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Mercury in PDB 1pj0: Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH

Enzymatic activity of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH

All present enzymatic activity of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH:
1.17.4.1;

Protein crystallography data

The structure of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH, PDB code: 1pj0 was solved by W.C.Voegtli, M.Sommerhalter, L.Saleh, J.Baldwin, 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) 19.32 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.000, 84.400, 114.600, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.6

Other elements in 1pj0:

The structure of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH (pdb code 1pj0). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 9 binding sites of Mercury where determined in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH, PDB code: 1pj0:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Mercury binding site 1 out of 9 in 1pj0

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Mercury binding site 1 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg378

b:26.1
occ:1.00
SG A:CYS272 2.4 18.6 1.0
OH A:TYR194 2.8 20.5 1.0
CB A:CYS272 3.3 17.6 1.0
O A:ALA265 3.5 24.5 1.0
CZ A:TYR194 3.8 19.3 1.0
CA A:LYS269 3.8 24.9 1.0
CE2 A:TYR194 3.8 19.2 1.0
CE A:MET198 4.0 18.5 1.0
CD2 A:LEU321 4.1 16.5 1.0
SG A:CYS268 4.1 30.3 1.0
N A:LYS269 4.1 25.6 1.0
C A:ALA265 4.4 24.1 1.0
O A:HOH426 4.4 23.5 1.0
CB A:LYS269 4.5 26.4 1.0
C A:CYS268 4.5 26.2 1.0
O A:LYS269 4.6 23.2 1.0
CA A:ALA265 4.6 23.4 1.0
O A:CYS268 4.7 25.9 1.0
CA A:CYS272 4.7 17.3 1.0
C A:LYS269 4.7 24.1 1.0
CB A:ALA265 4.8 22.4 1.0
CG A:LEU321 4.9 16.3 1.0
CG A:MET198 5.0 18.1 1.0

Mercury binding site 2 out of 9 in 1pj0

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Mercury binding site 2 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg379

b:22.8
occ:1.00
SG A:CYS196 2.3 18.3 1.0
O A:CYS196 3.1 15.1 1.0
CB A:CYS196 3.3 16.1 1.0
CA A:CYS196 3.4 15.7 1.0
CD1 A:TYR157 3.6 14.1 1.0
CE1 A:TYR157 3.6 14.7 1.0
C A:CYS196 3.6 15.5 1.0
CG2 A:VAL200 3.7 12.9 1.0
CG A:TYR157 3.9 14.4 1.0
CZ A:TYR157 3.9 14.5 1.0
CD2 A:TYR157 4.1 14.1 1.0
CB A:TYR156 4.2 23.8 1.0
CE2 A:TYR157 4.2 13.9 1.0
CD1 A:TYR156 4.2 27.4 1.0
N A:TYR157 4.2 18.1 1.0
CB A:SER199 4.3 14.4 1.0
CA A:TYR157 4.5 16.6 1.0
CG A:TYR156 4.5 26.7 1.0
C A:TYR156 4.6 19.9 1.0
OH A:TYR157 4.7 15.7 1.0
N A:VAL200 4.7 11.8 1.0
CB A:TYR157 4.7 15.4 1.0
O A:ILE153 4.7 20.5 1.0
N A:CYS196 4.8 15.4 1.0
N A:LEU197 4.8 14.9 1.0
OG A:SER199 4.9 15.4 1.0

Mercury binding site 3 out of 9 in 1pj0

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Mercury binding site 3 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg380

b:34.6
occ:1.00
SG A:CYS214 2.3 24.6 1.0
O A:VAL210 2.8 18.5 1.0
N A:CYS214 3.2 20.8 1.0
CB A:CYS214 3.5 21.8 1.0
CA A:CYS214 3.6 21.2 1.0
CB A:ALA213 3.7 20.4 1.0
CD1 A:LEU299 4.0 24.1 1.0
C A:ALA213 4.0 20.7 1.0
C A:VAL210 4.0 19.4 1.0
CG1 A:VAL210 4.1 20.0 1.0
CD1 A:LEU304 4.1 21.1 1.0
CA A:ALA213 4.4 20.3 1.0
O A:HOH452 4.5 37.1 1.0
CG A:LEU304 4.5 21.1 1.0
CA A:VAL210 4.7 18.9 1.0
O A:ALA213 4.8 20.4 1.0
CB A:LEU304 4.8 20.7 1.0
N A:ALA213 4.9 20.3 1.0
N A:SER211 5.0 19.2 1.0

