Atomistry » Mercury » PDB 1of5-1rsr » 1pfr
Atomistry »
  Mercury »
    PDB 1of5-1rsr »
      1pfr »

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

Go back to Mercury Binding Sites List in 1pfr
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

Go back to Mercury Binding Sites List in 1pfr
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

Go back to Mercury Binding Sites List in 1pfr
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

Go back to Mercury Binding Sites List in 1pfr
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

Go back to Mercury Binding Sites List in 1pfr
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

Go back to Mercury Binding Sites List in 1pfr
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy