Atomistry » Mercury » PDB 1of5-1rsr » 1pj0
Atomistry »
  Mercury »
    PDB 1of5-1rsr »
      1pj0 »

Mercury in PDB 1pj0: Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH

Enzymatic activity of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH

All present enzymatic activity of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH:
1.17.4.1;

Protein crystallography data

The structure of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH, PDB code: 1pj0 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) 19.32 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.000, 84.400, 114.600, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.6

Other elements in 1pj0:

The structure of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH (pdb code 1pj0). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 9 binding sites of Mercury where determined in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH, PDB code: 1pj0:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Mercury binding site 1 out of 9 in 1pj0

Go back to Mercury Binding Sites List in 1pj0
Mercury binding site 1 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg378

b:26.1
occ:1.00
SG A:CYS272 2.4 18.6 1.0
OH A:TYR194 2.8 20.5 1.0
CB A:CYS272 3.3 17.6 1.0
O A:ALA265 3.5 24.5 1.0
CZ A:TYR194 3.8 19.3 1.0
CA A:LYS269 3.8 24.9 1.0
CE2 A:TYR194 3.8 19.2 1.0
CE A:MET198 4.0 18.5 1.0
CD2 A:LEU321 4.1 16.5 1.0
SG A:CYS268 4.1 30.3 1.0
N A:LYS269 4.1 25.6 1.0
C A:ALA265 4.4 24.1 1.0
O A:HOH426 4.4 23.5 1.0
CB A:LYS269 4.5 26.4 1.0
C A:CYS268 4.5 26.2 1.0
O A:LYS269 4.6 23.2 1.0
CA A:ALA265 4.6 23.4 1.0
O A:CYS268 4.7 25.9 1.0
CA A:CYS272 4.7 17.3 1.0
C A:LYS269 4.7 24.1 1.0
CB A:ALA265 4.8 22.4 1.0
CG A:LEU321 4.9 16.3 1.0
CG A:MET198 5.0 18.1 1.0

Mercury binding site 2 out of 9 in 1pj0

Go back to Mercury Binding Sites List in 1pj0
Mercury binding site 2 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg379

b:22.8
occ:1.00
SG A:CYS196 2.3 18.3 1.0
O A:CYS196 3.1 15.1 1.0
CB A:CYS196 3.3 16.1 1.0
CA A:CYS196 3.4 15.7 1.0
CD1 A:TYR157 3.6 14.1 1.0
CE1 A:TYR157 3.6 14.7 1.0
C A:CYS196 3.6 15.5 1.0
CG2 A:VAL200 3.7 12.9 1.0
CG A:TYR157 3.9 14.4 1.0
CZ A:TYR157 3.9 14.5 1.0
CD2 A:TYR157 4.1 14.1 1.0
CB A:TYR156 4.2 23.8 1.0
CE2 A:TYR157 4.2 13.9 1.0
CD1 A:TYR156 4.2 27.4 1.0
N A:TYR157 4.2 18.1 1.0
CB A:SER199 4.3 14.4 1.0
CA A:TYR157 4.5 16.6 1.0
CG A:TYR156 4.5 26.7 1.0
C A:TYR156 4.6 19.9 1.0
OH A:TYR157 4.7 15.7 1.0
N A:VAL200 4.7 11.8 1.0
CB A:TYR157 4.7 15.4 1.0
O A:ILE153 4.7 20.5 1.0
N A:CYS196 4.8 15.4 1.0
N A:LEU197 4.8 14.9 1.0
OG A:SER199 4.9 15.4 1.0

Mercury binding site 3 out of 9 in 1pj0

Go back to Mercury Binding Sites List in 1pj0
Mercury binding site 3 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg380

b:34.6
occ:1.00
SG A:CYS214 2.3 24.6 1.0
O A:VAL210 2.8 18.5 1.0
N A:CYS214 3.2 20.8 1.0
CB A:CYS214 3.5 21.8 1.0
CA A:CYS214 3.6 21.2 1.0
CB A:ALA213 3.7 20.4 1.0
CD1 A:LEU299 4.0 24.1 1.0
C A:ALA213 4.0 20.7 1.0
C A:VAL210 4.0 19.4 1.0
CG1 A:VAL210 4.1 20.0 1.0
CD1 A:LEU304 4.1 21.1 1.0
CA A:ALA213 4.4 20.3 1.0
O A:HOH452 4.5 37.1 1.0
CG A:LEU304 4.5 21.1 1.0
CA A:VAL210 4.7 18.9 1.0
O A:ALA213 4.8 20.4 1.0
CB A:LEU304 4.8 20.7 1.0
N A:ALA213 4.9 20.3 1.0
N A:SER211 5.0 19.2 1.0

