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Mercury in PDB 1rsr: Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase

Enzymatic activity of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase

All present enzymatic activity of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase:
1.17.4.1;

Protein crystallography data

The structure of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase, PDB code: 1rsr was solved by M.E.Andersson, M.Hogbom, A.Rinaldo-Matthis, K.K.Andersson, 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.800, 84.200, 113.500, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1rsr:

The structure of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Mercury atom in the Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase (pdb code 1rsr). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 12 binding sites of Mercury where determined in the Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase, PDB code: 1rsr:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 12 in 1rsr

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Mercury binding site 1 out of 12 in the Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2001

b:27.9
occ:0.82
O A:HOH2132 2.2 32.2 1.0
SG A:CYS196 2.2 25.2 1.0
HG A:HG2008 3.0 46.0 0.3
O A:CYS196 3.1 21.3 1.0
HG A:HG2013 3.2 58.8 0.2
CB A:CYS196 3.4 23.1 1.0
CA A:CYS196 3.4 20.9 1.0
CD1 A:TYR157 3.5 21.9 1.0
CE1 A:TYR157 3.6 19.3 1.0
CB A:TYR156 3.6 39.1 1.0
C A:CYS196 3.6 20.1 1.0
CG A:TYR157 3.8 21.3 1.0
CZ A:TYR157 3.8 23.6 1.0
CG2 A:VAL200 3.9 25.5 1.0
CD2 A:TYR157 4.0 24.5 1.0
N A:TYR157 4.0 28.9 1.0
CE2 A:TYR157 4.0 21.6 1.0
O A:HOH2137 4.3 0.7 1.0
C A:TYR156 4.4 32.0 1.0
CB A:SER199 4.4 26.1 1.0
CA A:TYR157 4.4 25.8 1.0
OG A:SER199 4.5 34.3 1.0
CG A:TYR156 4.5 44.9 1.0
OH A:TYR157 4.5 23.2 1.0
CA A:TYR156 4.6 34.5 1.0
CB A:TYR157 4.6 25.2 1.0
O A:ILE153 4.7 37.4 1.0
N A:VAL200 4.7 21.3 1.0
N A:LEU197 4.8 18.6 1.0
N A:CYS196 4.9 19.5 1.0
CD2 A:TYR156 4.9 47.4 1.0
O A:TYR156 5.0 30.2 1.0

Mercury binding site 2 out of 12 in 1rsr

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Mercury binding site 2 out of 12 in the Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2005

b:28.9
occ:0.15
CB A:CYS272 2.4 33.0 1.0
HG A:HG2007 2.5 24.6 0.6
SG A:CYS272 2.7 52.7 1.0
O A:HOH2158 2.7 58.9 1.0
CA A:CYS272 3.0 28.2 1.0
CE2 A:TYR194 3.2 25.6 1.0
N A:CYS272 3.5 26.0 1.0
O A:CYS268 3.5 31.2 1.0
OH A:TYR194 3.8 26.2 1.0
CE A:MET198 3.8 19.2 1.0
CZ A:TYR194 3.9 25.8 1.0
C A:CYS268 4.0 31.7 1.0
CG A:MET198 4.0 20.9 1.0
CD2 A:TYR194 4.1 25.3 1.0
CD2 A:LEU195 4.1 30.1 1.0
CA A:LYS269 4.3 32.3 1.0
CB A:CYS268 4.3 33.3 1.0
N A:LYS269 4.4 32.3 1.0
O A:HOH2131 4.4 36.8 1.0
C A:CYS272 4.4 26.8 1.0
O A:LYS269 4.6 31.6 1.0
SD A:MET198 4.6 22.6 1.0
CB A:MET198 4.6 19.1 1.0
C A:GLU271 4.7 27.6 1.0
C A:LYS269 4.7 32.0 1.0
O A:ALA265 4.8 37.1 1.0
CA A:CYS268 4.8 33.4 1.0

Mercury binding site 3 out of 12 in 1rsr

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Mercury binding site 3 out of 12 in the Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2007

b:24.6
occ:0.60
O A:HOH2131 2.3 36.8 1.0
O A:HOH2158 2.4 58.9 1.0
HG A:HG2005 2.5 28.9 0.1
OH A:TYR194 2.9 26.2 1.0
O A:HOH2159 2.9 46.3 1.0
SG A:CYS272 2.9 52.7 1.0
CB A:CYS272 3.3 33.0 1.0
O A:ALA265 3.5 37.1 1.0
CZ A:TYR194 3.8 25.8 1.0
CE2 A:TYR194 3.8 25.6 1.0
CA A:LYS269 3.9 32.3 1.0
CE A:MET198 3.9 19.2 1.0
CD2 A:LEU321 4.0 29.0 1.0
N A:LYS269 4.3 32.3 1.0
C A:ALA265 4.5 39.0 1.0
CB A:LYS269 4.5 36.9 1.0
C A:CYS268 4.6 31.7 1.0
O A:HOH2116 4.6 26.7 1.0
CG A:LYS269 4.6 43.8 1.0
O A:CYS268 4.7 31.2 1.0
CA A:CYS272 4.7 28.2 1.0
O A:LYS269 4.7 31.6 1.0
C A:LYS269 4.8 32.0 1.0
CA A:ALA265 4.8 37.6 1.0
CB A:ALA265 5.0 37.7 1.0
CG A:LEU321 5.0 30.4 1.0

