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Mercury in PDB 1yfd: Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli

Enzymatic activity of Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli

All present enzymatic activity of Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli, PDB code: 1yfd was solved by M.Kolberg, D.T.Logan, G.Bleifuss, S.Poetsch, B.M.Sjoeberg, A.Graeslund, W.Lubitz, G.Lassmann, F.Lendzian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.46 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.040, 84.740, 115.030, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.6

Other elements in 1yfd:

The structure of Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Mercury atom in the Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli (pdb code 1yfd). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 13 binding sites of Mercury where determined in the Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli, PDB code: 1yfd:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 13 in 1yfd

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Mercury binding site 1 out of 13 in the Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg601

b:13.8
occ:0.90
 SG A:CYS196 2.3 11.6 1.0
O A:HOH623 2.5 18.7 1.0
O A:CYS196 3.2 10.7 1.0
CB A:CYS196 3.3 10.5 1.0
CA A:CYS196 3.4 10.6 1.0
CE1 A:TYR157 3.6 11.2 1.0
CD1 A:TYR157 3.6 10.8 1.0
C A:CYS196 3.6 9.9 1.0
CG2 A:VAL200 3.7 9.0 1.0
CG A:TYR157 3.9 11.1 1.0
CZ A:TYR157 3.9 10.0 1.0
CB A:TYR156 4.0 21.4 1.0
CD2 A:TYR157 4.1 10.8 1.0
CE2 A:TYR157 4.1 9.6 1.0
N A:TYR157 4.2 14.9 1.0
CD2 A:TYR156 4.2 26.3 1.0
CB A:SER199 4.3 10.7 1.0
CG A:TYR156 4.4 23.3 1.0
CA A:TYR157 4.5 14.0 1.0
C A:TYR156 4.5 17.3 1.0
OH A:TYR157 4.6 13.0 1.0
N A:VAL200 4.6 9.2 1.0
CB A:TYR157 4.7 12.8 1.0
O A:ILE153 4.8 16.7 1.0
N A:CYS196 4.8 10.3 1.0
N A:LEU197 4.8 10.2 1.0
OG A:SER199 4.9 13.3 1.0
CA A:TYR156 4.9 18.5 1.0
CB A:VAL200 5.0 9.3 1.0

Mercury binding site 2 out of 13 in 1yfd

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Mercury binding site 2 out of 13 in the Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg605

b:14.7
occ:0.90
 SG A:CYS272 2.3 12.1 1.0
O A:HOH766 2.4 22.0 1.0
OH A:TYR194 2.8 10.9 1.0
CB A:CYS272 3.2 12.7 1.0
O A:ALA265 3.5 16.9 1.0
CE A:MET198 3.7 11.3 1.0
CZ A:TYR194 3.9 8.9 1.0
CA A:LYS269 3.9 18.0 1.0
CE2 A:TYR194 4.0 8.9 1.0
CD2 A:LEU321 4.2 16.3 1.0
N A:LYS269 4.4 17.8 1.0
C A:ALA265 4.4 16.5 1.0
O A:LYS269 4.5 16.3 1.0
O A:HOH617 4.6 10.2 1.0
CA A:ALA265 4.6 16.3 1.0
CG A:LYS269 4.7 21.8 1.0
CA A:CYS272 4.7 13.3 1.0
O A:CYS268 4.7 18.2 1.0
C A:LYS269 4.7 16.8 1.0
C A:CYS268 4.7 18.2 1.0
CB A:ALA265 4.8 16.5 1.0
CB A:LYS269 4.8 18.8 1.0
CG A:LEU321 4.9 14.5 1.0
SD A:MET198 5.0 13.2 1.0

Mercury binding site 3 out of 13 in 1yfd

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Mercury binding site 3 out of 13 in the Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg606

b:15.8
occ:0.60
 SG A:CYS214 2.1 20.5 1.0
O A:VAL210 3.0 15.8 1.0
N A:CYS214 3.3 17.9 1.0
CB A:CYS214 3.4 17.7 1.0
CA A:CYS214 3.7 17.6 1.0
CD1 A:LEU304 3.8 19.3 1.0
CB A:ALA213 3.8 17.6 1.0
CD1 A:LEU299 3.9 21.0 1.0
C A:ALA213 4.0 17.4 1.0
CG1 A:VAL210 4.1 18.3 1.0
C A:VAL210 4.1 16.1 1.0
CG A:LEU304 4.4 19.3 1.0
CA A:ALA213 4.4 17.3 1.0
O A:HOH807 4.6 40.7 1.0
O A:ALA213 4.7 17.1 1.0
CB A:LEU304 4.8 18.7 1.0
CA A:VAL210 4.8 16.1 1.0
N A:ALA213 4.9 17.6 1.0
CG A:LEU299 5.0 20.1 1.0

Mercury binding site 4 out of 13 in 1yfd

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Mercury binding site 4 out of 13 in the Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg609

b:21.4
occ:0.40
 SG A:CYS305 2.1 25.4 1.0
OE2 A:GLU309 3.2 14.4 1.0
CB A:CYS305 3.3 19.5 1.0
C A:CYS305 3.5 18.2 1.0
O A:CYS305 3.6 17.3 1.0
CD A:GLU309 3.6 15.7 1.0
N A:GLN306 3.7 16.7 1.0
CA A:CYS305 4.0 19.0 1.0
OE1 A:GLU309 4.1 14.8 1.0
CA A:GLN306 4.1 17.0 1.0
CG A:GLU309 4.2 15.2 1.0
NH2 A:ARG328 4.4 37.0 1.0
CG A:GLN306 4.4 19.1 1.0
CE A:LYS284 4.4 16.7 1.0
NZ A:LYS284 4.5 17.9 1.0
CB A:GLN306 4.9 16.8 1.0
O A:ASP302 4.9 21.5 1.0

Mercury binding site 5 out of 13 in 1yfd

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Mercury binding site 5 out of 13 in the Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg602

b:31.1
occ:0.20
 SG B:CYS196 1.7 12.1 1.0
HG B:HG604 2.9 14.3 0.8
CB B:CYS196 3.1 12.7 1.0
CG2 B:VAL200 3.2 12.3 1.0
CE1 B:TYR157 3.2 13.7 1.0
C B:CYS196 3.4 11.7 1.0
O B:CYS196 3.4 11.7 1.0
CD1 B:TYR157 3.6 14.0 1.0
CA B:CYS196 3.7 12.8 1.0
N B:LEU197 3.8 11.1 1.0
CZ B:TYR157 4.0 13.0 1.0
CD2 B:LEU95 4.2 13.3 1.0
CA B:LEU197 4.3 11.6 1.0
OH B:TYR157 4.3 12.5 1.0
CB B:VAL200 4.4 11.2 1.0
CD2 B:LEU197 4.5 13.3 1.0
O B:HOH637 4.5 18.4 1.0
CD2 B:LEU160 4.5 11.8 1.0
CG B:TYR157 4.7 12.5 1.0
CG B:LEU197 4.9 12.9 1.0
CG B:LEU95 4.9 12.0 1.0
CE2 B:TYR157 4.9 13.2 1.0
CD1 B:LEU95 5.0 13.2 1.0

Mercury binding site 6 out of 13 in 1yfd

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Mercury binding site 6 out of 13 in the Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg603

b:20.4
occ:0.20
 HG B:HG613 2.1 27.2 0.3
O B:HOH752 2.4 14.2 1.0
O B:ALA265 2.8 26.3 1.0
O B:CYS268 3.2 28.9 1.0
C B:CYS268 3.2 29.4 1.0
CE1 B:TYR194 3.3 19.9 1.0
N B:LYS269 3.5 28.5 1.0
C B:ALA265 3.6 27.1 1.0
CB B:CYS272 3.7 24.8 1.0
CA B:ALA265 3.7 26.6 1.0
CA B:CYS268 3.8 30.2 1.0
CB B:CYS268 3.8 31.0 1.0
CA B:LYS269 3.9 28.3 1.0
CD1 B:TYR194 3.9 19.0 1.0
SG B:CYS268 4.0 34.8 1.0
N B:CYS268 4.1 30.1 1.0
CB B:ALA265 4.3 26.5 1.0
CZ B:TYR194 4.3 17.8 1.0
SG B:CYS272 4.5 26.9 1.0
OH B:TYR194 4.5 21.4 1.0
O B:ILE264 4.7 26.2 1.0
C B:LYS269 4.8 27.3 1.0
N B:GLU266 4.9 27.9 1.0
N B:ALA265 5.0 26.1 1.0
CB B:LYS269 5.0 28.4 1.0
CA B:CYS272 5.0 24.3 1.0

Mercury binding site 7 out of 13 in 1yfd

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Mercury binding site 7 out of 13 in the Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg604

b:14.3
occ:0.80
 O B:HOH637 1.9 18.4 1.0
SG B:CYS196 2.3 12.1 1.0
HG B:HG602 2.9 31.1 0.2
O B:CYS196 3.2 11.7 1.0
CB B:CYS196 3.4 12.7 1.0
CA B:CYS196 3.4 12.8 1.0
CG2 B:VAL200 3.5 12.3 1.0
C B:CYS196 3.6 11.7 1.0
CB B:TYR156 3.6 19.7 1.0
CD1 B:TYR157 3.6 14.0 1.0
CE1 B:TYR157 3.7 13.7 1.0
CG B:TYR157 3.8 12.5 1.0
CZ B:TYR157 3.9 13.0 1.0
CD2 B:TYR157 4.0 10.6 1.0
CE2 B:TYR157 4.0 13.2 1.0
N B:TYR157 4.0 13.9 1.0
C B:TYR156 4.3 15.5 1.0
CA B:TYR157 4.3 13.4 1.0
CB B:SER199 4.4 11.6 1.0
CB B:TYR157 4.6 13.0 1.0
CG B:TYR156 4.6 22.4 1.0
N B:VAL200 4.6 11.4 1.0
OH B:TYR157 4.6 12.5 1.0
CA B:TYR156 4.6 17.0 1.0
O B:ILE153 4.7 16.2 1.0
N B:LEU197 4.7 11.1 1.0
O B:TYR156 4.8 13.4 1.0
N B:CYS196 4.8 13.3 1.0
CB B:VAL200 4.8 11.2 1.0

Mercury binding site 8 out of 13 in 1yfd

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Mercury binding site 8 out of 13 in the Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg607

b:15.7
occ:0.50
 SG B:CYS214 1.9 23.1 1.0
CB B:CYS214 3.1 18.1 1.0
CD1 B:LEU304 3.1 8.8 1.0
ND2 B:ASN76 3.3 11.8 1.0
CD2 B:LEU304 3.5 20.4 1.0
CD1 B:LEU290 3.5 36.1 1.0
O B:VAL210 3.7 14.6 1.0
CG B:LEU304 4.0 20.0 1.0
N B:CYS214 4.1 16.9 1.0
CA B:CYS214 4.1 16.7 1.0
O B:HOH777 4.2 18.3 1.0
CG B:ASN76 4.2 13.8 1.0
CA B:SER211 4.4 14.0 1.0
C B:VAL210 4.5 15.5 1.0
CG1 B:VAL210 4.6 19.8 1.0
O B:SER211 4.6 12.2 1.0
N B:SER211 4.8 14.1 1.0
CB B:ASN76 4.8 13.6 1.0
C B:SER211 4.9 13.1 1.0
OD1 B:ASN76 4.9 16.1 1.0
O B:HOH773 5.0 36.2 1.0

Mercury binding site 9 out of 13 in 1yfd

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Mercury binding site 9 out of 13 in the Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg608

b:20.8
occ:0.50
 SG B:CYS272 2.4 26.9 1.0
CG B:LEU275 2.6 26.8 1.0
CD2 B:LEU275 2.9 26.4 1.0
CD1 B:LEU275 2.9 27.7 1.0
O B:CYS272 3.0 22.3 1.0
CA B:CYS272 3.2 24.3 1.0
CB B:CYS272 3.3 24.8 1.0
CB B:MET198 3.4 13.1 1.0
C B:CYS272 3.4 23.6 1.0
CD2 B:PHE276 3.6 22.0 1.0
CE2 B:PHE276 3.7 22.9 1.0
CG B:MET198 3.8 14.2 1.0
CB B:LEU275 3.9 24.4 1.0
SD B:MET198 4.1 18.2 1.0
N B:PHE276 4.4 21.8 1.0
CG B:PHE276 4.5 21.6 1.0
N B:CYS272 4.5 24.7 1.0
CD2 B:LEU195 4.6 20.1 1.0
CA B:MET198 4.6 11.9 1.0
N B:TYR273 4.6 22.4 1.0
C B:MET198 4.6 11.5 1.0
CZ B:PHE276 4.7 21.7 1.0
CA B:LEU275 4.8 23.6 1.0
O B:MET198 4.8 11.3 1.0
C B:LEU275 4.9 22.9 1.0

Mercury binding site 10 out of 13 in 1yfd

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Mercury binding site 10 out of 13 in the Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Crystal Structure of the Y122H Mutant of Ribonucleotide Reductase R2 Protein From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg610

b:24.9
occ:0.25
 SG B:CYS305 2.2 24.9 1.0
OE2 B:GLU309 2.6 21.0 1.0
O B:HOH794 2.9 38.9 1.0
CD B:GLU309 3.1 18.8 1.0
NE2 B:GLN306 3.2 30.9 1.0
HG B:HG611 3.4 20.3 0.2
CB B:CYS305 3.7 20.6 1.0
CG B:GLU309 3.7 17.2 1.0
OE1 B:GLU309 3.8 21.9 1.0
O B:CYS305 3.8 18.2 1.0
C B:CYS305 3.8 19.2 1.0
N B:GLN306 4.0 17.9 1.0
CA B:GLN306 4.3 18.3 1.0
CD B:GLN306 4.3 27.9 1.0
CA B:CYS305 4.4 19.9 1.0
CG B:GLN306 4.6 23.7 1.0
NH2 B:ARG328 4.9 35.1 1.0
CB B:GLU309 4.9 16.8 1.0

Reference:

M.Kolberg, D.T.Logan, G.Bleifuss, S.Poetsch, B.M.Sjoeberg, A.Graeslund, W.Lubitz, G.Lassmann, F.Lendzian. A New Tyrosyl Radical on PHE208 As Ligand to the Diiron Center in Escherichia Coli Ribonucleotide Reductase, Mutant R2-Y122H. Combined X-Ray Diffraction and Epr/Endor Studies J.Biol.Chem. V. 280 11233 2005.
ISSN: ISSN 0021-9258
PubMed: 15634667
DOI: 10.1074/JBC.M414634200
Page generated: Sun Aug 11 01:57:57 2024

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