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Iron in PDB 1pim: Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant

Enzymatic activity of Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant

All present enzymatic activity of Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant:
1.17.4.1;

Protein crystallography data

The structure of Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant, PDB code: 1pim was solved by W.C.Voegtli, N.Khidekel, J.Baldwin, B.A.Ley, J.M.Bollinger Jr., A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.75 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.100, 84.600, 114.800, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.6

Other elements in 1pim:

The structure of Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant also contains other interesting chemical elements:

Mercury (Hg) 7 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant (pdb code 1pim). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant, PDB code: 1pim:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1pim

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Iron binding site 1 out of 4 in the Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:34.4
occ:1.00
OE1 A:GLU115 2.1 25.2 1.0
OE1 A:GLU84 2.2 37.0 1.0
ND1 A:HIS118 2.3 13.1 1.0
OE2 A:GLU238 2.5 34.8 1.0
OE2 A:GLU84 2.5 38.5 1.0
CD A:GLU84 2.7 32.5 1.0
O A:HOH556 3.0 40.8 1.0
CE1 A:HIS118 3.1 16.8 1.0
CD A:GLU115 3.2 25.1 1.0
CG A:HIS118 3.4 14.2 1.0
FE A:FE402 3.4 25.9 1.0
CD A:GLU238 3.5 37.3 1.0
OE2 A:GLU115 3.6 26.6 1.0
CB A:HIS118 3.8 18.1 1.0
OE1 A:GLU238 4.2 33.4 1.0
CG A:GLU84 4.2 36.4 1.0
NE2 A:HIS118 4.3 15.3 1.0
CG A:GLU238 4.4 33.5 1.0
CZ A:PHE208 4.4 38.4 1.0
CD2 A:HIS118 4.5 18.6 1.0
CG A:GLU115 4.5 21.6 1.0
CA A:GLU115 4.5 17.6 1.0
CG2 A:ILE234 4.5 15.3 1.0
CE2 A:PHE208 4.6 38.2 1.0
CE1 A:HIS241 4.6 18.2 1.0
ND1 A:HIS241 4.7 16.0 1.0
CB A:GLU115 4.7 20.0 1.0
CE1 A:PHE208 4.9 42.7 1.0
CB A:GLU84 5.0 24.8 1.0

Iron binding site 2 out of 4 in 1pim

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Iron binding site 2 out of 4 in the Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:25.9
occ:1.00
OE2 A:GLU204 2.2 29.4 1.0
O A:HOH556 2.2 40.8 1.0
OE2 A:GLU115 2.2 26.6 1.0
ND1 A:HIS241 2.3 16.0 1.0
OE2 A:GLU238 2.3 34.8 1.0
OE1 A:GLU238 2.4 33.4 1.0
CD A:GLU238 2.6 37.3 1.0
CD A:GLU204 3.1 25.0 1.0
CE1 A:HIS241 3.1 18.2 1.0
CD A:GLU115 3.1 25.1 1.0
CG A:HIS241 3.3 19.1 1.0
OE1 A:GLU115 3.4 25.2 1.0
FE A:FE401 3.4 34.4 1.0
CG A:GLU204 3.7 28.0 1.0
CB A:HIS241 3.7 17.6 1.0
NE1 A:TRP111 3.9 22.5 1.0
OE1 A:GLU204 4.0 28.7 1.0
CG A:GLU238 4.2 33.5 1.0
NE2 A:HIS241 4.3 17.7 1.0
CD2 A:HIS241 4.4 17.5 1.0
CB A:GLU204 4.4 27.8 1.0
CD1 A:TRP111 4.5 23.9 1.0
CG A:GLU115 4.5 21.6 1.0
CA A:GLU238 4.6 17.9 1.0
NE2 A:GLN87 4.8 28.4 1.0
CB A:GLU238 4.8 22.2 1.0
OE1 A:GLU84 4.9 37.0 1.0
CE1 A:HIS118 5.0 16.8 1.0
ND1 A:HIS118 5.0 13.1 1.0

