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Mercury in PDB 1piu: Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster

Enzymatic activity of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster

All present enzymatic activity of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster:
1.17.4.1;

Protein crystallography data

The structure of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster, PDB code: 1piu 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) 20.75 / 2.20
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 (%) 19.1 / 23.2

Other elements in 1piu:

The structure of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster (pdb code 1piu). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 10 binding sites of Mercury where determined in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster, PDB code: 1piu:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 10 in 1piu

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Mercury binding site 1 out of 10 in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg501

b:27.1
occ:1.00
 SG A:CYS272 2.4 20.9 1.0
OH A:TYR194 2.7 21.1 1.0
CB A:CYS272 3.3 22.5 1.0
O A:ALA265 3.5 21.2 1.0
CA A:LYS269 3.7 31.9 1.0
CE A:MET198 3.7 17.7 1.0
CZ A:TYR194 3.7 18.4 1.0
CE2 A:TYR194 3.8 18.0 1.0
CB A:LYS269 3.9 34.4 1.0
CD2 A:LEU321 4.0 19.5 1.0
C A:ALA265 4.3 23.6 1.0
O A:HOH606 4.4 17.5 1.0
N A:LYS269 4.4 32.5 1.0
CA A:ALA265 4.6 22.2 1.0
O A:LYS269 4.6 27.5 1.0
C A:LYS269 4.6 28.6 1.0
O A:CYS268 4.7 33.1 1.0
CA A:CYS272 4.7 21.5 1.0
CB A:ALA265 4.7 18.7 1.0
C A:CYS268 4.8 35.8 1.0
CE1 A:TYR194 5.0 15.8 1.0

Mercury binding site 2 out of 10 in 1piu

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Mercury binding site 2 out of 10 in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg502

b:24.1
occ:1.00
 SG A:CYS196 2.4 20.5 1.0
O A:CYS196 3.2 8.8 1.0
CB A:CYS196 3.3 17.4 1.0
CA A:CYS196 3.4 12.6 1.0
CE1 A:TYR157 3.5 17.9 1.0
CD1 A:TYR157 3.5 15.3 1.0
C A:CYS196 3.6 12.4 1.0
CZ A:TYR157 3.7 18.0 1.0
CG A:TYR157 3.9 18.8 1.0
CE2 A:TYR157 4.0 15.9 1.0
CD2 A:TYR157 4.1 15.8 1.0
CD1 A:TYR156 4.2 39.7 1.0
CB A:SER199 4.3 16.2 1.0
N A:TYR157 4.4 24.7 1.0
CB A:TYR156 4.4 30.3 1.0
OH A:TYR157 4.4 17.8 1.0
CG A:TYR156 4.5 37.0 1.0
CA A:TYR157 4.5 22.0 1.0
N A:VAL200 4.8 13.9 1.0
O A:ILE153 4.8 20.9 1.0
CB A:TYR157 4.8 20.7 1.0
C A:TYR156 4.8 25.6 1.0
N A:CYS196 4.8 17.5 1.0
N A:LEU197 4.9 11.5 1.0
OG A:SER199 4.9 20.0 1.0

Mercury binding site 3 out of 10 in 1piu

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Mercury binding site 3 out of 10 in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg503

b:29.2
occ:1.00
 SG A:CYS214 2.3 19.4 1.0
O A:VAL210 2.9 18.4 1.0
N A:CYS214 3.3 17.7 1.0
CB A:CYS214 3.4 20.7 1.0
CA A:CYS214 3.6 19.4 1.0
CB A:ALA213 3.8 19.5 1.0
CD1 A:LEU304 3.9 22.5 1.0
CG1 A:VAL210 3.9 22.9 1.0
CD1 A:LEU299 4.0 27.5 1.0
C A:ALA213 4.0 18.8 1.0
C A:VAL210 4.0 21.1 1.0
O A:HOH694 4.3 32.6 1.0
CG A:LEU304 4.4 20.1 1.0
CA A:ALA213 4.4 19.9 1.0
CA A:VAL210 4.7 20.0 1.0
O A:ALA213 4.7 19.2 1.0
CB A:LEU304 4.8 20.3 1.0
N A:ALA213 4.9 21.8 1.0
CB A:VAL210 5.0 20.5 1.0

Mercury binding site 4 out of 10 in 1piu

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Mercury binding site 4 out of 10 in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg507

b:43.2
occ:0.50
 O A:HOH672 3.1 45.7 1.0
OE2 A:GLU309 3.3 19.4 1.0
CB A:CYS305 3.4 22.3 1.0
NZ A:LYS284 3.5 20.3 1.0
CD A:GLU309 3.5 19.4 1.0
C A:CYS305 3.5 22.6 1.0
O A:CYS305 3.6 23.8 1.0
N A:GLN306 3.7 21.6 1.0
CG A:GLU309 4.0 18.8 1.0
CA A:GLN306 4.0 23.4 1.0
OE1 A:GLU309 4.1 20.2 1.0
CA A:CYS305 4.1 23.6 1.0
CG A:GLN306 4.2 28.9 1.0
NH2 A:ARG328 4.5 51.5 1.0
CE A:LYS284 4.7 24.1 1.0
CB A:GLN306 4.7 22.0 1.0
O A:ASP302 4.9 29.5 1.0
SG A:CYS305 4.9 39.3 1.0
CZ A:ARG328 5.0 51.7 1.0

Mercury binding site 5 out of 10 in 1piu

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Mercury binding site 5 out of 10 in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg509

b:49.5
occ:0.50
 SG A:CYS268 2.6 45.6 1.0
CB A:CYS268 2.7 39.1 1.0
CD A:LYS191 2.9 41.4 1.0
O A:HOH656 2.9 30.4 1.0
O A:ILE264 3.3 23.0 1.0
N A:CYS268 3.4 39.7 1.0
CG2 A:ILE264 3.6 20.6 1.0
CA A:CYS268 3.6 39.0 1.0
CG A:LYS191 3.7 32.0 1.0
CE A:LYS191 3.9 44.0 1.0
CB A:GLU267 4.0 49.6 1.0
NZ A:LYS191 4.0 48.7 1.0
OE2 A:GLU267 4.0 81.2 1.0
C A:ILE264 4.1 22.7 1.0
C A:GLU267 4.1 41.2 1.0
CG A:GLU267 4.1 64.5 1.0
CA A:ILE264 4.2 23.1 1.0
CB A:LYS191 4.3 23.5 1.0
CD A:GLU267 4.3 73.8 1.0
CB A:ILE264 4.4 22.7 1.0
CA A:GLU267 4.6 43.3 1.0
O A:GLU267 4.8 40.1 1.0
CG1 A:ILE264 4.9 25.9 1.0
C A:CYS268 4.9 35.8 1.0

Mercury binding site 6 out of 10 in 1piu

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Mercury binding site 6 out of 10 in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg504

b:30.2
occ:1.00
 SG B:CYS196 2.8 13.1 1.0
CB B:CYS196 2.8 9.5 1.0
CA B:CYS196 2.9 15.8 1.0
O B:CYS196 3.2 13.7 1.0
C B:CYS196 3.4 11.5 1.0
CD1 B:TYR157 3.5 13.5 1.0
CG2 B:VAL200 3.6 16.3 1.0
CB B:TYR156 3.6 26.2 1.0
CE1 B:TYR157 3.6 15.8 1.0
CG B:TYR157 3.6 14.3 1.0
N B:TYR157 3.9 17.8 1.0
CD2 B:TYR157 3.9 14.6 1.0
CZ B:TYR157 3.9 17.1 1.0
CE2 B:TYR157 4.0 15.1 1.0
C B:TYR156 4.2 21.7 1.0
CB B:SER199 4.2 17.8 1.0
CA B:TYR157 4.2 17.3 1.0
N B:CYS196 4.3 17.8 1.0
CB B:TYR157 4.5 16.5 1.0
O B:ILE153 4.5 18.1 1.0
N B:LEU197 4.6 14.8 1.0
CA B:TYR156 4.6 22.6 1.0
N B:VAL200 4.6 14.6 1.0
CG B:TYR156 4.7 32.9 1.0
OH B:TYR157 4.7 14.8 1.0
O B:TYR156 4.7 18.9 1.0
CB B:VAL200 4.9 17.2 1.0
OG B:SER199 4.9 24.8 1.0
O B:LEU195 4.9 17.6 1.0

Mercury binding site 7 out of 10 in 1piu

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Mercury binding site 7 out of 10 in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg505

b:30.8
occ:0.50
 SG B:CYS272 2.5 41.5 1.0
SG B:CYS268 2.6 38.7 1.0
O B:CYS268 2.8 33.9 1.0
CB B:CYS268 3.2 37.5 1.0
C B:CYS268 3.4 35.9 1.0
CB B:CYS272 3.6 28.1 1.0
CD2 B:TYR194 3.7 21.1 1.0
CD2 B:LEU195 3.7 30.2 1.0
CA B:CYS268 3.8 38.1 1.0
CE2 B:TYR194 3.9 22.9 1.0
N B:CYS272 4.0 27.7 1.0
CA B:CYS272 4.2 27.1 1.0
N B:LYS269 4.3 35.9 1.0
O B:ALA265 4.5 30.6 1.0
N B:CYS268 4.6 38.8 1.0
CA B:LYS269 4.7 36.7 1.0
O B:HOH603 4.7 12.6 1.0
CG B:LEU195 4.8 29.9 1.0
CB B:GLU271 4.9 31.2 1.0
CG B:TYR194 4.9 18.6 1.0
CA B:ALA265 5.0 32.9 1.0

Mercury binding site 8 out of 10 in 1piu

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Mercury binding site 8 out of 10 in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg506

b:28.7
occ:0.50
 SG B:CYS214 2.7 17.1 1.0
O B:VAL210 2.8 21.3 1.0
N B:CYS214 3.1 21.7 1.0
CA B:CYS214 3.5 22.1 1.0
CB B:CYS214 3.5 23.1 1.0
CD1 B:LEU304 3.5 37.3 1.0
CB B:ALA213 3.6 17.7 1.0
CG1 B:VAL210 3.8 24.4 1.0
CG B:LEU304 3.8 35.5 1.0
C B:ALA213 3.8 21.5 1.0
CD1 B:LEU299 3.8 43.7 1.0
C B:VAL210 3.8 21.6 1.0
CA B:ALA213 4.2 21.2 1.0
CA B:VAL210 4.5 21.1 1.0
CB B:LEU304 4.5 31.4 1.0
O B:ALA213 4.6 22.0 1.0
N B:ALA213 4.8 19.4 1.0
CB B:VAL210 4.8 23.0 1.0
N B:SER211 4.9 20.8 1.0
CG B:LEU299 4.9 44.5 1.0
CD2 B:LEU299 4.9 45.0 1.0

Mercury binding site 9 out of 10 in 1piu

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Mercury binding site 9 out of 10 in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg508

b:33.3
occ:0.50
 O B:CYS272 2.8 23.8 1.0
CA B:CYS272 3.0 27.1 1.0
CB B:CYS272 3.1 28.1 1.0
CD2 B:LEU275 3.1 31.5 1.0
SG B:CYS272 3.2 41.5 1.0
C B:CYS272 3.2 23.7 1.0
CD1 B:LEU275 3.3 34.1 1.0
CB B:MET198 3.3 20.6 1.0
CB B:LEU275 3.5 29.5 1.0
CG B:LEU275 3.5 32.3 1.0
CD2 B:PHE276 3.5 31.5 1.0
CG B:MET198 3.6 24.3 1.0
CE2 B:PHE276 3.8 33.5 1.0
SD B:MET198 3.9 24.0 1.0
N B:PHE276 4.3 26.2 1.0
N B:CYS272 4.4 27.7 1.0
N B:TYR273 4.5 22.2 1.0
CG B:PHE276 4.5 29.9 1.0
CA B:LEU275 4.6 27.8 1.0
CA B:MET198 4.6 18.9 1.0
C B:LEU275 4.7 28.0 1.0
C B:MET198 4.7 19.0 1.0
O B:GLU271 4.8 30.2 1.0
CD1 B:LEU321 4.8 31.5 1.0
O B:MET198 4.9 17.4 1.0
CB B:PHE276 4.9 26.8 1.0
N B:LEU275 4.9 29.1 1.0

Mercury binding site 10 out of 10 in 1piu

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Mercury binding site 10 out of 10 in the Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Oxidized Ribonucleotide Reductase R2-D84E Mutant Containing Oxo-Bridged Diferric Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg510

b:51.1
occ:0.50
 CE B:LYS284 2.5 46.0 1.0
CD B:LYS284 2.7 42.3 1.0
CG B:LYS284 3.0 36.9 1.0
O B:CYS305 3.1 26.9 1.0
CB B:CYS305 3.2 27.1 1.0
OE2 B:GLU309 3.2 26.8 1.0
O B:HOH602 3.4 8.7 1.0
CA B:CYS305 3.5 26.6 1.0
CG B:GLU309 3.5 22.4 1.0
C B:CYS305 3.6 25.1 1.0
NZ B:LYS284 3.7 49.9 1.0
CD B:GLU309 3.8 27.2 1.0
SG B:CYS305 3.9 39.8 1.0
CB B:LYS284 4.1 31.6 1.0
CB B:VAL308 4.6 20.2 1.0
CG1 B:VAL308 4.8 18.6 1.0
CB B:GLU309 4.8 20.4 1.0
N B:GLN306 4.8 24.6 1.0
N B:GLU309 4.8 17.7 1.0
N B:CYS305 4.9 26.4 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 Aug 11 01:00:58 2024

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