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Mercury in PDB 1r65: Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli

Enzymatic activity of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli

All present enzymatic activity of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli, PDB code: 1r65 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) 25.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.170, 84.220, 114.220, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.6

Other elements in 1r65:

The structure of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Mercury atom in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli (pdb code 1r65). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 13 binding sites of Mercury where determined in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli, PDB code: 1r65:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 13 in 1r65

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Mercury binding site 1 out of 13 in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg901

b:35.1
occ:0.70
 SG A:CYS272 2.4 31.9 1.0
OH A:TYR194 2.7 25.3 1.0
CB A:CYS272 3.3 27.8 1.0
O A:ALA265 3.7 36.7 1.0
CE A:MET198 3.7 33.7 1.0
CZ A:TYR194 3.7 28.0 1.0
CE2 A:TYR194 3.8 25.9 1.0
CD2 A:LEU321 4.0 31.8 1.0
CA A:LYS269 4.0 36.7 1.0
O A:HOH1013 4.4 33.8 1.0
N A:LYS269 4.4 36.4 1.0
C A:ALA265 4.5 35.7 1.0
O A:LYS269 4.6 33.0 1.0
O A:CYS268 4.6 37.5 1.0
C A:CYS268 4.7 38.6 1.0
CA A:CYS272 4.7 27.6 1.0
CA A:ALA265 4.8 33.3 1.0
C A:LYS269 4.8 35.9 1.0
CG A:LYS269 4.8 49.0 1.0
CB A:LYS269 4.9 41.6 1.0
CG A:LEU321 4.9 29.2 1.0
CB A:ALA265 4.9 31.2 1.0

Mercury binding site 2 out of 13 in 1r65

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Mercury binding site 2 out of 13 in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg902

b:37.1
occ:0.80
 SG A:CYS196 2.4 31.2 1.0
O A:CYS196 3.1 25.9 1.0
HG A:HG910 3.1 46.0 0.3
CB A:CYS196 3.5 28.0 1.0
CA A:CYS196 3.5 25.4 1.0
CE1 A:TYR157 3.5 29.3 1.0
CD1 A:TYR157 3.5 25.9 1.0
C A:CYS196 3.6 23.9 1.0
CG2 A:VAL200 3.7 29.7 1.0
CZ A:TYR157 3.8 27.6 1.0
CB A:TYR156 3.8 42.3 1.0
CG A:TYR157 3.8 27.1 1.0
CE2 A:TYR157 4.0 28.0 1.0
CD2 A:TYR157 4.0 26.9 1.0
N A:TYR157 4.1 30.7 1.0
CB A:SER199 4.2 29.1 1.0
OH A:TYR157 4.5 30.7 1.0
C A:TYR156 4.5 34.2 1.0
CA A:TYR157 4.5 28.3 1.0
O A:ILE153 4.6 29.8 1.0
N A:VAL200 4.6 24.3 1.0
CG A:TYR156 4.7 49.9 1.0
CB A:TYR157 4.7 26.6 1.0
CA A:TYR156 4.8 35.5 1.0
N A:LEU197 4.8 24.0 1.0
CD2 A:TYR156 4.8 52.7 1.0
N A:CYS196 4.9 23.9 1.0
OG A:SER199 4.9 33.1 1.0
CB A:VAL200 5.0 25.4 1.0

Mercury binding site 3 out of 13 in 1r65

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Mercury binding site 3 out of 13 in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg903

b:40.2
occ:0.50
 SG A:CYS214 2.3 40.6 1.0
O A:VAL210 2.8 29.8 1.0
HG A:HG911 3.2 75.1 0.3
N A:CYS214 3.3 33.4 1.0
CB A:CYS214 3.6 37.0 1.0
CB A:ALA213 3.7 30.8 1.0
CA A:CYS214 3.8 34.1 1.0
C A:VAL210 4.0 30.4 1.0
C A:ALA213 4.0 31.6 1.0
CG1 A:VAL210 4.0 32.2 1.0
CD1 A:LEU299 4.1 40.2 1.0
CD1 A:LEU304 4.1 33.8 1.0
CA A:ALA213 4.4 31.5 1.0
CG A:LEU304 4.5 32.9 1.0
CA A:VAL210 4.7 28.9 1.0
CB A:LEU304 4.8 31.8 1.0
O A:ALA213 4.8 33.3 1.0
N A:ALA213 4.8 30.1 1.0
N A:SER211 5.0 28.9 1.0

