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Mercury in PDB 1pm2: Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)

Enzymatic activity of Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)

All present enzymatic activity of Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase):
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase), PDB code: 1pm2 was solved by W.C.Voegtli, M.Sommerhalter, J.Baldwin, L.Saleh, J.M.Bollingerjr., A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.950, 83.940, 114.340, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.5

Other elements in 1pm2:

The structure of Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Mercury Binding Sites:

Pages:

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

Binding sites:

The binding sites of Mercury atom in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) (pdb code 1pm2). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 14 binding sites of Mercury where determined in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase), PDB code: 1pm2:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 14 in 1pm2

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Mercury binding site 1 out of 14 in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)


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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg601

b:21.1
occ:0.78
 SG A:CYS272 2.4 21.4 1.0
OH A:TYR194 2.6 20.3 1.0
CB A:CYS272 3.3 18.3 1.0
O A:ALA265 3.6 24.2 1.0
CZ A:TYR194 3.7 20.6 1.0
CE2 A:TYR194 3.8 19.9 1.0
CA A:LYS269 3.8 23.0 1.0
HG A:HG609 3.8 34.2 0.3
CD2 A:LEU321 4.0 15.2 1.0
CE A:MET198 4.0 20.8 1.0
CB A:LYS269 4.2 25.1 1.0
C A:ALA265 4.4 24.3 1.0
O A:HOH667 4.4 26.1 1.0
N A:LYS269 4.5 22.9 1.0
O A:LYS269 4.5 21.3 1.0
CA A:ALA265 4.6 23.0 1.0
O A:CYS268 4.6 25.9 1.0
C A:LYS269 4.7 21.9 1.0
CB A:ALA265 4.8 22.4 1.0
CA A:CYS272 4.8 16.1 1.0
CG A:LEU321 4.8 15.6 1.0
C A:CYS268 4.8 25.5 1.0
CE1 A:TYR194 5.0 19.0 1.0

Mercury binding site 2 out of 14 in 1pm2

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Mercury binding site 2 out of 14 in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)


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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg602

b:18.2
occ:0.85
 SG A:CYS196 2.2 18.9 1.0
HG A:HG610 3.1 26.4 0.3
O A:CYS196 3.2 16.8 1.0
CB A:CYS196 3.4 15.7 1.0
CA A:CYS196 3.4 15.0 1.0
CD1 A:TYR157 3.6 16.3 1.0
C A:CYS196 3.6 15.5 1.0
CE1 A:TYR157 3.6 17.7 1.0
CG2 A:VAL200 3.6 15.6 1.0
CG A:TYR157 3.9 15.7 1.0
CZ A:TYR157 3.9 15.1 1.0
CB A:TYR156 4.1 26.9 1.0
CD2 A:TYR157 4.1 16.3 1.0
N A:TYR157 4.1 17.2 1.0
CE2 A:TYR157 4.2 15.6 1.0
CB A:SER199 4.2 15.6 1.0
CD1 A:TYR156 4.3 34.5 1.0
CG A:TYR156 4.4 32.9 1.0
CA A:TYR157 4.4 15.3 1.0
C A:TYR156 4.6 21.0 1.0
OH A:TYR157 4.7 19.6 1.0
O A:ILE153 4.7 17.7 1.0
N A:VAL200 4.7 14.3 1.0
CB A:TYR157 4.7 15.7 1.0
N A:LEU197 4.8 14.2 1.0
N A:CYS196 4.9 14.7 1.0
OG A:SER199 4.9 21.3 1.0
CB A:VAL200 5.0 15.1 1.0
CA A:TYR156 5.0 23.3 1.0

Mercury binding site 3 out of 14 in 1pm2

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Mercury binding site 3 out of 14 in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)


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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg603

b:21.5
occ:0.81
 SG A:CYS214 2.3 24.0 1.0
O A:VAL210 2.9 19.3 1.0
N A:CYS214 3.3 20.8 1.0
CB A:CYS214 3.5 20.3 1.0
CA A:CYS214 3.7 20.0 1.0
CB A:ALA213 3.8 19.1 1.0
C A:ALA213 4.0 19.5 1.0
CD1 A:LEU299 4.0 22.4 1.0
C A:VAL210 4.0 18.8 1.0
CG1 A:VAL210 4.1 19.8 1.0
CD1 A:LEU304 4.2 18.9 1.0
CA A:ALA213 4.4 19.7 1.0
CG A:LEU304 4.4 17.8 1.0
O A:ALA213 4.7 20.4 1.0
CA A:VAL210 4.8 17.8 1.0
CB A:LEU304 4.8 17.2 1.0
N A:ALA213 4.9 18.2 1.0

Mercury binding site 4 out of 14 in 1pm2

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Mercury binding site 4 out of 14 in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)


