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Mercury in PDB 1pfr: 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: 1pfr 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.300, 85.500, 115.700, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / n/a

Other elements in 1pfr:

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

Mercury binding site 1 out of 8 in 1pfr

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Mercury binding site 1 out of 8 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:Hg601

b:33.4
occ:1.00
 SG A:CYS196 2.2 14.9 1.0
O A:HOH612 2.7 17.6 1.0
HG A:HG603 3.1 31.8 0.3
O A:CYS196 3.1 13.2 1.0
CA A:CYS196 3.4 10.5 1.0
CB A:CYS196 3.5 11.1 1.0
CB A:TYR156 3.5 25.8 1.0
C A:CYS196 3.5 13.6 1.0
CG2 A:VAL200 3.6 16.3 1.0
CE1 A:TYR157 3.6 16.1 1.0
CD1 A:TYR157 3.6 16.2 1.0
CZ A:TYR157 3.7 22.6 1.0
CG A:TYR157 3.8 15.1 1.0
CE2 A:TYR157 3.9 15.5 1.0
CD2 A:TYR157 3.9 15.2 1.0
N A:TYR157 4.0 17.0 1.0
CB A:SER199 4.3 15.1 1.0
C A:TYR156 4.3 23.1 1.0
OH A:TYR157 4.4 24.0 1.0
CG A:TYR156 4.4 30.3 1.0
CA A:TYR157 4.5 15.8 1.0
N A:VAL200 4.5 12.8 1.0
CA A:TYR156 4.5 22.9 1.0
N A:LEU197 4.6 11.9 1.0
CB A:TYR157 4.7 15.8 1.0
O A:ILE153 4.8 27.1 1.0
O A:TYR156 4.8 22.8 1.0
N A:CYS196 4.8 11.2 1.0
CB A:VAL200 4.9 16.3 1.0

Mercury binding site 2 out of 8 in 1pfr

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Mercury binding site 2 out of 8 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:Hg602

b:37.1
occ:1.00
 O A:HOH667 2.3 38.2 1.0
SG A:CYS272 2.5 25.2 1.0
OH A:TYR194 3.0 17.6 1.0
CB A:CYS272 3.4 20.1 1.0
O A:ALA265 3.5 25.5 1.0
CE A:MET198 3.6 15.9 1.0
CE2 A:TYR194 3.7 16.0 1.0
CZ A:TYR194 3.8 19.2 1.0
CA A:LYS269 3.8 18.4 1.0
CD2 A:LEU321 3.9 21.7 1.0
CG A:LYS269 4.2 31.5 1.0
N A:LYS269 4.3 18.6 1.0
CB A:LYS269 4.3 20.4 1.0
C A:ALA265 4.3 26.1 1.0
CA A:ALA265 4.6 21.1 1.0
O A:LYS269 4.6 24.4 1.0
CB A:ALA265 4.7 21.5 1.0
O A:HOH661 4.7 25.1 1.0
C A:CYS268 4.8 25.7 1.0
C A:LYS269 4.8 23.9 1.0
CA A:CYS272 4.8 18.9 1.0
O A:CYS268 4.9 26.1 1.0

Mercury binding site 3 out of 8 in 1pfr

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Mercury binding site 3 out of 8 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:Hg603

b:31.8
occ:0.35
 SG A:CYS196 2.1 14.9 1.0
CG2 A:VAL200 3.1 16.3 1.0
HG A:HG601 3.1 33.4 1.0
CB A:CYS196 3.2 11.1 1.0
CE1 A:TYR157 3.3 16.1 1.0
C A:CYS196 3.4 13.6 1.0
O A:CYS196 3.5 13.2 1.0
N A:LEU197 3.7 11.9 1.0
CD2 A:LEU95 3.7 23.1 1.0
CA A:CYS196 3.9 10.5 1.0
CD1 A:TYR157 3.9 16.2 1.0
CZ A:TYR157 4.0 22.6 1.0
CA A:LEU197 4.1 12.8 1.0
CD1 A:LEU197 4.2 21.5 1.0
OH A:TYR157 4.2 24.0 1.0
CB A:VAL200 4.4 16.3 1.0
CG A:LEU95 4.6 20.3 1.0
CD1 A:LEU95 4.8 20.0 1.0
CD2 A:LEU160 4.8 16.7 1.0
CG A:TYR157 5.0 15.1 1.0

Mercury binding site 4 out of 8 in 1pfr

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Mercury binding site 4 out of 8 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:Hg604

b:38.5
occ:0.10
 SG A:CYS268 2.2 33.0 1.0
O A:HOH695 2.8 49.6 1.0
CB A:CYS268 3.3 28.1 1.0
CA A:CYS268 3.6 26.5 1.0
CD A:LYS191 3.7 44.1 1.0
CG A:LYS191 4.1 37.2 1.0
CG A:GLU271 4.1 39.5 1.0
N A:CYS268 4.2 26.3 1.0
O A:GLU267 4.2 30.0 1.0
OE2 A:GLU271 4.3 80.2 1.0
CD2 A:LEU195 4.3 24.1 1.0
CD A:GLU271 4.4 76.5 1.0
C A:GLU267 4.5 30.3 1.0
CE A:LYS191 4.6 54.4 1.0
CB A:LYS191 4.8 18.9 1.0
C A:CYS268 4.8 25.7 1.0
CD1 A:LEU195 5.0 19.1 1.0

