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Mercury in PDB 1pj1: Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5

Enzymatic activity of Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5

All present enzymatic activity of Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5:
1.17.4.1;

Protein crystallography data

The structure of Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5, PDB code: 1pj1 was solved by W.C.Voegtli, M.Sommerhalter, L.Saleh, J.Baldwin, J.M.Bollingerjr., A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.100, 84.200, 114.700, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.1

Other elements in 1pj1:

The structure of Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5 also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Mercury atom in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5 (pdb code 1pj1). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 15 binding sites of Mercury where determined in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5, PDB code: 1pj1:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 15 in 1pj1

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Mercury binding site 1 out of 15 in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5


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 Soaked with Ferrous Ions at pH 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg408

b:20.3
occ:0.50
 SG A:CYS272 2.6 31.2 1.0
OH A:TYR194 3.2 31.1 1.0
CB A:CYS272 3.4 27.9 1.0
CE2 A:TYR194 3.7 26.6 1.0
O A:ALA265 3.7 31.0 1.0
HG A:HG414 3.8 19.9 0.2
CZ A:TYR194 3.9 25.3 1.0
CA A:LYS269 4.0 31.6 1.0
CE A:MET198 4.0 19.4 1.0
CD2 A:LEU321 4.0 19.7 1.0
C A:ALA265 4.5 31.4 1.0
CB A:LYS269 4.5 35.6 1.0
N A:LYS269 4.6 30.5 1.0
O A:CYS268 4.6 28.9 1.0
CA A:ALA265 4.7 29.7 1.0
O A:LYS269 4.7 28.4 1.0
CB A:ALA265 4.7 28.4 1.0
CA A:CYS272 4.8 25.0 1.0
C A:CYS268 4.9 31.3 1.0
C A:LYS269 4.9 29.8 1.0
CG A:LEU321 4.9 19.6 1.0
CD2 A:TYR194 4.9 24.7 1.0

Mercury binding site 2 out of 15 in 1pj1

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Mercury binding site 2 out of 15 in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5


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 Soaked with Ferrous Ions at pH 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg409

b:12.1
occ:0.50
 SG A:CYS196 2.2 23.5 1.0
HG A:HG413 3.1 28.6 0.2
O A:CYS196 3.1 16.5 1.0
CB A:CYS196 3.3 17.5 1.0
CA A:CYS196 3.4 17.2 1.0
CD2 A:TYR157 3.5 12.4 1.0
C A:CYS196 3.6 16.0 1.0
CE2 A:TYR157 3.6 12.7 1.0
CB A:TYR156 3.7 39.7 1.0
CG A:TYR157 3.8 15.2 1.0
CZ A:TYR157 3.9 16.3 1.0
N A:TYR157 4.0 23.7 1.0
CD1 A:TYR157 4.1 16.6 1.0
CE1 A:TYR157 4.1 17.0 1.0
CB A:SER199 4.2 19.4 1.0
CA A:TYR157 4.4 20.5 1.0
C A:TYR156 4.4 28.7 1.0
O A:ILE153 4.6 23.7 1.0
CB A:TYR157 4.6 18.6 1.0
CG A:TYR156 4.6 49.3 1.0
N A:VAL200 4.7 14.6 1.0
OH A:TYR157 4.7 19.2 1.0
CA A:TYR156 4.7 32.5 1.0
N A:CYS196 4.8 18.1 1.0
N A:LEU197 4.8 17.2 1.0
OG A:SER199 4.9 23.9 1.0
CB A:VAL200 5.0 17.9 1.0

Mercury binding site 3 out of 15 in 1pj1

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Mercury binding site 3 out of 15 in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5


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 Soaked with Ferrous Ions at pH 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg410

b:30.2
occ:0.75
 SG A:CYS214 2.3 32.5 1.0
O A:VAL210 2.9 19.7 1.0
N A:CYS214 3.3 24.9 1.0
CB A:CYS214 3.6 26.4 1.0
CA A:CYS214 3.7 26.5 1.0
CB A:ALA213 3.7 25.0 1.0
C A:ALA213 4.0 23.7 1.0
CD1 A:LEU299 4.0 30.3 1.0
C A:VAL210 4.1 23.4 1.0
CD1 A:LEU304 4.1 25.8 1.0
CG1 A:VAL210 4.1 25.3 1.0
CA A:ALA213 4.4 23.9 1.0
CG A:LEU304 4.4 25.1 1.0
O A:ALA213 4.8 25.5 1.0
CA A:VAL210 4.8 22.3 1.0
CB A:LEU304 4.8 24.8 1.0
N A:ALA213 4.9 23.2 1.0

Mercury binding site 4 out of 15 in 1pj1

Go back to Mercury Binding Sites List in 1pj1
Mercury binding site 4 out of 15 in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5