Mercury binding site 4 out of 13 in 1r65

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Mercury binding site 4 out of 13 in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg907

b:51.9
occ:0.40
 OE2 A:GLU309 2.9 34.5 1.0
CD A:GLU309 3.3 33.9 1.0
O A:CYS305 3.5 29.2 1.0
C A:CYS305 3.5 31.2 1.0
CB A:CYS305 3.6 34.5 1.0
N A:GLN306 3.7 30.0 1.0
OE1 A:GLU309 3.9 34.6 1.0
CA A:GLN306 3.9 29.8 1.0
CG A:GLU309 4.0 30.9 1.0
CA A:CYS305 4.2 32.1 1.0
CG A:GLN306 4.3 36.1 1.0
NZ A:LYS284 4.3 41.4 1.0
NH2 A:ARG328 4.4 47.2 1.0
CE A:LYS284 4.6 36.8 1.0
CB A:GLN306 4.7 31.5 1.0
CB A:GLU309 4.8 27.4 1.0
O A:ASP302 4.9 36.2 1.0

Mercury binding site 5 out of 13 in 1r65

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Mercury binding site 5 out of 13 in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg910

b:46.0
occ:0.30
 SG A:CYS196 2.1 31.2 1.0
HG A:HG902 3.1 37.1 0.8
CB A:CYS196 3.2 28.0 1.0
CE1 A:TYR157 3.3 29.3 1.0
CG2 A:VAL200 3.3 29.7 1.0
O A:CYS196 3.3 25.9 1.0
C A:CYS196 3.4 23.9 1.0
N A:LEU197 3.8 24.0 1.0
CA A:CYS196 3.8 25.4 1.0
CD1 A:TYR157 3.9 25.9 1.0
CD2 A:LEU95 4.0 32.3 1.0
CZ A:TYR157 4.1 27.6 1.0
CA A:LEU197 4.2 24.0 1.0
CD2 A:LEU197 4.2 28.6 1.0
OH A:TYR157 4.3 30.7 1.0
CB A:VAL200 4.4 25.4 1.0
CG A:LEU95 4.6 28.8 1.0
CD1 A:LEU95 4.6 31.6 1.0
CD2 A:LEU160 4.7 25.0 1.0
CG A:LEU197 4.8 28.5 1.0

Mercury binding site 6 out of 13 in 1r65

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Mercury binding site 6 out of 13 in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg911

b:75.1
occ:0.30
 SG A:CYS214 2.3 40.6 1.0
HG A:HG903 3.2 40.2 0.5
OD1 A:ASN76 3.3 30.4 1.0
O A:VAL210 3.5 29.8 1.0
CB A:CYS214 3.6 37.0 1.0
CG1 A:VAL210 3.6 32.2 1.0
CD1 A:LEU290 3.7 38.9 1.0
NH2 A:ARG149 4.0 41.2 1.0
C A:VAL210 4.0 30.4 1.0
NE1 A:TRP286 4.1 33.7 1.0
CA A:SER211 4.1 31.1 1.0
CD1 A:LEU304 4.1 33.8 1.0
CD1 A:TRP286 4.3 32.8 1.0
CG A:ASN76 4.3 29.8 1.0
N A:SER211 4.3 28.9 1.0
NH1 A:ARG149 4.5 39.4 1.0
CZ A:ARG149 4.7 39.9 1.0
CG A:LEU290 4.7 40.5 1.0
CB A:VAL210 4.8 30.3 1.0
CA A:CYS214 4.8 34.1 1.0
N A:CYS214 4.9 33.4 1.0
CB A:ASN76 5.0 27.2 1.0
C A:SER211 5.0 31.6 1.0
CB A:SER211 5.0 32.7 1.0

Mercury binding site 7 out of 13 in 1r65

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Mercury binding site 7 out of 13 in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg904

b:39.0
occ:0.70
 SG B:CYS196 2.2 35.3 1.0
O B:CYS196 3.1 27.3 1.0
HG B:HG912 3.2 38.6 0.3
CB B:CYS196 3.4 29.6 1.0
CA B:CYS196 3.5 28.1 1.0
CB B:TYR156 3.6 40.0 1.0
CG2 B:VAL200 3.6 30.5 1.0
C B:CYS196 3.6 27.8 1.0
CD2 B:TYR157 3.7 30.4 1.0
CE2 B:TYR157 3.7 26.6 1.0
CG B:TYR157 3.8 26.9 1.0
CZ B:TYR157 3.9 28.9 1.0
CD1 B:TYR157 4.0 25.9 1.0
N B:TYR157 4.0 29.1 1.0
CE1 B:TYR157 4.0 26.9 1.0
CB B:SER199 4.2 30.8 1.0
C B:TYR156 4.3 32.6 1.0
CA B:TYR157 4.4 28.6 1.0
CG B:TYR156 4.5 45.7 1.0
CA B:TYR156 4.6 35.3 1.0
O B:ILE153 4.6 29.5 1.0
OH B:TYR157 4.6 30.2 1.0
CB B:TYR157 4.7 27.5 1.0
N B:VAL200 4.7 27.0 1.0
N B:LEU197 4.8 27.6 1.0
O B:TYR156 4.9 32.1 1.0
N B:CYS196 4.9 26.8 1.0
OG B:SER199 4.9 33.1 1.0
CB B:VAL200 4.9 26.8 1.0

