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Mercury in PDB 1biq: Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A

Enzymatic activity of Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A

All present enzymatic activity of Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A:
1.17.4.1;

Protein crystallography data

The structure of Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A, PDB code: 1biq was solved by D.T.Logan, F.Demare, B.O.Persson, A.Slaby, B.M.Sjoberg, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.053, 83.780, 113.953, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 26.6

Other elements in 1biq:

The structure of Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Mercury atom in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A (pdb code 1biq). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 16 binding sites of Mercury where determined in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A, PDB code: 1biq:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 16 in 1biq

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Mercury binding site 1 out of 16 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A


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 Mutant E238A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg380

b:23.3
occ:0.79
 SG A:CYS196 2.2 20.2 1.0
O A:CYS196 3.0 19.7 1.0
HG A:HG385 3.1 31.6 0.3
CA A:CYS196 3.3 16.8 1.0
CB A:CYS196 3.4 17.0 1.0
CD1 A:TYR157 3.4 16.1 1.0
C A:CYS196 3.5 18.6 1.0
CE1 A:TYR157 3.5 15.6 1.0
CB A:TYR156 3.6 35.2 1.0
CG2 A:VAL200 3.6 20.9 1.0
CG A:TYR157 3.7 15.7 1.0
CZ A:TYR157 3.9 19.9 1.0
N A:TYR157 4.0 22.0 1.0
CD2 A:TYR157 4.0 15.9 1.0
CE2 A:TYR157 4.1 15.4 1.0
CA A:TYR157 4.4 20.0 1.0
C A:TYR156 4.4 28.3 1.0
CG A:TYR156 4.5 43.6 1.0
CB A:SER199 4.5 19.2 1.0
CB A:TYR157 4.5 18.7 1.0
N A:LEU197 4.6 14.7 1.0
OH A:TYR157 4.6 17.3 1.0
N A:VAL200 4.7 16.2 1.0
CA A:TYR156 4.7 30.6 1.0
O A:ILE153 4.7 22.4 1.0
N A:CYS196 4.7 17.3 1.0
CB A:VAL200 4.9 20.8 1.0
O A:TYR156 4.9 25.4 1.0
OG A:SER199 4.9 33.6 1.0
CD2 A:TYR156 4.9 46.4 1.0

Mercury binding site 2 out of 16 in 1biq

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Mercury binding site 2 out of 16 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A


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 Mutant E238A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg381

b:25.0
occ:0.17
 SG A:CYS272 2.2 27.7 1.0
CD2 A:LEU195 2.5 27.3 1.0
CB A:CYS268 2.8 35.0 1.0
O A:CYS268 3.0 27.2 1.0
CE2 A:TYR194 3.2 26.4 1.0
C A:CYS268 3.5 29.3 1.0
CD2 A:TYR194 3.5 25.5 1.0
N A:CYS272 3.5 20.8 1.0
CB A:CYS272 3.5 23.0 1.0
CG A:LEU195 3.7 25.1 1.0
CA A:CYS272 3.8 22.1 1.0
CA A:CYS268 3.8 32.3 1.0
HG A:HG382 4.0 27.2 0.8
SG A:CYS268 4.1 40.5 1.0
N A:LYS269 4.2 25.5 1.0
CB A:GLU271 4.2 25.4 1.0
CD1 A:LEU195 4.4 26.6 1.0
C A:GLU271 4.4 24.5 1.0
CZ A:TYR194 4.4 30.8 1.0
CA A:LYS269 4.6 26.3 1.0
O A:ALA265 4.8 35.1 1.0
OH A:TYR194 4.8 27.3 1.0
N A:CYS268 4.8 33.4 1.0
CA A:GLU271 4.9 22.9 1.0
CG A:TYR194 4.9 22.9 1.0

Mercury binding site 3 out of 16 in 1biq

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Mercury binding site 3 out of 16 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A


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 Mutant E238A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg382

b:27.2
occ:0.77
 SG A:CYS272 2.2 27.7 1.0
OH A:TYR194 3.0 27.3 1.0
CB A:CYS272 3.2 23.0 1.0
O A:ALA265 3.6 35.1 1.0
CE2 A:TYR194 3.8 26.4 1.0
CA A:LYS269 3.8 26.3 1.0
CZ A:TYR194 3.9 30.8 1.0
CE A:MET198 4.0 19.1 1.0
HG A:HG381 4.0 25.0 0.2
CB A:LYS269 4.1 31.4 1.0
CD2 A:LEU321 4.1 28.6 1.0
N A:LYS269 4.3 25.5 1.0
CG A:LYS269 4.5 62.2 1.0
C A:ALA265 4.5 34.6 1.0
O A:LYS269 4.7 29.7 1.0
CA A:CYS272 4.7 22.1 1.0
O A:HOH477 4.7 29.6 1.0
C A:LYS269 4.7 28.7 1.0
C A:CYS268 4.8 29.3 1.0
CA A:ALA265 4.8 24.6 1.0
O A:CYS268 4.9 27.2 1.0
CG A:LEU321 4.9 25.3 1.0
CB A:ALA265 5.0 24.8 1.0

Mercury binding site 4 out of 16 in 1biq

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Mercury binding site 4 out of 16 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A


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 Mutant E238A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg383

b:23.2
occ:0.50
 SG A:CYS214 1.8 27.1 1.0
O A:VAL210 2.9 22.1 1.0
HG A:HG386 3.0 62.0 0.2
N A:CYS214 3.1 22.8 1.0
CB A:CYS214 3.2 24.4 1.0
CD2 A:LEU304 3.3 43.8 1.0
CB A:ALA213 3.3 26.8 1.0
CA A:CYS214 3.6 24.3 1.0
CG1 A:VAL210 3.8 24.4 1.0
C A:ALA213 3.9 25.7 1.0
C A:VAL210 4.0 22.0 1.0
CA A:ALA213 4.2 25.4 1.0
CD1 A:LEU299 4.3 38.8 1.0
CG A:LEU304 4.5 39.1 1.0
CA A:VAL210 4.5 20.7 1.0
O A:ALA213 4.7 25.9 1.0
CB A:VAL210 4.8 24.4 1.0
N A:ALA213 4.8 25.5 1.0
CB A:LEU304 4.9 30.8 1.0
CG A:LEU299 4.9 37.7 1.0

Mercury binding site 5 out of 16 in 1biq

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Mercury binding site 5 out of 16 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A


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 Mutant E238A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg384

b:34.7
occ:0.40
 OE2 A:GLU309 3.3 27.0 1.0
CB A:CYS305 3.4 27.1 1.0
NZ A:LYS284 3.5 29.4 1.0
C A:CYS305 3.5 28.0 1.0
N A:GLN306 3.6 25.1 1.0
O A:CYS305 3.6 26.3 1.0
CD A:GLU309 3.7 37.4 1.0
CA A:GLN306 3.9 25.1 1.0
CA A:CYS305 4.1 26.6 1.0
OE1 A:GLU309 4.1 28.2 1.0
CG A:GLN306 4.1 44.7 1.0
CG A:GLU309 4.2 20.1 1.0
NH2 A:ARG328 4.6 93.2 1.0
CB A:GLN306 4.6 26.3 1.0
CE A:LYS284 4.7 27.4 1.0
O A:ASP302 5.0 34.5 1.0
SG A:CYS305 5.0 31.0 0.5

Mercury binding site 6 out of 16 in 1biq

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Mercury binding site 6 out of 16 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A


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 Mutant E238A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg385

b:31.6
occ:0.29
 SG A:CYS196 2.1 20.2 1.0
HG A:HG380 3.1 23.3 0.8
CG2 A:VAL200 3.1 20.9 1.0
CB A:CYS196 3.1 17.0 1.0
CE1 A:TYR157 3.1 15.6 1.0
C A:CYS196 3.3 18.6 1.0
O A:CYS196 3.3 19.7 1.0
N A:LEU197 3.6 14.7 1.0
CD1 A:TYR157 3.7 16.1 1.0
CA A:CYS196 3.8 16.8 1.0
CZ A:TYR157 3.9 19.9 1.0
CD2 A:LEU95 4.0 21.8 1.0
CA A:LEU197 4.1 16.1 1.0
OH A:TYR157 4.1 17.3 1.0
CB A:VAL200 4.2 20.8 1.0
CD1 A:LEU95 4.3 20.9 1.0
CD2 A:LEU197 4.4 26.0 1.0
CG A:LEU95 4.5 22.2 1.0
CD2 A:LEU160 4.8 16.7 1.0
CG A:TYR157 4.9 15.7 1.0
CG A:LEU197 5.0 22.3 1.0

Mercury binding site 7 out of 16 in 1biq

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Mercury binding site 7 out of 16 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A


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 Mutant E238A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg386

b:62.0
occ:0.24
 SG A:CYS214 1.8 27.1 1.0
CB A:CYS214 2.8 24.4 1.0
HG A:HG383 3.0 23.2 0.5
CD2 A:LEU290 3.4 42.9 1.0
OD1 A:ASN76 3.5 31.2 1.0
O A:VAL210 3.5 22.1 1.0
CG1 A:VAL210 3.7 24.4 1.0
NE1 A:TRP286 4.1 45.7 1.0
CA A:CYS214 4.2 24.3 1.0
C A:VAL210 4.2 22.0 1.0
CA A:SER211 4.3 14.7 1.0
CG A:ASN76 4.3 35.9 1.0
CD2 A:LEU304 4.3 43.8 1.0
CD1 A:TRP286 4.3 45.7 1.0
N A:CYS214 4.4 22.8 1.0
NH2 A:ARG149 4.4 33.6 1.0
N A:SER211 4.6 15.2 1.0
CG A:LEU290 4.9 42.4 1.0
NH1 A:ARG149 4.9 32.2 1.0
O A:SER211 4.9 20.7 1.0
CB A:VAL210 5.0 24.4 1.0
C A:SER211 5.0 19.9 1.0
CB A:ASN76 5.0 20.5 1.0

Mercury binding site 8 out of 16 in 1biq

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Mercury binding site 8 out of 16 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A


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 Mutant E238A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg379

b:20.9
occ:0.31
 SG B:CYS196 1.9 20.0 1.0
HG B:HG381 2.9 22.5 0.6
CE1 B:TYR157 3.1 21.0 1.0
CB B:CYS196 3.2 17.2 1.0
O B:CYS196 3.3 20.0 1.0
C B:CYS196 3.4 19.6 1.0
CG2 B:VAL200 3.5 18.0 1.0
CD1 B:TYR157 3.6 19.1 1.0
CA B:CYS196 3.9 17.4 1.0
N B:LEU197 3.9 15.9 1.0
CZ B:TYR157 4.0 20.8 1.0
CD2 B:LEU95 4.2 27.2 1.0
OH B:TYR157 4.3 20.8 1.0
CA B:LEU197 4.3 15.9 1.0
CD2 B:LEU160 4.4 17.7 1.0
CB B:VAL200 4.5 18.2 1.0
CD2 B:LEU197 4.5 19.4 1.0
CG B:TYR157 4.7 16.7 1.0
CG B:LEU95 5.0 23.5 1.0
CB B:ALA94 5.0 17.3 1.0
CG B:LEU197 5.0 18.3 1.0
CE2 B:TYR157 5.0 15.7 1.0

Mercury binding site 9 out of 16 in 1biq

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Mercury binding site 9 out of 16 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A


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 Mutant E238A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg380

b:24.9
occ:0.31
 SG B:CYS272 2.0 37.5 0.5
SG B:CYS268 2.0 49.4 1.0
CD2 B:LEU195 2.5 34.1 1.0
O B:CYS268 3.0 41.0 1.0
CB B:CYS268 3.2 45.6 1.0
CB B:CYS272 3.3 33.8 1.0
C B:CYS268 3.5 43.4 1.0
CD2 B:TYR194 3.6 28.7 1.0
CE2 B:TYR194 3.8 30.3 1.0
N B:CYS272 3.8 34.2 1.0
CA B:CYS268 3.8 44.7 1.0
CG B:LEU195 4.0 30.5 1.0
CA B:CYS272 4.0 33.7 1.0
CD1 B:LEU195 4.4 31.1 1.0
N B:LYS269 4.4 38.0 1.0
O B:ALA265 4.4 49.1 1.0
CB B:GLU271 4.5 38.9 1.0
HG B:HG383 4.6 32.1 0.3
C B:GLU271 4.7 39.2 1.0
CG B:TYR194 4.8 26.6 1.0
N B:CYS268 4.9 45.8 1.0

Mercury binding site 10 out of 16 in 1biq

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Mercury binding site 10 out of 16 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238A


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 Mutant E238A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg381

b:22.5
occ:0.61
 SG B:CYS196 2.2 20.0 1.0
HG B:HG379 2.9 20.9 0.3
O B:CYS196 3.0 20.0 1.0
CA B:CYS196 3.4 17.4 1.0
CB B:CYS196 3.5 17.2 1.0
CD1 B:TYR157 3.5 19.1 1.0
C B:CYS196 3.5 19.6 1.0
CG2 B:VAL200 3.6 18.0 1.0
CE1 B:TYR157 3.6 21.0 1.0
CB B:TYR156 3.6 25.9 1.0
CG B:TYR157 3.7 16.7 1.0
CZ B:TYR157 3.9 20.8 1.0
N B:TYR157 3.9 18.2 1.0
OG B:SER199 3.9 43.7 1.0
CD2 B:TYR157 4.0 15.8 1.0
CE2 B:TYR157 4.1 15.7 1.0
C B:TYR156 4.2 22.7 1.0
CA B:TYR157 4.3 18.2 1.0
CB B:SER199 4.5 25.5 1.0
CA B:TYR156 4.5 22.3 1.0
CB B:TYR157 4.5 17.1 1.0
O B:ILE153 4.6 22.6 1.0
N B:VAL200 4.6 15.5 1.0
OH B:TYR157 4.6 20.8 1.0
CG B:TYR156 4.7 31.5 1.0
O B:TYR156 4.7 20.8 1.0
N B:LEU197 4.7 15.9 1.0
CB B:VAL200 4.8 18.2 1.0
N B:CYS196 4.9 19.3 1.0

Reference:

D.T.Logan, F.Demare, B.O.Persson, A.Slaby, B.M.Sjoberg, P.Nordlund. Crystal Structures of Two Self-Hydroxylating Ribonucleotide Reductase Protein R2 Mutants: Structural Basis For the Oxygen-Insertion Step of Hydroxylation Reactions Catalyzed By Diiron Proteins. Biochemistry V. 37 10798 1998.
ISSN: ISSN 0006-2960
PubMed: 9692970
DOI: 10.1021/BI9806403
Page generated: Sat Aug 10 23:19:18 2024

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