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 Soaked with Ferrous Ions at pH 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg411

b:47.7
occ:0.40
 OE2 A:GLU309 3.3 26.6 1.0
CD A:GLU309 3.4 24.9 1.0
CB A:CYS305 3.4 27.4 1.0
C A:CYS305 3.5 23.2 1.0
O A:CYS305 3.6 22.8 1.0
N A:GLN306 3.7 23.4 1.0
OE1 A:GLU309 3.8 26.5 1.0
CG A:GLU309 4.0 22.6 1.0
CA A:GLN306 4.0 22.7 1.0
CA A:CYS305 4.1 25.3 1.0
NZ A:LYS284 4.2 31.1 1.0
CE A:LYS284 4.3 26.6 1.0
CG A:GLN306 4.3 25.1 1.0
O A:HOH558 4.4 43.2 1.0
NH1 A:ARG328 4.5 56.0 1.0
CB A:GLN306 4.8 23.9 1.0
SG A:CYS305 4.9 37.3 1.0
O A:ASP302 4.9 28.8 1.0
CB A:GLU309 5.0 20.5 1.0

Mercury binding site 5 out of 15 in 1pj1

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Mercury binding site 5 out of 15 in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5


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 Soaked with Ferrous Ions at pH 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg412

b:80.8
occ:0.25
 CB A:CYS268 2.8 35.4 1.0
SG A:CYS268 3.4 32.7 1.0
CD A:LYS191 3.5 39.0 1.0
N A:CYS268 3.6 34.4 1.0
CA A:CYS268 3.7 33.2 1.0
CE A:LYS191 3.7 43.6 1.0
CG A:LYS191 3.7 33.0 1.0
O A:ILE264 3.8 25.0 1.0
CG2 A:ILE264 3.9 21.4 1.0
C A:GLU267 4.1 37.8 1.0
CB A:GLU267 4.1 46.2 1.0
CB A:LYS191 4.2 26.2 1.0
NZ A:LYS191 4.2 46.7 1.0
O A:GLU267 4.6 39.2 1.0
C A:ILE264 4.6 24.2 1.0
OE1 A:GLU267 4.7 57.4 1.0
CA A:GLU267 4.7 40.2 1.0
CA A:ILE264 4.8 23.9 1.0
CB A:ILE264 4.9 22.9 1.0

Mercury binding site 6 out of 15 in 1pj1

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Mercury binding site 6 out of 15 in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5


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 Soaked with Ferrous Ions at pH 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg413

b:28.6
occ:0.25
 SG A:CYS196 2.1 23.5 1.0
HG A:HG409 3.1 12.1 0.5
CE2 A:TYR157 3.2 12.7 1.0
O A:CYS196 3.3 16.5 1.0
CB A:CYS196 3.4 17.5 1.0
C A:CYS196 3.4 16.0 1.0
CD2 A:TYR157 3.8 12.4 1.0
N A:LEU197 3.9 17.2 1.0
CG1 A:VAL200 3.9 23.2 1.0
CA A:CYS196 4.0 17.2 1.0
CZ A:TYR157 4.0 16.3 1.0
CD2 A:LEU95 4.0 21.3 1.0
CD1 A:LEU197 4.2 31.3 1.0
CB A:VAL200 4.2 17.9 1.0
CA A:LEU197 4.3 17.8 1.0
OH A:TYR157 4.3 19.2 1.0
CD1 A:LEU95 4.6 20.1 1.0
CG A:LEU95 4.6 19.5 1.0
CD2 A:LEU160 4.8 16.2 1.0
CG A:TYR157 4.9 15.2 1.0
CG A:LEU197 5.0 26.8 1.0

Mercury binding site 7 out of 15 in 1pj1

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Mercury binding site 7 out of 15 in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5


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 Soaked with Ferrous Ions at pH 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg414

b:19.9
occ:0.25
 SG A:CYS272 2.2 31.2 1.0
SG A:CYS268 2.5 32.7 1.0
O A:CYS268 2.7 28.9 1.0
CD2 A:LEU195 3.1 23.1 1.0
CE2 A:TYR194 3.2 26.6 1.0
CB A:CYS268 3.3 35.4 1.0
CD2 A:TYR194 3.3 24.7 1.0
C A:CYS268 3.4 31.3 1.0
CB A:CYS272 3.6 27.9 1.0
N A:CYS272 3.7 25.5 1.0
HG A:HG408 3.8 20.3 0.5
CA A:CYS268 3.9 33.2 1.0
CA A:CYS272 4.0 25.0 1.0
CG A:LEU195 4.2 22.7 1.0
N A:LYS269 4.2 30.5 1.0
CZ A:TYR194 4.4 25.3 1.0
CB A:GLU271 4.4 33.4 1.0
O A:ALA265 4.5 31.0 1.0
CA A:LYS269 4.6 31.6 1.0
C A:GLU271 4.7 28.0 1.0
CG A:TYR194 4.7 23.0 1.0
N A:CYS268 4.8 34.4 1.0
OH A:TYR194 4.9 31.1 1.0

