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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

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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

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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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