Mercury binding site 4 out of 9 in 1pj0

Go back to Mercury Binding Sites List in 1pj0
Mercury binding site 4 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg381

b:44.5
occ:0.50
OE2 A:GLU309 3.1 19.7 1.0
CB A:CYS305 3.4 23.2 1.0
CD A:GLU309 3.4 18.7 1.0
NZ A:LYS284 3.4 24.4 1.0
C A:CYS305 3.5 21.0 1.0
O A:CYS305 3.6 20.9 1.0
N A:GLN306 3.7 19.8 1.0
OE1 A:GLU309 3.9 19.2 1.0
CG A:GLU309 4.0 17.4 1.0
CA A:GLN306 4.0 19.3 1.0
CA A:CYS305 4.1 21.8 1.0
CG A:GLN306 4.3 22.5 1.0
NH2 A:ARG328 4.5 36.9 1.0
CE A:LYS284 4.7 25.1 1.0
SG A:CYS305 4.8 29.9 1.0
CB A:GLN306 4.8 20.4 1.0
O A:ASP302 4.9 23.8 1.0
CZ A:ARG328 4.9 36.5 1.0
CB A:GLU309 4.9 16.4 1.0

Mercury binding site 5 out of 9 in 1pj0

Go back to Mercury Binding Sites List in 1pj0
Mercury binding site 5 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg382

b:0.1
occ:0.50
CB A:CYS268 2.7 28.0 1.0
CA A:CYS268 3.0 27.4 1.0
N A:CYS268 3.1 27.5 1.0
O A:ILE264 3.5 22.0 1.0
C A:GLU267 3.7 28.2 1.0
CG2 A:ILE264 3.8 21.4 1.0
CD A:LYS191 4.0 24.5 1.0
CG A:LYS191 4.1 22.7 1.0
O A:GLU267 4.2 28.1 1.0
CB A:GLU267 4.2 29.9 1.0
SG A:CYS268 4.3 30.3 1.0
C A:ILE264 4.4 21.9 1.0
CB A:LYS191 4.5 19.5 1.0
C A:CYS268 4.5 26.2 1.0
CE A:LYS191 4.5 26.6 1.0
CA A:GLU267 4.6 28.5 1.0
CA A:ILE264 4.7 21.5 1.0
CB A:ILE264 4.8 21.4 1.0
OE1 A:GLU267 5.0 34.8 1.0

Mercury binding site 6 out of 9 in 1pj0

Go back to Mercury Binding Sites List in 1pj0
Mercury binding site 6 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg378

b:32.3
occ:1.00
CB B:CYS196 2.6 13.9 1.0
CA B:CYS196 2.8 16.2 1.0
SG B:CYS196 2.9 6.6 1.0
O B:CYS196 3.1 16.8 1.0
C B:CYS196 3.3 16.1 1.0
CG2 B:VAL200 3.4 17.1 1.0
CB B:TYR156 3.6 21.9 1.0
CD1 B:TYR157 3.6 16.4 1.0
CG B:TYR157 3.7 15.2 1.0
CE1 B:TYR157 3.7 14.8 1.0
CD2 B:TYR157 3.8 15.0 1.0
CZ B:TYR157 3.9 15.2 1.0
N B:TYR157 3.9 18.1 1.0
CE2 B:TYR157 3.9 14.7 1.0
C B:TYR156 4.2 19.4 1.0
N B:CYS196 4.2 18.1 1.0
CB B:SER199 4.3 18.5 1.0
CA B:TYR157 4.3 16.4 1.0
CB B:TYR157 4.5 15.6 1.0
N B:LEU197 4.5 16.7 1.0
O B:ILE153 4.5 22.8 1.0
CA B:TYR156 4.5 20.5 1.0
N B:VAL200 4.6 15.8 1.0
CG B:TYR156 4.6 24.1 1.0
O B:TYR156 4.7 18.6 1.0
OH B:TYR157 4.7 14.2 1.0
CB B:VAL200 4.8 16.0 1.0
O B:LEU195 4.9 19.6 1.0
OG B:SER199 5.0 22.5 1.0