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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg609

b:34.2
occ:0.35
 SG A:CYS272 2.2 21.4 1.0
O A:CYS268 2.5 25.9 1.0
CD2 A:LEU195 2.8 19.7 1.0
CE2 A:TYR194 2.8 19.9 1.0
C A:CYS268 3.3 25.5 1.0
CD2 A:TYR194 3.3 21.0 1.0
CB A:CYS268 3.4 27.8 1.0
CB A:CYS272 3.6 18.3 1.0
N A:CYS272 3.7 16.0 1.0
HG A:HG601 3.8 21.1 0.8
CA A:CYS268 4.0 26.3 1.0
CA A:CYS272 4.0 16.1 1.0
CZ A:TYR194 4.0 20.6 1.0
CG A:LEU195 4.1 18.3 1.0
N A:LYS269 4.1 22.9 1.0
OH A:TYR194 4.3 20.3 1.0
CA A:LYS269 4.3 23.0 1.0
CB A:GLU271 4.4 21.8 1.0
O A:ALA265 4.5 24.2 1.0
C A:GLU271 4.5 15.8 1.0
CG A:TYR194 4.7 16.8 1.0
C A:LYS269 4.9 21.9 1.0
CD1 A:LEU195 4.9 20.6 1.0
CA A:GLU271 4.9 18.6 1.0
N A:CYS268 4.9 28.3 1.0
O A:ILE264 5.0 22.1 1.0

Mercury binding site 5 out of 14 in 1pm2

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Mercury binding site 5 out of 14 in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)


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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg610

b:26.4
occ:0.28
 SG A:CYS196 2.2 18.9 1.0
CG2 A:VAL200 2.9 15.6 1.0
HG A:HG602 3.1 18.2 0.8
CE1 A:TYR157 3.3 17.7 1.0
O A:CYS196 3.3 16.8 1.0
CB A:CYS196 3.4 15.7 1.0
C A:CYS196 3.4 15.5 1.0
N A:LEU197 3.8 14.2 1.0
CD1 A:TYR157 3.9 16.3 1.0
CA A:CYS196 4.0 15.0 1.0
CZ A:TYR157 4.1 15.1 1.0
CB A:VAL200 4.1 15.1 1.0
CA A:LEU197 4.2 15.4 1.0
OH A:TYR157 4.3 19.6 1.0
CD2 A:LEU95 4.3 20.1 1.0
CD2 A:LEU197 4.3 19.9 1.0
CD2 A:LEU160 4.8 13.7 1.0
CG A:LEU95 4.8 18.3 1.0
CG A:LEU197 4.9 19.9 1.0
CG1 A:VAL200 5.0 16.0 1.0

Mercury binding site 6 out of 14 in 1pm2

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Mercury binding site 6 out of 14 in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)


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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg614

b:22.4
occ:0.43
 SG A:CYS305 2.3 30.2 1.0
OE2 A:GLU309 3.4 21.8 1.0
CB A:CYS305 3.4 20.9 1.0
CD A:GLU309 3.5 18.6 1.0
C A:CYS305 3.6 19.4 1.0
O A:CYS305 3.7 17.8 1.0
N A:GLN306 3.7 18.5 1.0
OE1 A:GLU309 3.9 19.5 1.0
CG A:GLU309 4.0 16.7 1.0
CA A:GLN306 4.0 18.2 1.0
CA A:CYS305 4.1 19.9 1.0
NZ A:LYS284 4.2 24.8 1.0
CG A:GLN306 4.3 24.6 1.0
CE A:LYS284 4.3 19.9 1.0
O A:HOH732 4.4 29.8 1.0
CB A:GLN306 4.8 19.8 1.0
NH2 A:ARG328 4.9 42.9 1.0
O A:ASP302 4.9 22.3 1.0

Mercury binding site 7 out of 14 in 1pm2

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Mercury binding site 7 out of 14 in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)


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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg604

b:21.1
occ:0.70
 SG B:CYS196 2.2 18.2 1.0
O B:CYS196 3.0 14.3 1.0
HG B:HG612 3.0 18.4 0.4
CB B:CYS196 3.3 15.0 1.0
CA B:CYS196 3.4 14.9 1.0
CG2 B:VAL200 3.4 18.5 1.0
C B:CYS196 3.5 14.4 1.0
CD1 B:TYR157 3.6 14.5 1.0
CB B:TYR156 3.6 20.6 1.0
CG B:TYR157 3.7 12.8 1.0
CE1 B:TYR157 3.7 15.0 1.0
CD2 B:TYR157 3.9 12.2 1.0
N B:TYR157 3.9 15.1 1.0
CZ B:TYR157 3.9 14.7 1.0
CE2 B:TYR157 4.0 14.1 1.0
C B:TYR156 4.1 16.4 1.0
CB B:SER199 4.2 15.6 1.0
CA B:TYR157 4.2 13.1 1.0
OG B:SER199 4.4 20.6 1.0
O B:ILE153 4.5 15.5 1.0
CB B:TYR157 4.5 12.6 1.0
N B:VAL200 4.5 14.2 1.0
CA B:TYR156 4.5 18.2 1.0
O B:TYR156 4.6 16.6 1.0
N B:LEU197 4.7 13.7 1.0
CG B:TYR156 4.7 23.3 1.0
CB B:VAL200 4.7 15.3 1.0
OH B:TYR157 4.8 14.6 1.0
N B:CYS196 4.8 14.4 1.0