Mercury binding site 8 out of 15 in 1pj1

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Mercury binding site 8 out of 15 in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5


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 Soaked with Ferrous Ions at pH 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg410

b:20.0
occ:0.50
 SG B:CYS196 2.1 20.9 1.0
HG B:HG417 3.0 17.3 0.4
O B:CYS196 3.0 14.9 1.0
CB B:CYS196 3.3 16.8 1.0
CA B:CYS196 3.3 15.3 1.0
CG2 B:VAL200 3.5 18.5 1.0
C B:CYS196 3.5 13.9 1.0
CB B:TYR156 3.6 24.5 1.0
CD1 B:TYR157 3.6 14.7 1.0
CG B:TYR157 3.7 13.8 1.0
CD2 B:TYR157 3.8 12.5 1.0
CE1 B:TYR157 3.8 13.3 1.0
N B:TYR157 3.8 17.7 1.0
CE2 B:TYR157 3.9 13.1 1.0
CZ B:TYR157 3.9 14.2 1.0
C B:TYR156 4.1 19.2 1.0
CB B:SER199 4.2 15.7 1.0
CA B:TYR157 4.2 16.4 1.0
OG B:SER199 4.3 20.4 1.0
CB B:TYR157 4.4 14.8 1.0
CA B:TYR156 4.5 21.4 1.0
O B:ILE153 4.5 18.9 1.0
N B:VAL200 4.6 15.6 1.0
O B:TYR156 4.6 15.9 1.0
CG B:TYR156 4.7 27.4 1.0
N B:LEU197 4.7 13.5 1.0
N B:CYS196 4.7 16.0 1.0
CB B:VAL200 4.8 15.6 1.0
OH B:TYR157 4.8 13.6 1.0

Mercury binding site 9 out of 15 in 1pj1

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Mercury binding site 9 out of 15 in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5


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 Soaked with Ferrous Ions at pH 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg411

b:25.8
occ:0.75
 SG B:CYS272 2.3 26.9 1.0
SG B:CYS268 2.3 33.3 1.0
O B:CYS268 2.7 32.1 1.0
O B:HOH512 3.0 30.0 1.0
CB B:CYS268 3.2 33.7 1.0
CB B:CYS272 3.4 22.0 1.0
C B:CYS268 3.4 33.5 1.0
CD2 B:TYR194 3.6 20.6 1.0
CD2 B:LEU195 3.6 24.9 1.0
N B:CYS272 3.9 22.2 1.0
CA B:CYS268 3.9 33.4 1.0
CE2 B:TYR194 4.0 21.9 1.0
CA B:CYS272 4.1 22.1 1.0
N B:LYS269 4.3 34.9 1.0
O B:ALA265 4.4 25.9 1.0
CG B:LEU195 4.6 22.2 1.0
CA B:LYS269 4.7 37.1 1.0
N B:CYS268 4.8 33.7 1.0
CG B:TYR194 4.8 19.3 1.0
CB B:GLU271 4.8 24.8 1.0
C B:GLU271 4.9 23.8 1.0
CA B:ALA265 4.9 26.5 1.0

Mercury binding site 10 out of 15 in 1pj1

Go back to Mercury Binding Sites List in 1pj1
Mercury binding site 10 out of 15 in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5


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-D84E/W48F Soaked with Ferrous Ions at pH 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg412

b:19.6
occ:0.25
 SG B:CYS214 2.6 32.9 1.0
O B:VAL210 2.8 27.6 1.0
N B:CYS214 3.5 27.3 1.0
CD1 B:LEU304 3.5 45.6 1.0
CB B:ALA213 3.7 25.8 1.0
CG B:LEU304 3.7 43.5 1.0
CB B:CYS214 3.8 29.6 1.0
CG1 B:VAL210 3.9 28.9 1.0
C B:VAL210 3.9 26.2 1.0
CA B:CYS214 3.9 27.8 1.0
C B:ALA213 4.1 25.9 1.0
CD1 B:LEU299 4.2 49.9 1.0
CD2 B:LEU299 4.2 50.8 1.0
CA B:ALA213 4.4 25.0 1.0
CB B:LEU304 4.4 40.7 1.0
CA B:VAL210 4.5 27.0 1.0
N B:ALA213 4.8 23.0 1.0
CG B:LEU299 4.8 49.0 1.0
CB B:VAL210 4.9 27.4 1.0
O B:ALA213 4.9 26.2 1.0
N B:SER211 4.9 25.5 1.0
CD2 B:LEU304 4.9 45.3 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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