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Mercury in PDB 1rnr: Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein

Enzymatic activity of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein

All present enzymatic activity of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein:
1.17.4.1;

Protein crystallography data

The structure of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein, PDB code: 1rnr was solved by A.Aberg, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.100, 85.300, 115.700, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / n/a

Other elements in 1rnr:

The structure of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Mercury atom in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein (pdb code 1rnr). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 14 binding sites of Mercury where determined in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein, PDB code: 1rnr:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 14 in 1rnr

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Mercury binding site 1 out of 14 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg403

b:26.4
occ:1.00
 SG A:CYS196 2.0 13.9 1.0
O A:HOH417 3.0 36.1 1.0
HG A:HG406 3.1 10.6 0.1
O A:CYS196 3.3 14.1 1.0
CB A:CYS196 3.3 15.5 1.0
CA A:CYS196 3.4 14.4 1.0
CE1 A:TYR157 3.5 12.1 1.0
CD1 A:TYR157 3.5 14.3 1.0
C A:CYS196 3.6 14.0 1.0
CB A:TYR156 3.7 35.1 1.0
CZ A:TYR157 3.7 15.1 1.0
CG A:TYR157 3.8 15.2 1.0
CG2 A:VAL200 3.9 13.3 1.0
CE2 A:TYR157 3.9 13.2 1.0
CD2 A:TYR157 4.0 14.5 1.0
N A:TYR157 4.2 21.1 1.0
CB A:SER199 4.3 15.7 1.0
OH A:TYR157 4.4 18.1 1.0
CG A:TYR156 4.4 41.7 1.0
C A:TYR156 4.6 25.2 1.0
CA A:TYR157 4.6 20.4 1.0
N A:VAL200 4.7 14.8 1.0
N A:LEU197 4.7 12.4 1.0
CB A:TYR157 4.8 16.8 1.0
CD1 A:TYR156 4.8 45.6 1.0
CA A:TYR156 4.8 28.9 1.0
N A:CYS196 4.8 14.2 1.0
O A:ILE153 4.8 35.0 1.0
OG A:SER199 4.9 20.3 1.0

Mercury binding site 2 out of 14 in 1rnr

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Mercury binding site 2 out of 14 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg404

b:27.2
occ:1.00
 HG A:HG407 1.8 42.0 0.3
SG A:CYS272 2.2 42.2 1.0
OH A:TYR194 3.0 16.3 1.0
CB A:CYS272 3.3 29.3 1.0
O A:ALA265 3.7 21.6 1.0
CA A:LYS269 3.7 24.4 1.0
CE A:MET198 3.8 5.8 1.0
CE2 A:TYR194 3.9 13.0 1.0
CZ A:TYR194 3.9 15.3 1.0
CD2 A:LEU321 3.9 9.2 1.0
CB A:LYS269 4.3 25.8 1.0
N A:LYS269 4.3 21.6 1.0
CG A:LYS269 4.4 31.3 1.0
C A:ALA265 4.5 21.6 1.0
O A:LYS269 4.5 24.8 1.0
O A:HOH429 4.5 8.0 1.0
CA A:ALA265 4.6 19.9 1.0
C A:LYS269 4.7 24.6 1.0
CB A:ALA265 4.7 16.9 1.0
C A:CYS268 4.8 22.8 1.0
CA A:CYS272 4.8 26.4 1.0
O A:CYS268 4.8 21.9 1.0
CG A:LEU321 4.8 11.1 1.0
CG A:MET198 5.0 12.4 1.0

Mercury binding site 3 out of 14 in 1rnr

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Mercury binding site 3 out of 14 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg405

b:28.8
occ:0.75
 SG A:CYS214 2.0 22.4 1.0
O A:HOH414 2.3 25.8 1.0
O A:VAL210 3.0 24.0 1.0
N A:CYS214 3.1 24.3 1.0
CB A:CYS214 3.2 24.4 1.0
CA A:CYS214 3.5 24.5 1.0
CB A:ALA213 3.7 26.2 1.0
CD1 A:LEU304 3.8 26.0 1.0
C A:ALA213 3.9 23.8 1.0
C A:VAL210 3.9 22.9 1.0
CG1 A:VAL210 4.0 15.4 1.0
CG A:LEU304 4.2 26.1 1.0
CD1 A:LEU299 4.3 26.6 1.0
CA A:ALA213 4.4 25.5 1.0
CA A:VAL210 4.5 20.2 1.0
O A:ALA213 4.6 22.5 1.0
CD2 A:LEU299 4.7 26.5 1.0
CB A:LEU304 4.8 23.5 1.0
N A:ALA213 4.8 27.6 1.0
O A:HOH419 4.9 23.4 1.0
CG A:LEU299 4.9 27.2 1.0
N A:SER211 4.9 24.1 1.0
CB A:VAL210 4.9 16.8 1.0

Mercury binding site 4 out of 14 in 1rnr

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Mercury binding site 4 out of 14 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg406

b:10.6
occ:0.10
 SG A:CYS196 1.8 13.9 1.0
CB A:CYS196 3.0 15.5 1.0
HG A:HG403 3.1 26.4 1.0
CE1 A:TYR157 3.1 12.1 1.0
CD1 A:LEU95 3.5 12.6 1.0
CG2 A:VAL200 3.5 13.3 1.0
C A:CYS196 3.5 14.0 1.0
CD1 A:TYR157 3.7 14.3 1.0
O A:CYS196 3.8 14.1 1.0
N A:LEU197 3.8 12.4 1.0
CA A:CYS196 3.8 14.4 1.0
CZ A:TYR157 3.9 15.1 1.0
OH A:TYR157 4.1 18.1 1.0
CA A:LEU197 4.4 14.4 1.0
CD2 A:LEU95 4.5 11.8 1.0
CD2 A:LEU197 4.5 12.2 1.0
CG A:LEU95 4.5 14.0 1.0
CD2 A:LEU160 4.6 11.5 1.0
CB A:VAL200 4.7 14.3 1.0
CG A:TYR157 4.9 15.2 1.0
CG A:LEU197 5.0 15.3 1.0
CE2 A:TYR157 5.0 13.2 1.0
O A:LEU193 5.0 11.6 1.0

Mercury binding site 5 out of 14 in 1rnr

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Mercury binding site 5 out of 14 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg407

b:42.0
occ:0.30
 SG A:CYS272 1.7 42.2 1.0
HG A:HG404 1.8 27.2 1.0
CB A:CYS272 1.8 29.3 1.0
CE2 A:TYR194 3.3 13.0 1.0
CA A:CYS272 3.3 26.4 1.0
OH A:TYR194 3.5 16.3 1.0
O A:CYS268 3.7 21.9 1.0
CA A:LYS269 3.8 24.4 1.0
N A:CYS272 3.8 24.3 1.0
CE A:MET198 3.8 5.8 1.0
CZ A:TYR194 3.9 15.3 1.0
C A:CYS268 4.0 22.8 1.0
CG A:MET198 4.1 12.4 1.0
O A:LYS269 4.1 24.8 1.0
N A:LYS269 4.1 21.6 1.0
C A:LYS269 4.3 24.6 1.0
C A:CYS272 4.3 24.6 1.0
O A:ALA265 4.4 21.6 1.0
CD2 A:TYR194 4.4 17.1 1.0
CD2 A:LEU321 4.5 9.2 1.0
SD A:MET198 4.6 12.4 1.0
CD2 A:LEU195 4.7 20.6 1.0
CB A:LYS269 4.8 25.8 1.0
N A:TYR273 4.9 22.6 1.0

Mercury binding site 6 out of 14 in 1rnr

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Mercury binding site 6 out of 14 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg408

b:26.7
occ:0.30
 OE1 A:GLU309 3.3 30.9 1.0
CB A:CYS305 3.4 30.4 1.0
O A:HOH468 3.4 50.1 1.0
C A:CYS305 3.6 23.5 1.0
N A:GLN306 3.6 22.0 1.0
CD A:GLU309 3.7 32.0 1.0
O A:CYS305 3.8 23.9 1.0
NZ A:LYS284 3.8 6.9 1.0
OE2 A:GLU309 3.9 36.4 1.0
CA A:GLN306 3.9 23.1 1.0
CA A:CYS305 4.1 25.6 1.0
CB A:GLN306 4.2 26.1 1.0
CE A:LYS284 4.5 10.7 1.0
CB A:GLU309 4.7 25.2 1.0
CG A:GLU309 4.7 28.9 1.0
NH2 A:ARG328 4.8 51.5 1.0
SG A:CYS305 4.8 46.5 1.0
O A:ASP302 4.9 31.1 1.0

Mercury binding site 7 out of 14 in 1rnr

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Mercury binding site 7 out of 14 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg403

b:32.2
occ:1.00
 SG B:CYS196 2.0 11.7 1.0
O B:HOH421 2.3 9.7 1.0
HG B:HG408 2.6 36.2 0.3
O B:CYS196 3.1 13.3 1.0
CB B:TYR156 3.4 30.3 1.0
CA B:CYS196 3.4 15.7 1.0
CB B:CYS196 3.5 14.7 1.0
C B:CYS196 3.5 14.1 1.0
CD1 B:TYR157 3.7 11.9 1.0
CE1 B:TYR157 3.7 12.6 1.0
CG2 B:VAL200 3.8 22.2 1.0
CG B:TYR157 3.8 11.7 1.0
CZ B:TYR157 3.9 11.8 1.0
N B:TYR157 3.9 19.5 1.0
O B:HOH412 3.9 34.4 1.0
CD2 B:TYR157 4.0 10.3 1.0
CE2 B:TYR157 4.0 10.9 1.0
C B:TYR156 4.2 23.7 1.0
CB B:SER199 4.3 19.1 1.0
CA B:TYR157 4.4 17.2 1.0
CA B:TYR156 4.5 25.7 1.0
CG B:TYR156 4.5 34.0 1.0
OH B:TYR157 4.6 10.2 1.0
O B:ILE153 4.6 29.4 1.0
CB B:TYR157 4.6 15.0 1.0
N B:VAL200 4.6 18.4 1.0
N B:LEU197 4.7 14.2 1.0
O B:TYR156 4.8 24.9 1.0
N B:CYS196 4.8 17.9 1.0