Mercury binding site 8 out of 14 in 1pm2

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Mercury binding site 8 out of 14 in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)


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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg605

b:19.4
occ:0.53
 SG B:CYS272 2.3 27.2 1.0
SG B:CYS268 2.4 31.9 1.0
O B:CYS268 2.6 34.6 1.0
CB B:CYS268 3.2 32.8 1.0
C B:CYS268 3.3 33.9 1.0
CB B:CYS272 3.4 24.0 1.0
CD2 B:TYR194 3.7 18.5 1.0
CD2 B:LEU195 3.8 21.9 1.0
CA B:CYS268 3.9 33.7 1.0
N B:CYS272 4.0 23.5 1.0
CE2 B:TYR194 4.0 20.7 1.0
CA B:CYS272 4.2 23.0 1.0
N B:LYS269 4.3 33.5 1.0
O B:ALA265 4.4 28.5 1.0
HG B:HG606 4.5 58.0 0.4
CG B:LEU195 4.6 20.9 1.0
CA B:LYS269 4.7 33.2 1.0
N B:CYS268 4.7 34.2 1.0
CB B:GLU271 4.8 26.3 1.0
CG B:TYR194 4.9 17.9 1.0
CA B:ALA265 4.9 29.9 1.0
C B:GLU271 4.9 24.7 1.0

Mercury binding site 9 out of 14 in 1pm2

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Mercury binding site 9 out of 14 in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)


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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg606

b:58.0
occ:0.36
 O B:HOH806 2.3 33.5 1.0
OH B:TYR194 3.6 18.9 1.0
CE2 B:TYR194 3.6 20.7 1.0
O B:ALA265 3.9 28.5 1.0
CD2 B:LEU321 3.9 22.1 1.0
CE B:MET198 4.0 24.0 1.0
CZ B:TYR194 4.1 19.1 1.0
CA B:LYS269 4.1 33.2 1.0
CB B:CYS272 4.1 24.0 1.0
SG B:CYS272 4.3 27.2 1.0
CB B:LYS269 4.4 35.6 1.0
O B:HOH780 4.5 35.8 1.0
HG B:HG605 4.5 19.4 0.5
C B:ALA265 4.6 31.2 1.0
CB B:ALA265 4.6 30.8 1.0
CG B:LEU321 4.8 22.4 1.0
CD2 B:TYR194 4.8 18.5 1.0
N B:LYS269 4.8 33.5 1.0
O B:LYS269 4.9 30.2 1.0
CA B:ALA265 4.9 29.9 1.0
O B:CYS268 5.0 34.6 1.0

Mercury binding site 10 out of 14 in 1pm2

Go back to Mercury Binding Sites List in 1pm2
Mercury binding site 10 out of 14 in the Crystal Structure of Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase)


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 Manganese Substituted R2-D84E (D84E Mutant of the R2 Subunit of E. Coli Ribonucleotide Reductase) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg607

b:22.5
occ:0.49
 HG B:HG613 2.6 30.6 0.4
O B:VAL210 2.8 17.9 1.0
SG B:CYS214 3.3 39.2 1.0
N B:CYS214 3.5 22.2 1.0
CB B:ALA213 3.5 20.9 1.0
CD1 B:LEU304 3.7 32.7 1.0
CB B:CYS214 3.8 26.6 1.0
CD1 B:LEU299 3.9 39.7 1.0
CG B:LEU304 3.9 32.4 1.0
C B:VAL210 3.9 18.6 1.0
CG1 B:VAL210 3.9 22.6 1.0
CA B:CYS214 4.0 23.6 1.0
C B:ALA213 4.1 20.2 1.0
CA B:ALA213 4.3 19.9 1.0
CB B:LEU304 4.4 29.7 1.0
CA B:VAL210 4.6 20.1 1.0
N B:ALA213 4.7 19.1 1.0
N B:SER211 4.9 17.7 1.0
O B:ALA213 4.9 19.7 1.0
CB B:VAL210 4.9 20.2 1.0
CA B:LEU304 5.0 26.3 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: Sun Aug 11 01:06:33 2024

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