0
occ:0.70
 OD1 B:ASP84 2.0 26.4 1.0
OZ B:DAH208 2.0 44.4 1.0
OE2 B:DAH208 2.1 42.0 1.0
ND1 B:HIS118 2.3 8.4 1.0
OE1 B:GLU115 2.3 22.2 1.0
OE2 B:GLU238 2.4 27.6 1.0
CZ B:DAH208 2.7 43.5 1.0
CE2 B:DAH208 2.8 42.8 1.0
CG B:ASP84 2.9 27.6 1.0
CE1 B:HIS118 3.1 5.5 1.0
OD2 B:ASP84 3.2 32.0 1.0
CG B:HIS118 3.4 7.2 1.0
FE B:FE402 3.5 20.0 1.0
CD B:GLU115 3.5 20.0 1.0
CD B:GLU238 3.5 26.5 1.0
CB B:HIS118 3.9 9.8 1.0
CE1 B:DAH208 4.0 43.7 1.0
OE2 B:GLU115 4.0 24.2 1.0
CD2 B:DAH208 4.1 41.2 1.0
OE1 B:GLU238 4.2 28.8 1.0
NE2 B:HIS118 4.3 6.2 1.0
CB B:ASP84 4.3 22.3 1.0
CG B:GLU238 4.4 24.7 1.0
CD2 B:HIS118 4.5 4.6 1.0
CG2 B:ILE234 4.5 10.2 1.0
CA B:GLU115 4.6 11.1 1.0
CG B:GLU115 4.7 16.9 1.0
ND1 B:HIS241 4.8 9.3 1.0
CA B:ASP84 4.8 20.6 1.0
CB B:GLU115 4.8 12.7 1.0
CE1 B:HIS241 4.9 7.1 1.0

Iron binding site 4 out of 4 in 1rnr

Go back to Iron Binding Sites List in 1rnr
Iron binding site 4 out of 4 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:20.0
occ:1.00
 OE2 B:GLU204 1.9 24.1 1.0
OE1 B:GLU238 1.9 28.8 1.0
OE2 B:GLU238 2.1 27.6 1.0
ND1 B:HIS241 2.3 9.3 1.0
CD B:GLU238 2.3 26.5 1.0
OE2 B:GLU115 2.3 24.2 1.0
CD B:GLU204 3.0 24.9 1.0
OE1 B:GLU115 3.0 22.2 1.0
CD B:GLU115 3.1 20.0 1.0
OZ B:DAH208 3.1 44.4 1.0
CE1 B:HIS241 3.2 7.1 1.0
CG B:HIS241 3.3 12.0 1.0
FE B:FE401 3.5 17.0 0.7
CZ B:DAH208 3.6 43.5 1.0
CB B:HIS241 3.7 15.2 1.0
CG B:GLU204 3.7 27.0 1.0
CG B:GLU238 3.9 24.7 1.0
CE1 B:DAH208 3.9 43.7 1.0
OE1 B:GLU204 3.9 26.8 1.0
NE1 B:TRP111 4.0 10.8 1.0
NE2 B:HIS241 4.4 8.5 1.0
CE2 B:DAH208 4.4 42.8 1.0
CD1 B:TRP111 4.4 9.5 1.0
CD2 B:HIS241 4.4 10.8 1.0
CG B:GLU115 4.5 16.9 1.0
CB B:GLU204 4.6 25.2 1.0
CA B:GLU238 4.7 16.6 1.0
CB B:GLU238 4.7 19.5 1.0
OE2 B:DAH208 4.7 42.0 1.0
CE1 B:HIS118 4.8 5.5 1.0
OE1 B:GLN87 4.8 19.0 1.0
CD1 B:DAH208 4.8 42.1 1.0
ND1 B:HIS118 4.9 8.4 1.0
OD1 B:ASP84 5.0 26.4 1.0

Reference:

A.Aberg, M.Ormo, P.Nordlund, B.M.Sjoberg. Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein. Biochemistry V. 32 9845 1993.
ISSN: ISSN 0006-2960
PubMed: 8373782
DOI: 10.1021/BI00088A040
Page generated: Sun Dec 13 14:30:35 2020

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