Mercury binding site 8 out of 14 in 1rnr

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Mercury binding site 8 out of 14 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg404

b:46.6
occ:0.40
 CD1 B:LEU304 2.3 28.9 1.0
HG B:HG407 2.7 30.9 0.3
CD2 B:LEU304 2.8 31.1 1.0
O B:VAL210 2.8 26.5 1.0
SG B:CYS214 3.0 38.8 1.0
CG B:LEU304 3.1 30.2 1.0
CG1 B:VAL210 3.5 26.6 1.0
CB B:ALA213 3.6 21.2 1.0
N B:CYS214 3.7 22.6 1.0
C B:VAL210 3.9 25.1 1.0
CD2 B:LEU299 3.9 33.2 1.0
CB B:CYS214 4.2 28.0 1.0
C B:ALA213 4.3 21.0 1.0
CA B:VAL210 4.3 26.4 1.0
CA B:CYS214 4.3 23.3 1.0
CD1 B:LEU299 4.4 34.5 1.0
CB B:LEU304 4.4 29.5 1.0
CA B:ALA213 4.5 20.9 1.0
CG B:LEU299 4.6 34.0 1.0
CB B:VAL210 4.6 26.6 1.0
N B:SER211 4.9 25.8 1.0

Mercury binding site 9 out of 14 in 1rnr

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Mercury binding site 9 out of 14 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg405

b:31.5
occ:0.40
 O B:HOH413 1.9 45.1 1.0
SG B:CYS272 3.2 55.6 1.0
CE B:MET198 3.3 25.1 1.0
OH B:TYR194 3.4 24.1 1.0
CE2 B:TYR194 3.7 23.6 1.0
HG B:HG409 3.7 56.4 0.1
CD2 B:LEU321 3.7 34.1 1.0
O B:ALA265 3.8 39.4 1.0
CB B:CYS272 4.0 45.8 1.0
CZ B:TYR194 4.0 23.4 1.0
CA B:LYS269 4.2 42.7 1.0
C B:ALA265 4.3 39.7 1.0
CA B:ALA265 4.4 38.0 1.0
CB B:ALA265 4.5 37.5 1.0
N B:LYS269 4.5 42.8 1.0
CG B:LYS269 4.5 46.2 1.0
CG B:LEU321 4.7 35.2 1.0
C B:CYS268 4.8 44.1 1.0
CD2 B:TYR194 4.8 20.9 1.0
CB B:LYS269 4.9 42.7 1.0
CD1 B:LEU321 5.0 34.0 1.0

Mercury binding site 10 out of 14 in 1rnr

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Mercury binding site 10 out of 14 in the Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg406

b:36.0
occ:0.40
 CG B:MET198 2.8 25.7 1.0
O B:CYS272 3.0 41.3 1.0
CA B:CYS272 3.0 43.4 1.0
CB B:CYS272 3.2 45.8 1.0
C B:CYS272 3.4 40.5 1.0
SG B:CYS272 3.5 55.6 1.0
CD2 B:PHE276 3.6 28.4 1.0
CB B:MET198 3.7 22.2 1.0
CB B:LEU275 3.8 38.1 1.0
CD2 B:LEU275 3.9 42.9 1.0
CE2 B:PHE276 3.9 28.4 1.0
SD B:MET198 4.2 27.4 1.0
N B:CYS272 4.2 43.4 1.0
N B:PHE276 4.3 32.9 1.0
CG B:LEU275 4.4 42.2 1.0
O B:GLU271 4.5 45.2 1.0
C B:MET198 4.6 20.1 1.0
CG B:PHE276 4.6 26.5 1.0
O B:MET198 4.6 19.5 1.0
N B:TYR273 4.7 38.0 1.0
CA B:MET198 4.7 21.0 1.0
CA B:LEU275 4.7 36.3 1.0
CE B:MET198 4.7 25.1 1.0
C B:LEU275 4.8 34.6 1.0
C B:GLU271 4.8 43.7 1.0

Reference:

A.Aberg, M.Ormo, P.Nordlund, B.M.Sjoberg. Autocatalytic Generation of Dopa in the Engineered Protein R2 F208Y From Escherichia Coli Ribonucleotide Reductase and Crystal Structure of the Dopa-208 Protein. Biochemistry V. 32 9845 1993.
ISSN: ISSN 0006-2960
PubMed: 8373782
DOI: 10.1021/BI00088A040
Page generated: Sun Aug 11 01:27:06 2024

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