Mercury binding site 5 out of 8 in 1pfr

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Mercury binding site 5 out of 8 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
B:Hg605

b:38.9
occ:0.90
 SG B:CYS196 2.3 17.9 1.0
O B:HOH617 2.4 18.8 1.0
HG B:HG606 3.0 25.7 0.5
O B:CYS196 3.1 10.7 1.0
CB B:CYS196 3.2 13.4 1.0
CA B:CYS196 3.4 12.3 1.0
CG2 B:VAL200 3.4 18.2 1.0
CD1 B:TYR157 3.4 11.3 1.0
C B:CYS196 3.5 13.8 1.0
CG B:TYR157 3.5 9.7 1.0
CE1 B:TYR157 3.6 12.8 1.0
CB B:TYR156 3.6 20.2 1.0
CD2 B:TYR157 3.7 10.5 1.0
CZ B:TYR157 3.8 15.1 1.0
N B:TYR157 3.8 14.2 1.0
CE2 B:TYR157 3.8 9.9 1.0
C B:TYR156 4.1 19.4 1.0
CA B:TYR157 4.2 12.5 1.0
CB B:TYR157 4.3 10.7 1.0
CB B:SER199 4.4 18.3 1.0
O B:ILE153 4.5 24.3 1.0
CA B:TYR156 4.5 17.6 1.0
N B:VAL200 4.6 13.8 1.0
OH B:TYR157 4.6 16.0 1.0
O B:TYR156 4.6 19.6 1.0
N B:LEU197 4.7 13.0 1.0
CG B:TYR156 4.7 23.8 1.0
CB B:VAL200 4.8 18.1 1.0
N B:CYS196 4.8 13.1 1.0

Mercury binding site 6 out of 8 in 1pfr

Go back to Mercury Binding Sites List in 1pfr
Mercury binding site 6 out of 8 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
B:Hg606

b:25.7
occ:0.50
 SG B:CYS196 1.8 17.9 1.0
CE1 B:TYR157 3.0 12.8 1.0
HG B:HG605 3.0 38.9 0.9
CG2 B:VAL200 3.1 18.2 1.0
CB B:CYS196 3.4 13.4 1.0
C B:CYS196 3.4 13.8 1.0
O B:CYS196 3.4 10.7 1.0
CD1 B:TYR157 3.5 11.3 1.0
N B:LEU197 3.7 13.0 1.0
CZ B:TYR157 3.8 15.1 1.0
CA B:CYS196 3.9 12.3 1.0
CA B:LEU197 4.1 13.8 1.0
OH B:TYR157 4.2 16.0 1.0
CD2 B:LEU95 4.4 24.7 1.0
CB B:VAL200 4.4 18.1 1.0
CD1 B:LEU197 4.5 20.9 1.0
CG B:TYR157 4.6 9.7 1.0
CD2 B:LEU160 4.8 19.2 1.0
CE2 B:TYR157 4.8 9.9 1.0

Mercury binding site 7 out of 8 in 1pfr

Go back to Mercury Binding Sites List in 1pfr
Mercury binding site 7 out of 8 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:Hg607

b:18.4
occ:0.15
 CB B:CYS268 2.2 37.6 1.0
SG B:CYS272 2.3 23.7 1.0
O B:CYS268 2.8 32.9 1.0
C B:CYS268 3.0 35.3 1.0
CA B:CYS268 3.1 36.5 1.0
SG B:CYS268 3.2 42.0 1.0
CD2 B:TYR194 3.5 21.3 1.0
CE2 B:TYR194 3.6 22.1 1.0
CB B:CYS272 3.6 19.7 1.0
CD2 B:LEU195 3.8 21.0 1.0
N B:LYS269 3.9 30.7 1.0
N B:CYS272 4.0 20.2 1.0
CG B:LEU195 4.2 19.0 1.0
CA B:CYS272 4.3 19.4 1.0
N B:CYS268 4.4 37.5 1.0
O B:ALA265 4.5 36.6 1.0
CA B:LYS269 4.6 30.2 1.0
O B:HOH660 4.6 20.3 1.0
CG B:GLU271 4.7 35.0 1.0
CG B:TYR194 4.8 20.4 1.0
O B:ILE264 4.8 30.3 1.0
C B:GLU271 5.0 24.6 1.0
CZ B:TYR194 5.0 30.8 1.0

Mercury binding site 8 out of 8 in 1pfr

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Mercury binding site 8 out of 8 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:Hg608

b:20.9
occ:0.15
 SG B:CYS214 2.3 34.7 1.0
CB B:CYS214 2.3 29.5 1.0
CA B:CYS214 2.8 27.4 1.0
CG2 B:ILE72 3.2 25.7 1.0
O B:CYS214 3.3 29.4 1.0
C B:CYS214 3.4 29.7 1.0
SD B:MET296 3.5 63.4 1.0
CD2 B:LEU299 3.8 45.0 1.0
N B:CYS214 4.2 26.0 1.0
CE2 B:PHE218 4.2 29.1 1.0
CG B:MET296 4.3 59.0 1.0
CB B:ILE72 4.6 25.3 1.0
N B:SER215 4.6 23.1 1.0
CZ B:PHE291 4.6 48.8 1.0
CZ B:PHE218 4.7 26.8 1.0
CB B:ALA217 4.7 22.1 1.0
CD2 B:PHE218 4.7 26.8 1.0
O B:HOH610 4.8 10.2 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 01:00:58 2024

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