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Mercury in PDB 1xik: Ribonucleoside-Diphosphate Reductase 1 Beta Chain

Enzymatic activity of Ribonucleoside-Diphosphate Reductase 1 Beta Chain

All present enzymatic activity of Ribonucleoside-Diphosphate Reductase 1 Beta Chain:
1.17.4.1;

Protein crystallography data

The structure of Ribonucleoside-Diphosphate Reductase 1 Beta Chain, PDB code: 1xik was solved by D.T.Logan, X.-D.Su, A.Aberg, K.Regnstrom, J.Hajdu, H.Eklund, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.440, 83.530, 113.700, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 28

Other elements in 1xik:

The structure of Ribonucleoside-Diphosphate Reductase 1 Beta Chain also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain (pdb code 1xik). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 10 binding sites of Mercury where determined in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain, PDB code: 1xik:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 10 in 1xik

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Mercury binding site 1 out of 10 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg378

b:33.9
occ:0.82
 SG A:CYS196 2.3 26.7 1.0
O A:HOH399 2.5 28.9 1.0
HG A:HG381 3.0 27.3 0.3
O A:CYS196 3.2 21.8 1.0
CA A:CYS196 3.3 20.8 1.0
CB A:TYR156 3.3 40.1 1.0
CB A:CYS196 3.3 22.2 1.0
CD1 A:TYR157 3.5 21.5 1.0
CG2 A:VAL200 3.5 23.6 1.0
C A:CYS196 3.6 21.9 1.0
CE1 A:TYR157 3.6 21.0 1.0
CG A:TYR157 3.7 20.4 1.0
N A:TYR157 3.7 28.2 1.0
CZ A:TYR157 3.9 23.6 1.0
CD2 A:TYR157 4.0 19.6 1.0
CE2 A:TYR157 4.1 19.4 1.0
C A:TYR156 4.1 34.5 1.0
CA A:TYR157 4.2 25.3 1.0
CA A:TYR156 4.3 35.1 1.0
CB A:SER199 4.4 23.4 1.0
OG A:SER199 4.4 35.8 1.0
CG A:TYR156 4.4 48.2 1.0
CB A:TYR157 4.4 23.8 1.0
O A:ILE153 4.6 32.4 1.0
N A:VAL200 4.7 20.3 1.0
OH A:TYR157 4.7 22.6 1.0
N A:CYS196 4.7 21.1 1.0
N A:LEU197 4.7 18.8 1.0
O A:TYR156 4.8 33.6 1.0
CB A:VAL200 4.9 23.2 1.0
CD2 A:TYR156 5.0 51.2 1.0

Mercury binding site 2 out of 10 in 1xik

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Mercury binding site 2 out of 10 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg379

b:36.1
occ:0.43
 SG A:CYS272 2.2 35.7 1.0
SG A:CYS268 2.7 47.3 1.0
O A:CYS268 2.9 34.8 1.0
CD2 A:TYR194 3.2 28.2 1.0
CD2 A:LEU195 3.2 33.6 1.0
CB A:CYS268 3.3 42.6 1.0
C A:CYS268 3.3 37.3 1.0
CE2 A:TYR194 3.4 28.8 1.0
CB A:CYS272 3.6 30.3 1.0
CA A:CYS268 3.8 40.8 1.0
N A:CYS272 3.8 27.3 1.0
HG A:HG380 3.9 38.5 0.4
CA A:CYS272 4.0 28.2 1.0
N A:LYS269 4.1 32.5 1.0
CG A:LEU195 4.2 31.3 1.0
O A:ALA265 4.4 41.4 1.0
CG A:TYR194 4.5 27.3 1.0
CA A:LYS269 4.6 32.2 1.0
CB A:GLU271 4.6 33.8 1.0
N A:CYS268 4.7 41.6 1.0
CZ A:TYR194 4.7 40.4 1.0
C A:GLU271 4.8 31.8 1.0

Mercury binding site 3 out of 10 in 1xik

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Mercury binding site 3 out of 10 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg380

b:38.5
occ:0.37
 SG A:CYS272 3.1 35.7 1.0
CE2 A:TYR194 3.4 28.8 1.0
OH A:TYR194 3.5 47.5 1.0
CB A:CYS272 3.5 30.3 1.0
O A:ALA265 3.6 41.4 1.0
CZ A:TYR194 3.8 40.4 1.0
CE A:MET198 3.9 25.6 1.0
CA A:LYS269 3.9 32.2 1.0
HG A:HG379 3.9 36.1 0.4
CD2 A:LEU321 4.0 31.3 1.0
CG A:LYS269 4.2 53.5 1.0
CB A:LYS269 4.3 35.9 1.0
C A:ALA265 4.4 42.2 1.0
N A:LYS269 4.4 32.5 1.0
CD2 A:TYR194 4.6 28.2 1.0
CA A:ALA265 4.6 34.1 1.0
CB A:ALA265 4.7 34.5 1.0
O A:LYS269 4.8 35.6 1.0
C A:CYS268 4.9 37.3 1.0
O A:CYS268 4.9 34.8 1.0
C A:LYS269 4.9 35.2 1.0
CG A:LEU321 5.0 30.0 1.0
CA A:CYS272 5.0 28.2 1.0