Iron binding site 3 out of 4 in 1pim

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Iron binding site 3 out of 4 in the Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:30.1
occ:1.00
OE2 B:GLU115 2.1 26.1 1.0
ND1 B:HIS118 2.3 15.5 1.0
OE1 B:GLU84 2.3 40.0 1.0
OE2 B:GLU84 2.4 32.1 1.0
OE2 B:GLU238 2.4 25.4 1.0
CD B:GLU84 2.5 36.2 1.0
O B:HOH556 2.9 27.2 1.0
CE1 B:HIS118 3.1 22.6 1.0
CD B:GLU115 3.2 20.6 1.0
CG B:HIS118 3.4 18.0 1.0
FE B:FE404 3.5 20.4 1.0
CD B:GLU238 3.6 34.4 1.0
OE1 B:GLU115 3.6 18.5 1.0
CB B:HIS118 3.8 17.7 1.0
CG B:GLU84 3.9 36.2 1.0
CE2 B:PHE208 4.2 35.3 1.0
NE2 B:HIS118 4.3 16.9 1.0
OE1 B:GLU238 4.3 32.9 1.0
CZ B:PHE208 4.3 34.8 1.0
CG2 B:ILE234 4.4 9.6 1.0
CD2 B:HIS118 4.4 16.5 1.0
CG B:GLU238 4.4 27.9 1.0
CG B:GLU115 4.4 16.4 1.0
CA B:GLU115 4.5 17.5 1.0
CE1 B:HIS241 4.6 18.3 1.0
CB B:GLU115 4.6 16.0 1.0
ND1 B:HIS241 4.7 15.3 1.0
CD2 B:PHE208 4.9 38.4 1.0

Iron binding site 4 out of 4 in 1pim

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Iron binding site 4 out of 4 in the Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe404

b:20.4
occ:1.00
OE1 B:GLU115 2.1 18.5 1.0
OE1 B:GLU238 2.2 32.9 1.0
ND1 B:HIS241 2.2 15.3 1.0
OE2 B:GLU204 2.3 18.2 1.0
OE2 B:GLU238 2.3 25.4 1.0
O B:HOH556 2.4 27.2 1.0
CD B:GLU238 2.5 34.4 1.0
CD B:GLU115 3.0 20.6 1.0
CE1 B:HIS241 3.1 18.3 1.0
OE2 B:GLU115 3.2 26.1 1.0
CD B:GLU204 3.3 21.1 1.0
CG B:HIS241 3.3 18.0 1.0
FE B:FE403 3.5 30.1 1.0
CB B:HIS241 3.7 18.3 1.0
CG B:GLU204 3.9 28.4 1.0
NE1 B:TRP111 4.0 15.1 1.0
CG B:GLU238 4.1 27.9 1.0
OE1 B:GLU204 4.2 29.6 1.0
NE2 B:HIS241 4.3 16.4 1.0
CG B:GLU115 4.4 16.4 1.0
CD2 B:HIS241 4.4 15.3 1.0
CD1 B:TRP111 4.5 15.0 1.0
CB B:GLU204 4.6 23.9 1.0
CA B:GLU238 4.7 16.7 1.0
OE1 B:GLU84 4.7 40.0 1.0
CB B:GLU238 4.8 17.9 1.0
NE2 B:GLN87 4.9 26.8 1.0

Reference:

W.C.Voegtli, N.Khidekel, J.Baldwin, B.A.Ley, J.M.Bollinger Jr., A.C.Rosenzweig. Crystal Structure of the Ribonucleotide Reductase R2 Mutant That Accumulates A U-1,2-Peroxodiiron(III) Intermediate During Oxygen Activation J.Am.Chem.Soc. V. 122 3255 2000.
ISSN: ISSN 0002-7863
DOI: 10.1021/JA991839L
Page generated: Sun Dec 13 14:28:29 2020

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