Mercury binding site 8 out of 13 in 1r65

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Mercury binding site 8 out of 13 in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg905

b:0.2
occ:0.40
 SG B:CYS268 2.5 59.5 1.0
CD2 B:LEU195 2.6 37.7 1.0
CB B:CYS268 3.1 59.5 1.0
CD2 B:TYR194 3.3 36.0 1.0
O B:CYS268 3.3 58.1 1.0
CE2 B:TYR194 3.4 38.0 1.0
CB B:CYS272 3.6 50.8 1.0
CG B:LEU195 3.7 35.9 1.0
C B:CYS268 3.8 58.7 1.0
CA B:CYS268 4.1 58.9 1.0
N B:CYS272 4.1 49.5 1.0
CA B:CYS272 4.1 48.8 1.0
SG B:CYS272 4.5 61.3 1.0
HG B:HG908 4.5 42.6 0.3
CD1 B:LEU195 4.6 39.1 1.0
CG B:TYR194 4.6 33.3 1.0
CZ B:TYR194 4.7 36.5 1.0
N B:CYS268 4.8 58.7 1.0
CA B:LEU195 4.8 29.4 1.0
N B:LYS269 4.8 58.9 1.0
CB B:LEU195 4.8 33.2 1.0
CB B:GLU271 4.9 51.1 1.0
N B:LEU195 5.0 28.6 1.0

Mercury binding site 9 out of 13 in 1r65

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Mercury binding site 9 out of 13 in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg906

b:62.9
occ:0.40
 CD1 B:LEU304 2.5 48.8 1.0
SG B:CYS214 2.7 35.9 1.0
O B:VAL210 2.8 26.8 1.0
CB B:ALA213 3.2 33.8 1.0
N B:CYS214 3.4 34.7 1.0
HG B:HG914 3.4 42.3 0.3
CG B:LEU304 3.6 46.5 1.0
CD2 B:LEU304 3.6 48.8 1.0
C B:VAL210 3.9 28.3 1.0
CB B:CYS214 3.9 35.7 1.0
C B:ALA213 3.9 34.3 1.0
CG1 B:VAL210 3.9 33.8 1.0
CA B:CYS214 4.0 32.2 1.0
CA B:ALA213 4.1 33.7 1.0
CD1 B:LEU299 4.2 53.0 1.0
CB B:LEU304 4.3 43.7 1.0
CA B:VAL210 4.5 29.6 1.0
N B:ALA213 4.6 31.5 1.0
CD2 B:LEU299 4.7 52.2 1.0
O B:ALA213 4.8 34.5 1.0
CB B:VAL210 4.9 31.1 1.0
N B:SER211 5.0 26.8 1.0
CA B:LEU304 5.0 41.3 1.0

Mercury binding site 10 out of 13 in 1r65

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Mercury binding site 10 out of 13 in the Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Crystal Structure of Ferrous Soaked Ribonucleotide Reductase R2 Subunit (Wildtype) at pH 5 From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg908

b:42.6
occ:0.30
 OH B:TYR194 2.9 41.6 1.0
O B:ALA265 3.5 52.2 1.0
SG B:CYS272 3.5 61.3 1.0
CE2 B:TYR194 3.6 38.0 1.0
CB B:CYS272 3.6 50.8 1.0
CZ B:TYR194 3.7 36.5 1.0
CD2 B:LEU321 3.9 40.7 1.0
CE B:MET198 4.0 42.3 1.0
CA B:LYS269 4.2 59.4 1.0
C B:ALA265 4.3 52.1 1.0
HG B:HG905 4.5 0.2 0.4
CA B:ALA265 4.6 50.6 1.0
N B:LYS269 4.7 58.9 1.0
CB B:ALA265 4.8 50.2 1.0
O B:CYS268 4.8 58.1 1.0
CB B:LYS269 4.9 63.5 1.0
CG B:LEU321 4.9 43.1 1.0
CD2 B:TYR194 4.9 36.0 1.0
O B:LYS269 5.0 57.1 1.0
C B:CYS268 5.0 58.7 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 01:17:04 2024

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