Mercury binding site 4 out of 9 in 1pj0

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Mercury binding site 4 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg381

b:44.5
occ:0.50
OE2 A:GLU309 3.1 19.7 1.0
CB A:CYS305 3.4 23.2 1.0
CD A:GLU309 3.4 18.7 1.0
NZ A:LYS284 3.4 24.4 1.0
C A:CYS305 3.5 21.0 1.0
O A:CYS305 3.6 20.9 1.0
N A:GLN306 3.7 19.8 1.0
OE1 A:GLU309 3.9 19.2 1.0
CG A:GLU309 4.0 17.4 1.0
CA A:GLN306 4.0 19.3 1.0
CA A:CYS305 4.1 21.8 1.0
CG A:GLN306 4.3 22.5 1.0
NH2 A:ARG328 4.5 36.9 1.0
CE A:LYS284 4.7 25.1 1.0
SG A:CYS305 4.8 29.9 1.0
CB A:GLN306 4.8 20.4 1.0
O A:ASP302 4.9 23.8 1.0
CZ A:ARG328 4.9 36.5 1.0
CB A:GLU309 4.9 16.4 1.0

Mercury binding site 5 out of 9 in 1pj0

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Mercury binding site 5 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg382

b:0.1
occ:0.50
CB A:CYS268 2.7 28.0 1.0
CA A:CYS268 3.0 27.4 1.0
N A:CYS268 3.1 27.5 1.0
O A:ILE264 3.5 22.0 1.0
C A:GLU267 3.7 28.2 1.0
CG2 A:ILE264 3.8 21.4 1.0
CD A:LYS191 4.0 24.5 1.0
CG A:LYS191 4.1 22.7 1.0
O A:GLU267 4.2 28.1 1.0
CB A:GLU267 4.2 29.9 1.0
SG A:CYS268 4.3 30.3 1.0
C A:ILE264 4.4 21.9 1.0
CB A:LYS191 4.5 19.5 1.0
C A:CYS268 4.5 26.2 1.0
CE A:LYS191 4.5 26.6 1.0
CA A:GLU267 4.6 28.5 1.0
CA A:ILE264 4.7 21.5 1.0
CB A:ILE264 4.8 21.4 1.0
OE1 A:GLU267 5.0 34.8 1.0

Mercury binding site 6 out of 9 in 1pj0

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Mercury binding site 6 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg378

b:32.3
occ:1.00
CB B:CYS196 2.6 13.9 1.0
CA B:CYS196 2.8 16.2 1.0
SG B:CYS196 2.9 6.6 1.0
O B:CYS196 3.1 16.8 1.0
C B:CYS196 3.3 16.1 1.0
CG2 B:VAL200 3.4 17.1 1.0
CB B:TYR156 3.6 21.9 1.0
CD1 B:TYR157 3.6 16.4 1.0
CG B:TYR157 3.7 15.2 1.0
CE1 B:TYR157 3.7 14.8 1.0
CD2 B:TYR157 3.8 15.0 1.0
CZ B:TYR157 3.9 15.2 1.0
N B:TYR157 3.9 18.1 1.0
CE2 B:TYR157 3.9 14.7 1.0
C B:TYR156 4.2 19.4 1.0
N B:CYS196 4.2 18.1 1.0
CB B:SER199 4.3 18.5 1.0
CA B:TYR157 4.3 16.4 1.0
CB B:TYR157 4.5 15.6 1.0
N B:LEU197 4.5 16.7 1.0
O B:ILE153 4.5 22.8 1.0
CA B:TYR156 4.5 20.5 1.0
N B:VAL200 4.6 15.8 1.0
CG B:TYR156 4.6 24.1 1.0
O B:TYR156 4.7 18.6 1.0
OH B:TYR157 4.7 14.2 1.0
CB B:VAL200 4.8 16.0 1.0
O B:LEU195 4.9 19.6 1.0
OG B:SER199 5.0 22.5 1.0

Mercury binding site 7 out of 9 in 1pj0

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Mercury binding site 7 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg379

b:26.1
occ:0.50
SG B:CYS272 2.3 29.9 1.0
SG B:CYS268 2.5 38.5 1.0
O B:CYS268 2.6 37.2 1.0
CB B:CYS268 3.2 38.1 1.0
C B:CYS268 3.3 37.2 1.0
CB B:CYS272 3.4 27.3 1.0
CD2 B:TYR194 3.5 19.6 1.0
CE2 B:TYR194 3.8 21.0 1.0
CA B:CYS268 3.9 37.7 1.0
N B:CYS272 4.0 27.7 1.0
CD2 B:LEU195 4.0 24.6 1.0
CA B:CYS272 4.2 27.0 1.0
N B:LYS269 4.2 36.4 1.0
O B:ALA265 4.5 36.0 1.0
CA B:LYS269 4.5 35.7 1.0
N B:CYS268 4.7 38.1 1.0
CG B:TYR194 4.7 19.5 1.0
O B:HOH388 4.8 25.5 1.0
CB B:GLU271 4.8 30.5 1.0
CA B:ALA265 4.9 35.7 1.0
C B:GLU271 5.0 29.1 1.0

Mercury binding site 8 out of 9 in 1pj0

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Mercury binding site 8 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg380

b:41.2
occ:0.50
SG B:CYS214 2.6 18.4 1.0
O B:VAL210 2.8 20.9 1.0
N B:CYS214 3.1 22.7 1.0
CD1 B:LEU304 3.1 31.3 1.0
CA B:CYS214 3.5 22.7 1.0
CB B:CYS214 3.5 21.8 1.0
CG B:LEU304 3.6 31.0 1.0
CB B:ALA213 3.6 22.3 1.0
CG1 B:VAL210 3.8 22.0 1.0
C B:VAL210 3.9 20.7 1.0
C B:ALA213 3.9 22.4 1.0
CD2 B:LEU299 4.2 42.7 1.0
CA B:ALA213 4.3 21.7 1.0
CD1 B:LEU299 4.3 42.6 1.0
CB B:LEU304 4.3 30.1 1.0
CA B:VAL210 4.5 21.1 1.0
N B:ALA213 4.6 21.1 1.0
CG B:LEU299 4.6 42.4 1.0
O B:ALA213 4.7 22.5 1.0
CD2 B:LEU304 4.8 31.0 1.0
CB B:VAL210 4.8 21.4 1.0
N B:SER211 4.9 20.1 1.0

Mercury binding site 9 out of 9 in 1pj0

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Mercury binding site 9 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg381

b:61.7
occ:0.50
O B:CYS272 2.8 24.9 1.0
CA B:CYS272 2.9 27.0 1.0
CB B:CYS272 3.0 27.3 1.0
CB B:MET198 3.1 19.6 1.0
CG B:MET198 3.2 22.8 1.0
C B:CYS272 3.2 25.9 1.0
SG B:CYS272 3.3 29.9 1.0
CD1 B:LEU275 3.4 27.0 1.0
SD B:MET198 3.5 23.6 1.0
CB B:LEU275 3.6 25.9 1.0
CD2 B:LEU275 3.6 26.7 1.0
CG B:LEU275 3.7 26.6 1.0
CD2 B:PHE276 3.9 24.9 1.0
N B:PHE276 4.3 24.8 1.0
N B:CYS272 4.3 27.7 1.0
CA B:MET198 4.4 18.3 1.0
N B:TYR273 4.4 25.8 1.0
CD1 B:LEU321 4.5 28.0 1.0
C B:MET198 4.6 18.0 1.0
CE2 B:PHE276 4.6 24.5 1.0
CA B:LEU275 4.7 25.3 1.0
C B:LEU275 4.7 25.2 1.0
CG B:PHE276 4.7 24.2 1.0
CB B:PHE276 4.8 24.1 1.0
O B:GLU271 4.8 28.6 1.0
O B:MET198 4.9 18.2 1.0
CE B:MET198 4.9 23.8 1.0
CA B:PHE276 4.9 24.2 1.0
N B:SER199 5.0 18.2 1.0

Reference:

W.C.Voegtli, M.Sommerhalter, L.Saleh, J.Baldwin, J.M.Bollinger Jr., A.C.Rosenzweig. Variable Coordination Geometries at the Diiron(II) Active Site of Ribonucleotide Reductase R2. J.Am.Chem.Soc. V. 125 15822 2003.
ISSN: ISSN 0002-7863
PubMed: 14677973
DOI: 10.1021/JA0370387
Page generated: Sun Dec 13 19:04:39 2020

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