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Mercury in PDB 1piy: Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH

Enzymatic activity of Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH

All present enzymatic activity of Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH:
1.17.4.1;

Protein crystallography data

The structure of Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH, PDB code: 1piy 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) 24.08 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.900, 84.600, 114.100, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 24.6

Other elements in 1piy:

The structure of Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Mercury atom in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH (pdb code 1piy). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 14 binding sites of Mercury where determined in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH, PDB code: 1piy:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 14 in 1piy

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Mercury binding site 1 out of 14 in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion 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 Soaked with Ferrous Ion at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg378

b:11.8
occ:0.70
 SG A:CYS272 2.3 16.3 1.0
OH A:TYR194 2.8 13.4 1.0
CB A:CYS272 3.2 16.6 1.0
O A:ALA265 3.5 19.1 1.0
CZ A:TYR194 3.8 13.4 1.0
CE A:MET198 3.9 13.7 1.0
CA A:LYS269 3.9 19.3 1.0
CE2 A:TYR194 3.9 13.4 1.0
CD2 A:LEU321 4.0 15.1 1.0
N A:LYS269 4.4 19.6 1.0
C A:ALA265 4.4 19.1 1.0
CG A:LYS269 4.4 19.7 1.0
O A:LYS269 4.5 18.9 1.0
O A:HOH391 4.5 13.8 1.0
CB A:LYS269 4.6 19.5 1.0
O A:CYS268 4.6 19.8 1.0
CA A:CYS272 4.7 16.8 1.0
CA A:ALA265 4.7 18.9 1.0
C A:LYS269 4.7 19.0 1.0
C A:CYS268 4.7 19.8 1.0
CB A:ALA265 4.9 18.9 1.0
CG A:LEU321 4.9 15.1 1.0

Mercury binding site 2 out of 14 in 1piy

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Mercury binding site 2 out of 14 in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion 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 Soaked with Ferrous Ion at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg379

b:13.8
occ:0.80
 SG A:CYS196 2.3 13.8 1.0
HG A:HG383 3.1 31.4 0.3
O A:CYS196 3.3 13.3 1.0
CB A:CYS196 3.4 13.4 1.0
CA A:CYS196 3.4 13.4 1.0
CD1 A:TYR157 3.6 16.6 1.0
CE1 A:TYR157 3.6 16.5 1.0
CG2 A:VAL200 3.6 13.0 1.0
C A:CYS196 3.6 13.3 1.0
CG A:TYR157 3.8 16.7 1.0
CZ A:TYR157 3.9 16.5 1.0
CD2 A:TYR157 4.0 16.6 1.0
CD2 A:TYR156 4.0 19.6 1.0
CE2 A:TYR157 4.1 16.5 1.0
N A:TYR157 4.2 17.6 1.0
CB A:TYR156 4.2 19.0 1.0
CB A:SER199 4.2 13.1 1.0
CA A:TYR157 4.4 17.1 1.0
CG A:TYR156 4.5 19.5 1.0
C A:TYR156 4.6 18.2 1.0
O A:ILE153 4.6 20.0 1.0
OH A:TYR157 4.6 16.5 1.0
N A:VAL200 4.6 12.9 1.0
CB A:TYR157 4.6 16.9 1.0
N A:LEU197 4.8 13.2 1.0
N A:CYS196 4.9 13.3 1.0
CB A:VAL200 4.9 13.0 1.0
OG A:SER199 5.0 13.3 1.0

Mercury binding site 3 out of 14 in 1piy

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Mercury binding site 3 out of 14 in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion 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 Soaked with Ferrous Ion at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg380

b:20.1
occ:0.75
 SG A:CYS214 2.2 17.1 1.0
O A:VAL210 2.9 15.4 1.0
N A:CYS214 3.3 16.1 1.0
CB A:CYS214 3.5 16.4 1.0
HG A:HG384 3.6 67.4 0.3
CB A:ALA213 3.7 15.8 1.0
CA A:CYS214 3.7 16.3 1.0
CG1 A:VAL210 4.0 15.4 1.0
CD1 A:LEU299 4.0 19.6 1.0
C A:ALA213 4.0 16.0 1.0
C A:VAL210 4.0 15.4 1.0
CD1 A:LEU304 4.2 17.9 1.0
CA A:ALA213 4.4 15.9 1.0
CG A:LEU304 4.5 17.9 1.0
CA A:VAL210 4.6 15.4 1.0
O A:ALA213 4.8 16.0 1.0
N A:ALA213 4.9 15.8 1.0
CB A:LEU304 4.9 17.9 1.0
CB A:VAL210 5.0 15.4 1.0