Mercury binding site 4 out of 10 in 1xik

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Mercury binding site 4 out of 10 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg381

b:27.3
occ:0.35
 SG A:CYS196 2.0 26.7 1.0
HG A:HG378 3.0 33.9 0.8
CG2 A:VAL200 3.1 23.6 1.0
CB A:CYS196 3.1 22.2 1.0
CE1 A:TYR157 3.3 21.0 1.0
C A:CYS196 3.3 21.9 1.0
O A:CYS196 3.3 21.8 1.0
N A:LEU197 3.7 18.8 1.0
CA A:CYS196 3.7 20.8 1.0
CD1 A:TYR157 3.7 21.5 1.0
CZ A:TYR157 4.0 23.6 1.0
CA A:LEU197 4.1 19.1 1.0
CB A:VAL200 4.2 23.2 1.0
OH A:TYR157 4.3 22.6 1.0
CD2 A:LEU95 4.5 35.2 1.0
CD2 A:LEU160 4.5 24.4 1.0
CD2 A:LEU197 4.6 32.5 1.0
CG A:TYR157 4.8 20.4 1.0
CG A:LEU95 4.9 31.0 1.0
CG A:LEU197 5.0 28.1 1.0
N A:CYS196 5.0 21.1 1.0

Mercury binding site 5 out of 10 in 1xik

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Mercury binding site 5 out of 10 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg382

b:32.0
occ:0.20
 SG A:CYS214 2.4 42.9 0.5
O A:VAL210 3.0 30.2 1.0
CD2 A:LEU304 3.0 50.7 1.0
N A:CYS214 3.3 33.9 1.0
CB A:ALA213 3.6 32.5 1.0
CB A:CYS214 3.7 38.7 1.0
CA A:CYS214 3.8 36.6 1.0
C A:ALA213 4.0 34.8 1.0
C A:VAL210 4.1 31.2 1.0
CG1 A:VAL210 4.1 31.3 1.0
CA A:ALA213 4.3 31.5 1.0
CG A:LEU304 4.3 49.8 1.0
CD1 A:LEU299 4.4 73.9 1.0
N A:ALA213 4.7 31.8 1.0
O A:ALA213 4.8 33.6 1.0
CA A:VAL210 4.8 26.9 1.0
CD2 A:LEU299 4.9 76.2 1.0
CG A:LEU299 5.0 74.0 1.0

Mercury binding site 6 out of 10 in 1xik

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Mercury binding site 6 out of 10 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg383

b:26.9
occ:0.10
 SG A:CYS214 2.3 43.1 0.5
CB A:CYS214 2.7 38.7 1.0
O A:CYS214 2.8 36.0 1.0
CA A:CYS214 2.8 36.6 1.0
CD2 A:LEU299 3.0 76.2 1.0
C A:CYS214 3.0 38.3 1.0
CE2 A:PHE218 3.5 33.7 1.0
CG2 A:ILE72 3.7 39.0 1.0
SG A:CYS214 3.8 42.9 0.5
CB A:ALA217 3.8 33.9 1.0
CD2 A:PHE218 3.9 31.3 1.0
N A:SER215 4.2 34.5 1.0
N A:CYS214 4.2 33.9 1.0
CG A:LEU299 4.3 74.0 1.0
CZ A:PHE218 4.4 30.9 1.0
CD1 A:LEU299 4.4 73.9 1.0
SD A:MET296 4.6 99.0 1.0
O A:ALA213 4.7 33.6 1.0
CE A:MET296 4.9 95.6 1.0
C A:ALA213 4.9 34.8 1.0

Mercury binding site 7 out of 10 in 1xik

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Mercury binding site 7 out of 10 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg378

b:35.0
occ:0.77
 SG B:CYS196 2.2 22.7 1.0
HG B:HG380 3.0 34.0 0.6
CE1 B:TYR157 3.1 18.2 1.0
O B:CYS196 3.2 21.1 1.0
CG2 B:VAL200 3.2 18.6 1.0
C B:CYS196 3.3 21.2 1.0
CB B:CYS196 3.3 18.7 1.0
CD1 B:TYR157 3.5 18.5 1.0
N B:LEU197 3.8 19.7 1.0
CA B:CYS196 3.9 18.2 1.0
CZ B:TYR157 4.0 23.0 1.0
CA B:LEU197 4.1 19.7 1.0
OH B:TYR157 4.3 21.2 1.0
CB B:VAL200 4.3 18.8 1.0
CD2 B:LEU160 4.4 17.7 1.0
CG B:TYR157 4.6 17.3 1.0
CD2 B:LEU197 4.8 27.8 1.0
CD2 B:LEU95 4.8 26.9 1.0
CG B:LEU197 4.8 25.1 1.0
CE2 B:TYR157 5.0 17.6 1.0
CG B:LEU95 5.0 25.2 1.0

Mercury binding site 8 out of 10 in 1xik

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Mercury binding site 8 out of 10 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg379

b:36.0
occ:0.81
 SG B:CYS272 2.2 30.7 1.0
SG B:CYS268 2.2 35.3 1.0
O B:CYS268 2.8 33.1 1.0
O B:HOH485 2.9 28.8 1.0
CB B:CYS268 3.1 31.8 1.0
CB B:CYS272 3.2 26.4 1.0
C B:CYS268 3.3 34.6 1.0
CD2 B:LEU195 3.5 26.7 1.0
CD2 B:TYR194 3.6 26.9 1.0
CA B:CYS268 3.8 32.1 1.0
N B:CYS272 3.9 26.1 1.0
CE2 B:TYR194 3.9 27.9 1.0
CA B:CYS272 4.0 25.6 1.0
N B:LYS269 4.1 31.6 1.0
O B:ALA265 4.3 37.1 1.0
CG B:LEU195 4.3 24.2 1.0
N B:CYS268 4.6 33.6 1.0
CA B:LYS269 4.6 31.4 1.0
CB B:GLU271 4.7 28.5 1.0
CA B:ALA265 4.8 29.5 1.0
CG B:TYR194 4.8 24.3 1.0
C B:GLU271 4.8 29.9 1.0
C B:ALA265 5.0 36.1 1.0

Mercury binding site 9 out of 10 in 1xik

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Mercury binding site 9 out of 10 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg380

b:34.0
occ:0.59
 SG B:CYS196 2.2 22.7 1.0
O B:HOH402 2.3 26.7 1.0
O B:CYS196 2.9 21.1 1.0
HG B:HG378 3.0 35.0 0.8
CG2 B:VAL200 3.3 18.6 1.0
CA B:CYS196 3.3 18.2 1.0
CB B:CYS196 3.3 18.7 1.0
C B:CYS196 3.4 21.2 1.0
CD1 B:TYR157 3.4 18.5 1.0
CG B:TYR157 3.6 17.3 1.0
CE1 B:TYR157 3.6 18.2 1.0
CB B:TYR156 3.6 24.4 1.0
N B:TYR157 3.8 18.2 1.0
CD2 B:TYR157 3.9 17.5 1.0
CZ B:TYR157 3.9 23.0 1.0
CA B:TYR157 4.1 17.4 1.0
CE2 B:TYR157 4.1 17.6 1.0
C B:TYR156 4.1 23.8 1.0
CB B:SER199 4.2 22.0 1.0
OG B:SER199 4.2 31.4 1.0
CB B:TYR157 4.3 17.4 1.0
O B:ILE153 4.4 27.1 1.0
N B:VAL200 4.5 15.9 1.0
CA B:TYR156 4.5 22.0 1.0
O B:TYR156 4.6 23.6 1.0
N B:LEU197 4.6 19.7 1.0
CB B:VAL200 4.6 18.8 1.0
CG B:TYR156 4.7 27.9 1.0
OH B:TYR157 4.7 21.2 1.0
N B:CYS196 4.8 18.7 1.0

Mercury binding site 10 out of 10 in 1xik

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Mercury binding site 10 out of 10 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg381

b:37.6
occ:0.29
 SG B:CYS214 2.5 32.6 0.5
CE B:MET296 2.7 95.3 1.0
O B:CYS214 3.1 29.2 1.0
CA B:CYS214 3.1 27.1 1.0
CB B:CYS214 3.2 28.5 1.0
SD B:MET296 3.2 98.7 1.0
CG2 B:ILE72 3.3 30.0 1.0
CE1 B:PHE218 3.3 26.4 1.0
C B:CYS214 3.3 29.0 1.0
SG B:CYS214 3.6 33.1 0.5
CD1 B:PHE218 3.8 24.6 1.0
CD2 B:LEU299 4.0 58.8 1.0
CB B:ALA217 4.2 26.9 1.0
CZ B:PHE218 4.2 23.4 1.0
N B:CYS214 4.5 27.1 1.0
N B:SER215 4.5 24.5 1.0
CZ B:PHE291 4.6 68.0 1.0
CG B:MET296 4.6 94.8 1.0
CB B:ILE72 4.7 30.8 1.0
CB B:MET296 4.7 91.7 1.0

Reference:

D.T.Logan, X.D.Su, A.Aberg, K.Regnstrom, J.Hajdu, H.Eklund, P.Nordlund. Crystal Structure of Reduced Protein R2 of Ribonucleotide Reductase: the Structural Basis For Oxygen Activation at A Dinuclear Iron Site. Structure V. 4 1053 1996.
ISSN: ISSN 0969-2126
PubMed: 8805591
DOI: 10.1016/S0969-2126(96)00112-8
Page generated: Sun Aug 11 01:51:57 2024

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