Mercury binding site 7 out of 9 in 1pj0

Go back to Mercury Binding Sites List in 1pj0
Mercury binding site 7 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg379

b:26.1
occ:0.50
SG B:CYS272 2.3 29.9 1.0
SG B:CYS268 2.5 38.5 1.0
O B:CYS268 2.6 37.2 1.0
CB B:CYS268 3.2 38.1 1.0
C B:CYS268 3.3 37.2 1.0
CB B:CYS272 3.4 27.3 1.0
CD2 B:TYR194 3.5 19.6 1.0
CE2 B:TYR194 3.8 21.0 1.0
CA B:CYS268 3.9 37.7 1.0
N B:CYS272 4.0 27.7 1.0
CD2 B:LEU195 4.0 24.6 1.0
CA B:CYS272 4.2 27.0 1.0
N B:LYS269 4.2 36.4 1.0
O B:ALA265 4.5 36.0 1.0
CA B:LYS269 4.5 35.7 1.0
N B:CYS268 4.7 38.1 1.0
CG B:TYR194 4.7 19.5 1.0
O B:HOH388 4.8 25.5 1.0
CB B:GLU271 4.8 30.5 1.0
CA B:ALA265 4.9 35.7 1.0
C B:GLU271 5.0 29.1 1.0

Mercury binding site 8 out of 9 in 1pj0

Go back to Mercury Binding Sites List in 1pj0
Mercury binding site 8 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg380

b:41.2
occ:0.50
SG B:CYS214 2.6 18.4 1.0
O B:VAL210 2.8 20.9 1.0
N B:CYS214 3.1 22.7 1.0
CD1 B:LEU304 3.1 31.3 1.0
CA B:CYS214 3.5 22.7 1.0
CB B:CYS214 3.5 21.8 1.0
CG B:LEU304 3.6 31.0 1.0
CB B:ALA213 3.6 22.3 1.0
CG1 B:VAL210 3.8 22.0 1.0
C B:VAL210 3.9 20.7 1.0
C B:ALA213 3.9 22.4 1.0
CD2 B:LEU299 4.2 42.7 1.0
CA B:ALA213 4.3 21.7 1.0
CD1 B:LEU299 4.3 42.6 1.0
CB B:LEU304 4.3 30.1 1.0
CA B:VAL210 4.5 21.1 1.0
N B:ALA213 4.6 21.1 1.0
CG B:LEU299 4.6 42.4 1.0
O B:ALA213 4.7 22.5 1.0
CD2 B:LEU304 4.8 31.0 1.0
CB B:VAL210 4.8 21.4 1.0
N B:SER211 4.9 20.1 1.0

Mercury binding site 9 out of 9 in 1pj0

Go back to Mercury Binding Sites List in 1pj0
Mercury binding site 9 out of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg381

b:61.7
occ:0.50
O B:CYS272 2.8 24.9 1.0
CA B:CYS272 2.9 27.0 1.0
CB B:CYS272 3.0 27.3 1.0
CB B:MET198 3.1 19.6 1.0
CG B:MET198 3.2 22.8 1.0
C B:CYS272 3.2 25.9 1.0
SG B:CYS272 3.3 29.9 1.0
CD1 B:LEU275 3.4 27.0 1.0
SD B:MET198 3.5 23.6 1.0
CB B:LEU275 3.6 25.9 1.0
CD2 B:LEU275 3.6 26.7 1.0
CG B:LEU275 3.7 26.6 1.0
CD2 B:PHE276 3.9 24.9 1.0
N B:PHE276 4.3 24.8 1.0
N B:CYS272 4.3 27.7 1.0
CA B:MET198 4.4 18.3 1.0
N B:TYR273 4.4 25.8 1.0
CD1 B:LEU321 4.5 28.0 1.0
C B:MET198 4.6 18.0 1.0
CE2 B:PHE276 4.6 24.5 1.0
CA B:LEU275 4.7 25.3 1.0
C B:LEU275 4.7 25.2 1.0
CG B:PHE276 4.7 24.2 1.0
CB B:PHE276 4.8 24.1 1.0
O B:GLU271 4.8 28.6 1.0
O B:MET198 4.9 18.2 1.0
CE B:MET198 4.9 23.8 1.0
CA B:PHE276 4.9 24.2 1.0
N B:SER199 5.0 18.2 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: Wed Oct 28 18:40:22 2020

Last articles

Xe in 6AYK
Xe in 6QII
Xe in 6ASM
Xe in 5NSW
Xe in 6FY9
Xe in 5O1K
Xe in 5O27
Xe in 5M69
Xe in 5KPU
Xe in 5I63
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy