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Mercury in PDB 1jqc: Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine

Enzymatic activity of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine

All present enzymatic activity of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine:
1.17.4.1;

Protein crystallography data

The structure of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine, PDB code: 1jqc was solved by M.Hogbom, M.E.Andersson, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.00 / 1.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.848, 84.554, 114.286, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.9

Other elements in 1jqc:

The structure of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Mercury Binding Sites:

Pages:

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

Binding sites:

The binding sites of Mercury atom in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine (pdb code 1jqc). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 13 binding sites of Mercury where determined in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine, PDB code: 1jqc:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 13 in 1jqc

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Mercury binding site 1 out of 13 in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg901

b:16.1
occ:0.82
 SG A:CYS196 2.3 16.0 1.0
HG A:HG908 3.0 25.7 0.2
O A:HOH950 3.1 31.0 1.0
O A:CYS196 3.4 13.9 1.0
CB A:CYS196 3.4 11.2 1.0
CA A:CYS196 3.4 13.5 1.0
CE1 A:TYR157 3.5 15.3 1.0
CD1 A:TYR157 3.5 14.0 1.0
CG2 A:VAL200 3.7 15.6 1.0
C A:CYS196 3.7 13.4 1.0
CG A:TYR157 3.8 13.2 1.0
CZ A:TYR157 3.8 14.0 1.0
CB A:TYR156 3.9 29.2 1.0
CD2 A:TYR157 4.0 12.0 1.0
CE2 A:TYR157 4.1 13.5 1.0
N A:TYR157 4.1 13.0 1.0
OG A:SER199 4.2 35.5 1.0
CB A:SER199 4.3 19.9 1.0
CA A:TYR157 4.4 13.6 1.0
C A:TYR156 4.6 23.9 1.0
OH A:TYR157 4.6 18.5 1.0
CB A:TYR157 4.6 15.7 1.0
N A:VAL200 4.7 13.0 1.0
O A:ILE153 4.7 16.7 1.0
CG A:TYR156 4.8 37.8 1.0
N A:CYS196 4.8 13.1 1.0
N A:LEU197 4.9 11.2 1.0
CA A:TYR156 5.0 22.6 1.0
CD2 A:TYR156 5.0 38.5 1.0

Mercury binding site 2 out of 13 in 1jqc

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Mercury binding site 2 out of 13 in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg907

b:14.5
occ:0.67
 SG A:CYS272 2.3 17.7 1.0
O A:HOH1070 2.6 36.4 1.0
OH A:TYR194 2.7 18.4 1.0
CB A:CYS272 3.2 10.0 1.0
O A:ALA265 3.5 20.2 1.0
CA A:LYS269 3.8 20.5 1.0
CZ A:TYR194 3.8 14.7 1.0
CE A:MET198 3.9 14.1 1.0
CE2 A:TYR194 3.9 13.8 1.0
O A:HOH997 3.9 25.3 1.0
CD2 A:LEU321 4.0 20.9 1.0
CG A:LYS269 4.0 34.2 1.0
CB A:LYS269 4.3 26.2 1.0
N A:LYS269 4.3 22.1 1.0
C A:ALA265 4.4 19.6 1.0
O A:HOH920 4.5 15.7 1.0
CA A:ALA265 4.6 17.6 1.0
O A:LYS269 4.6 17.8 1.0
CA A:CYS272 4.7 14.0 1.0
C A:LYS269 4.7 20.5 1.0
C A:CYS268 4.7 22.0 1.0
O A:CYS268 4.7 19.9 1.0
CB A:ALA265 4.8 16.9 1.0
CG A:LEU321 4.9 19.1 1.0

Mercury binding site 3 out of 13 in 1jqc

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Mercury binding site 3 out of 13 in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg908

b:25.7
occ:0.17
 SG A:CYS196 1.8 16.0 1.0
HG A:HG901 3.0 16.1 0.8
CG2 A:VAL200 3.1 15.6 1.0
CE1 A:TYR157 3.1 15.3 1.0
CB A:CYS196 3.2 11.2 1.0
C A:CYS196 3.4 13.4 1.0
O A:CYS196 3.5 13.9 1.0
CD1 A:TYR157 3.7 14.0 1.0
CD2 A:LEU95 3.7 17.6 1.0
CA A:CYS196 3.8 13.5 1.0
N A:LEU197 3.9 11.2 1.0
CZ A:TYR157 4.0 14.0 1.0
OH A:TYR157 4.2 18.5 1.0
CA A:LEU197 4.3 13.4 1.0
CD1 A:LEU95 4.4 20.0 1.0
CB A:VAL200 4.4 13.8 1.0
CG A:LEU95 4.4 18.1 1.0
CD2 A:LEU197 4.5 20.5 1.0
CD2 A:LEU160 4.7 13.8 1.0
CG A:TYR157 4.8 13.2 1.0
CG A:LEU197 5.0 15.4 1.0

Mercury binding site 4 out of 13 in 1jqc

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Mercury binding site 4 out of 13 in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg909

b:17.7
occ:0.55
 SG A:CYS214 2.4 28.0 1.0
O A:VAL210 2.9 20.4 1.0
CD1 A:LEU304 3.0 35.8 1.0
N A:CYS214 3.3 20.2 1.0
CB A:CYS214 3.5 21.1 1.0
CA A:CYS214 3.6 17.9 1.0
CB A:ALA213 3.8 24.1 1.0
CG1 A:VAL210 3.9 21.4 1.0
CD1 A:LEU299 3.9 23.1 1.0
C A:VAL210 4.0 16.8 1.0
C A:ALA213 4.0 20.9 1.0
CG A:LEU304 4.2 24.2 1.0
CD2 A:LEU304 4.2 25.3 1.0
CA A:ALA213 4.4 19.6 1.0
CA A:VAL210 4.6 20.3 1.0
O A:HOH957 4.7 31.5 1.0
O A:ALA213 4.7 22.3 1.0
CB A:LEU304 4.9 18.9 1.0
N A:ALA213 4.9 20.5 1.0
CB A:VAL210 4.9 24.0 1.0

Mercury binding site 5 out of 13 in 1jqc

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Mercury binding site 5 out of 13 in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg912

b:25.9
occ:0.50
 O A:HOH978 2.2 19.7 1.0
OE2 A:GLU309 3.4 25.0 1.0
CB A:CYS305 3.4 24.6 1.0
C A:CYS305 3.5 18.8 1.0
CD A:GLU309 3.6 18.1 1.0
O A:CYS305 3.7 19.9 1.0
N A:GLN306 3.7 16.5 1.0
CG A:GLU309 3.9 16.8 1.0
CE A:LYS284 4.0 11.6 1.0
CA A:CYS305 4.1 22.3 1.0
CA A:GLN306 4.1 17.5 1.0
OE1 A:GLU309 4.1 21.9 1.0
NZ A:LYS284 4.2 29.1 1.0
CG A:GLN306 4.3 27.4 1.0
O A:HOH1048 4.5 35.5 1.0
SG A:CYS305 4.8 48.3 1.0
CB A:GLN306 4.9 23.1 1.0
NH2 A:ARG328 4.9 45.2 1.0
O A:ASP302 4.9 24.7 1.0

Mercury binding site 6 out of 13 in 1jqc

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Mercury binding site 6 out of 13 in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg902

b:27.0
occ:0.30
 SG B:CYS196 1.8 18.0 1.0
HG B:HG904 3.0 14.9 0.7
CE1 B:TYR157 3.1 16.8 1.0
CG2 B:VAL200 3.2 16.6 1.0
CB B:CYS196 3.3 12.6 1.0
C B:CYS196 3.5 10.7 1.0
O B:CYS196 3.5 15.5 1.0
CD1 B:TYR157 3.6 15.5 1.0
N B:LEU197 3.9 14.0 1.0
CZ B:TYR157 3.9 14.7 1.0
CA B:CYS196 3.9 11.7 1.0
CD2 B:LEU95 4.0 17.5 1.0
OH B:TYR157 4.2 18.0 1.0
CA B:LEU197 4.3 12.8 1.0
CD2 B:LEU197 4.3 18.7 1.0
CB B:VAL200 4.5 17.1 1.0
CD2 B:LEU160 4.6 17.0 1.0
CG B:TYR157 4.6 14.3 1.0
CG B:LEU95 4.7 18.3 1.0
CG B:LEU197 4.8 19.2 1.0
CD1 B:LEU95 4.8 19.1 1.0
CE2 B:TYR157 4.9 14.7 1.0

Mercury binding site 7 out of 13 in 1jqc

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Mercury binding site 7 out of 13 in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg903

b:34.5
occ:0.30
 O B:HOH920 2.3 11.5 1.0
CD2 B:LEU195 2.5 28.6 1.0
SG B:CYS272 2.5 51.8 1.0
SG B:CYS268 2.8 45.3 1.0
CB B:CYS268 3.2 40.6 1.0
O B:CYS268 3.3 31.9 1.0
CD1 B:TYR194 3.4 24.6 1.0
CE1 B:TYR194 3.5 30.3 1.0
CG B:LEU195 3.6 32.1 1.0
CB B:CYS272 3.8 35.1 1.0
C B:CYS268 3.8 35.7 1.0
CA B:CYS268 4.0 36.1 1.0
N B:CYS272 4.2 25.0 1.0
CD1 B:LEU195 4.2 33.2 1.0
CA B:CYS272 4.2 32.8 1.0
HG B:HG915 4.3 25.5 0.3
CG B:TYR194 4.7 22.3 1.0
O B:ALA265 4.7 30.3 1.0
N B:CYS268 4.8 38.8 1.0
N B:LYS269 4.8 30.4 1.0
CZ B:TYR194 4.8 24.2 1.0
CB B:LEU195 4.8 22.1 1.0
CA B:LEU195 4.9 22.1 1.0
N B:LEU195 5.0 17.5 1.0
CB B:GLU271 5.0 33.0 1.0

Mercury binding site 8 out of 13 in 1jqc

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Mercury binding site 8 out of 13 in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg904

b:14.9
occ:0.65
 SG B:CYS196 2.3 18.0 1.0
O B:HOH942 2.9 33.2 1.0
HG B:HG902 3.0 27.0 0.3
O B:CYS196 3.2 15.5 1.0
CB B:CYS196 3.3 12.6 1.0
CA B:CYS196 3.4 11.7 1.0
CD1 B:TYR157 3.5 15.5 1.0
CG2 B:VAL200 3.6 16.6 1.0
C B:CYS196 3.6 10.7 1.0
CE1 B:TYR157 3.6 16.8 1.0
CB B:TYR156 3.7 24.1 1.0
CG B:TYR157 3.7 14.3 1.0
N B:TYR157 3.8 14.3 1.0
CD2 B:TYR157 3.9 12.1 1.0
CZ B:TYR157 3.9 14.7 1.0
CE2 B:TYR157 4.0 14.7 1.0
CB B:SER199 4.2 18.7 1.0
C B:TYR156 4.2 21.0 1.0
CA B:TYR157 4.2 14.2 1.0
OG B:SER199 4.3 35.7 1.0
CB B:TYR157 4.5 14.5 1.0
O B:ILE153 4.6 18.0 1.0
CA B:TYR156 4.6 20.3 1.0
N B:VAL200 4.6 15.2 1.0
CG B:TYR156 4.7 32.6 1.0
OH B:TYR157 4.7 18.0 1.0
O B:TYR156 4.7 21.1 1.0
N B:LEU197 4.8 14.0 1.0
N B:CYS196 4.8 15.1 1.0
CB B:VAL200 5.0 17.1 1.0

Mercury binding site 9 out of 13 in 1jqc

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Mercury binding site 9 out of 13 in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg906

b:20.3
occ:0.29
 O B:HOH1246 2.9 64.5 1.0
CE B:MET296 2.9 61.1 1.0
O B:CYS214 3.1 21.1 1.0
CG2 B:ILE72 3.1 25.2 1.0
CB B:CYS214 3.1 31.9 1.0
CA B:CYS214 3.2 20.5 1.0
SD B:MET296 3.2 60.0 1.0
CE2 B:PHE218 3.4 23.3 1.0
C B:CYS214 3.4 22.3 1.0
CD2 B:PHE218 4.0 20.8 1.0
CD2 B:LEU299 4.0 29.8 1.0
CZ B:PHE218 4.1 24.3 1.0
CZ B:PHE291 4.4 44.4 1.0
CB B:ILE72 4.5 23.9 1.0
N B:CYS214 4.5 17.3 1.0
N B:SER215 4.6 17.9 1.0
CB B:ALA217 4.7 19.8 1.0
SG B:CYS214 4.8 51.7 1.0
CG B:MET296 4.9 60.8 1.0
HG B:HG914 4.9 21.6 0.3

Mercury binding site 10 out of 13 in 1jqc

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Mercury binding site 10 out of 13 in the Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Mn Substituted Ribonucleotide Reductase R2 From E. Coli Oxidized By Hydrogen Peroxide and Hydroxylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg911

b:28.5
occ:0.60
 CG B:MET198 2.6 27.1 1.0
CG B:LEU275 2.6 37.0 1.0
CD2 B:LEU275 2.7 41.0 1.0
O B:CYS272 2.8 28.0 1.0
CD1 B:LEU275 3.0 37.4 1.0
CA B:CYS272 3.1 32.8 1.0
C B:CYS272 3.3 30.7 1.0
CB B:MET198 3.4 18.4 1.0
CB B:CYS272 3.4 35.1 1.0
CD2 B:PHE276 3.5 32.3 1.0
CE2 B:PHE276 3.6 31.9 1.0
SG B:CYS272 3.7 51.8 1.0
CB B:LEU275 4.0 31.2 1.0
SD B:MET198 4.1 22.0 1.0
N B:PHE276 4.4 25.1 1.0
N B:CYS272 4.5 25.0 1.0
CG B:PHE276 4.5 24.8 1.0
CA B:MET198 4.5 20.6 1.0
N B:TYR273 4.6 25.1 1.0
C B:MET198 4.6 15.7 1.0
CD2 B:LEU195 4.7 28.6 1.0
CZ B:PHE276 4.7 26.6 1.0
CE B:MET198 4.8 27.8 1.0
O B:MET198 4.8 16.4 1.0
C B:LEU275 4.9 28.7 1.0
CA B:LEU275 4.9 28.3 1.0
CD1 B:LEU321 5.0 28.6 1.0
O B:GLU271 5.0 31.3 1.0
N B:SER199 5.0 14.9 1.0

Reference:

M.Hogbom, M.E.Andersson, P.Nordlund. Crystal Structures of Oxidized Dinuclear Manganese Centres in Mn-Substituted Class I Ribonucleotide Reductase From Escherichia Coli: Carboxylate Shifts with Implications For O2 Activation and Radical Generation. J.Biol.Inorg.Chem. V. 6 315 2001.
ISSN: ISSN 0949-8257
PubMed: 11315567
DOI: 10.1007/S007750000205
Page generated: Sun Aug 11 00:17:41 2024

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