Mercury binding site 4 out of 14 in 1piy

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Mercury binding site 4 out of 14 in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion 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 Soaked with Ferrous Ion at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg381

b:19.4
occ:0.40
 OE2 A:GLU309 3.4 15.0 1.0
CB A:CYS305 3.4 18.0 1.0
CD A:GLU309 3.5 14.8 1.0
C A:CYS305 3.6 17.3 1.0
O A:CYS305 3.7 17.3 1.0
N A:GLN306 3.7 16.9 1.0
CG A:GLU309 3.9 14.7 1.0
OE1 A:GLU309 4.0 14.9 1.0
CA A:GLN306 4.1 16.5 1.0
CA A:CYS305 4.1 17.7 1.0
CE A:LYS284 4.4 18.7 1.0
NZ A:LYS284 4.4 18.9 1.0
CG A:GLN306 4.4 16.9 1.0
SG A:CYS305 4.9 19.4 1.0
CB A:GLN306 4.9 16.6 1.0
NH2 A:ARG328 4.9 19.9 1.0
CB A:GLU309 4.9 14.5 1.0
O A:ASP302 5.0 19.1 1.0

Mercury binding site 5 out of 14 in 1piy

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Mercury binding site 5 out of 14 in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion 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 Soaked with Ferrous Ion at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg382

b:75.4
occ:0.30
 SG A:CYS268 3.0 21.1 1.0
CG A:GLU271 3.6 18.7 1.0
CB A:CYS268 3.7 20.3 1.0
CE A:LYS191 3.9 15.6 1.0
CA A:CYS268 4.2 20.1 1.0
CD1 A:LEU195 4.4 13.6 1.0
CD A:GLU271 4.6 19.0 1.0
CB A:GLU271 4.6 18.2 1.0
NZ A:LYS191 4.7 15.9 1.0
OE1 A:GLU271 4.7 19.3 1.0
CD A:LYS191 5.0 15.4 1.0

Mercury binding site 6 out of 14 in 1piy

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Mercury binding site 6 out of 14 in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion 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 Soaked with Ferrous Ion at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg383

b:31.4
occ:0.30
 SG A:CYS196 2.0 13.8 1.0
CG2 A:VAL200 3.0 13.0 1.0
HG A:HG379 3.1 13.8 0.8
CE1 A:TYR157 3.2 16.5 1.0
CB A:CYS196 3.3 13.4 1.0
C A:CYS196 3.5 13.3 1.0
O A:CYS196 3.5 13.3 1.0
CD2 A:LEU95 3.7 14.2 1.0
N A:LEU197 3.8 13.2 1.0
CD1 A:TYR157 3.8 16.6 1.0
CA A:CYS196 3.9 13.4 1.0
CZ A:TYR157 4.0 16.5 1.0
CA A:LEU197 4.2 13.1 1.0
OH A:TYR157 4.2 16.5 1.0
CD2 A:LEU197 4.3 13.4 1.0
CB A:VAL200 4.3 13.0 1.0
CG A:LEU95 4.3 14.1 1.0
CD1 A:LEU95 4.3 14.2 1.0
CD2 A:LEU160 4.8 15.6 1.0
CG A:LEU197 4.9 13.3 1.0
CG A:TYR157 5.0 16.7 1.0

Mercury binding site 7 out of 14 in 1piy

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Mercury binding site 7 out of 14 in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion 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 Soaked with Ferrous Ion at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg384

b:67.4
occ:0.30
 SG A:CYS214 2.6 17.1 1.0
OD1 A:ASN76 3.1 14.8 1.0
CB A:CYS214 3.6 16.4 1.0
HG A:HG380 3.6 20.1 0.8
NH2 A:ARG149 3.7 23.9 1.0
O A:VAL210 3.8 15.4 1.0
CG1 A:VAL210 3.8 15.4 1.0
NE1 A:TRP286 3.8 19.2 1.0
CA A:SER211 4.0 15.4 1.0
CG A:ASN76 4.0 14.8 1.0
CD1 A:LEU290 4.0 21.0 1.0
NH1 A:ARG149 4.1 23.9 1.0
C A:VAL210 4.2 15.4 1.0
CD1 A:TRP286 4.2 19.2 1.0
N A:SER211 4.3 15.4 1.0
CZ A:ARG149 4.3 23.8 1.0
CB A:ASN76 4.6 14.8 1.0
CD1 A:LEU304 4.6 17.9 1.0
CB A:SER211 4.7 15.5 1.0
CG A:LEU290 4.8 21.1 1.0
CB A:VAL210 4.9 15.4 1.0
CA A:CYS214 4.9 16.3 1.0
C A:SER211 4.9 15.5 1.0
ND2 A:ASN76 5.0 14.7 1.0
CE2 A:TRP286 5.0 19.2 1.0

Mercury binding site 8 out of 14 in 1piy

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Mercury binding site 8 out of 14 in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion 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 Soaked with Ferrous Ion at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg378

b:19.3
occ:0.70
 SG B:CYS196 2.2 16.7 1.0
HG B:HG382 3.0 16.3 0.3
O B:CYS196 3.0 16.7 1.0
CB B:CYS196 3.4 16.6 1.0
CA B:CYS196 3.4 16.7 1.0
CG2 B:VAL200 3.5 16.8 1.0
C B:CYS196 3.5 16.7 1.0
CD2 B:TYR157 3.6 17.2 1.0
CB B:TYR156 3.6 19.5 1.0
CE2 B:TYR157 3.7 17.0 1.0
CG B:TYR157 3.7 17.2 1.0
CD1 B:TYR157 3.8 17.1 1.0
CZ B:TYR157 3.8 17.0 1.0
CE1 B:TYR157 3.8 17.0 1.0
N B:TYR157 3.9 18.2 1.0
C B:TYR156 4.2 18.8 1.0
CB B:SER199 4.2 16.9 1.0
CA B:TYR157 4.3 17.7 1.0
OG B:SER199 4.4 17.2 1.0
N B:VAL200 4.5 16.7 1.0
CB B:TYR157 4.5 17.5 1.0
O B:ILE153 4.5 22.5 1.0
CA B:TYR156 4.5 19.3 1.0
OH B:TYR157 4.6 16.9 1.0
N B:LEU197 4.7 16.6 1.0
CG B:TYR156 4.7 19.8 1.0
O B:TYR156 4.7 18.7 1.0
CB B:VAL200 4.8 16.7 1.0
N B:CYS196 4.8 16.8 1.0

Mercury binding site 9 out of 14 in 1piy

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Mercury binding site 9 out of 14 in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion 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 Soaked with Ferrous Ion at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg379

b:21.6
occ:0.40
 SG B:CYS268 2.5 31.9 1.0
O B:CYS268 2.8 31.8 1.0
CB B:CYS268 3.3 31.9 1.0
C B:CYS268 3.4 31.8 1.0
CB B:CYS272 3.4 30.6 1.0
CD2 B:TYR194 3.6 17.2 1.0
CE2 B:TYR194 3.9 17.3 1.0
CA B:CYS268 3.9 31.8 1.0
CD2 B:LEU195 4.0 17.4 1.0
N B:CYS272 4.0 30.7 1.0
CA B:CYS272 4.1 30.5 1.0
N B:LYS269 4.3 31.8 1.0
O B:ALA265 4.4 31.3 1.0
SG B:CYS272 4.5 31.1 1.0
CA B:LYS269 4.7 31.7 1.0
CG B:LEU195 4.7 17.3 1.0
N B:CYS268 4.7 31.8 1.0
CB B:GLU271 4.9 31.0 1.0
CG B:TYR194 4.9 17.1 1.0
CA B:ALA265 5.0 31.2 1.0

Mercury binding site 10 out of 14 in 1piy

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Mercury binding site 10 out of 14 in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg380

b:26.9
occ:0.40
 CD1 B:LEU304 2.4 26.6 1.0
SG B:CYS214 2.5 12.9 1.0
O B:VAL210 2.7 16.4 1.0
CD2 B:LEU304 2.8 26.6 1.0
CG B:LEU304 3.2 26.6 1.0
N B:CYS214 3.2 15.4 1.0
CB B:ALA213 3.5 15.7 1.0
CB B:CYS214 3.6 14.8 1.0
CA B:CYS214 3.6 15.2 1.0
CG1 B:VAL210 3.7 16.6 1.0
HG B:HG384 3.7 33.5 0.3
C B:VAL210 3.8 16.4 1.0
C B:ALA213 3.9 15.6 1.0
CD1 B:LEU299 4.1 31.2 1.0
CA B:ALA213 4.2 15.7 1.0
CB B:LEU304 4.3 26.5 1.0
CA B:VAL210 4.4 16.5 1.0
N B:ALA213 4.6 15.7 1.0
CB B:VAL210 4.7 16.6 1.0
O B:ALA213 4.7 15.6 1.0
N B:SER211 4.8 16.3 1.0
CD2 B:LEU299 4.9 31.2 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 Aug 11 01:02:47 2024

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