Mercury binding site 4 out of 12 in 1rsr

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Mercury binding site 4 out of 12 in the Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2008

b:46.0
occ:0.35
SG A:CYS196 2.2 25.2 1.0
O A:HOH2137 2.8 0.7 1.0
HG A:HG2001 3.0 27.9 0.8
CE1 A:TYR157 3.2 19.3 1.0
O A:CYS196 3.3 21.3 1.0
CB A:CYS196 3.4 23.1 1.0
C A:CYS196 3.4 20.1 1.0
CG2 A:VAL200 3.4 25.5 1.0
N A:LEU197 3.8 18.6 1.0
CD1 A:TYR157 3.9 21.9 1.0
CA A:CYS196 3.9 20.9 1.0
CZ A:TYR157 3.9 23.6 1.0
CD2 A:LEU95 4.0 22.5 1.0
OH A:TYR157 4.2 23.2 1.0
CA A:LEU197 4.2 19.1 1.0
CD2 A:LEU197 4.2 23.6 1.0
CB A:VAL200 4.3 24.1 1.0
CD1 A:LEU95 4.6 22.1 1.0
CG A:LEU95 4.6 21.4 1.0
CG A:LEU197 4.8 21.2 1.0
CD2 A:LEU160 4.9 21.0 1.0
CG A:TYR157 5.0 21.3 1.0
CE2 A:TYR157 5.0 21.6 1.0

Mercury binding site 5 out of 12 in 1rsr

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Mercury binding site 5 out of 12 in the Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2009

b:28.1
occ:0.50
O A:HOH2136 2.2 30.6 1.0
O A:HOH2138 2.2 49.8 1.0
SG A:CYS214 2.4 34.2 1.0
O A:VAL210 2.9 31.4 1.0
N A:CYS214 3.3 30.6 1.0
CB A:CYS214 3.5 30.7 1.0
CA A:CYS214 3.7 31.5 1.0
CB A:ALA213 3.8 31.9 1.0
CD1 A:LEU299 3.9 49.9 1.0
C A:VAL210 4.0 32.1 1.0
C A:ALA213 4.0 31.5 1.0
CG1 A:VAL210 4.1 30.4 1.0
CA A:ALA213 4.4 31.1 1.0
CD1 A:LEU304 4.5 39.2 1.0
CG A:LEU304 4.5 38.4 1.0
CA A:VAL210 4.6 29.4 1.0
O A:ALA213 4.8 32.5 1.0
O A:HOH2150 4.8 37.4 1.0
CB A:LEU304 4.9 35.8 1.0
N A:ALA213 4.9 31.9 1.0
CB A:VAL210 5.0 29.5 1.0

Mercury binding site 6 out of 12 in 1rsr

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Mercury binding site 6 out of 12 in the Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2013

b:58.8
occ:0.20
O A:HOH2132 2.2 32.2 1.0
HG A:HG2001 3.2 27.9 0.8
CG2 A:VAL200 3.3 25.5 1.0
OG A:SER199 3.3 34.3 1.0
N A:VAL200 3.6 21.3 1.0
CA A:VAL200 3.7 21.5 1.0
CE2 A:TYR157 3.7 21.6 1.0
C A:SER199 3.7 22.7 1.0
CG2 A:ILE153 3.8 40.3 1.0
O A:SER199 3.9 20.6 1.0
CB A:SER199 4.0 26.1 1.0
CZ A:TYR157 4.0 23.6 1.0
CB A:VAL200 4.1 24.1 1.0
OH A:TYR157 4.2 23.2 1.0
CD2 A:TYR157 4.3 24.5 1.0
CD1 A:LEU203 4.3 35.5 1.0
O A:CYS196 4.3 21.3 1.0
O A:ILE153 4.5 37.4 1.0
CA A:SER199 4.5 21.9 1.0
CA A:ILE153 4.5 41.0 1.0
CB A:ILE153 4.7 42.2 1.0
NE2 A:GLN87 4.7 22.8 1.0
CE1 A:TYR157 4.8 19.3 1.0
CB A:LEU203 4.8 32.8 1.0
C A:ILE153 4.9 39.4 1.0
O A:HOH2025 4.9 38.9 1.0
CG1 A:ILE153 4.9 43.5 1.0
O A:HOH2137 5.0 0.7 1.0

Mercury binding site 7 out of 12 in 1rsr

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Mercury binding site 7 out of 12 in the Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg2002

b:33.2
occ:0.60
SG B:CYS196 2.4 25.0 1.0
HG B:HG2004 2.9 31.9 0.6
CE1 B:TYR157 3.1 19.8 1.0
O B:CYS196 3.2 17.7 1.0
CB B:CYS196 3.3 22.4 1.0
CG2 B:VAL200 3.3 25.2 1.0
C B:CYS196 3.3 19.1 1.0
CD1 B:TYR157 3.5 16.5 1.0
N B:LEU197 3.8 18.9 1.0
CA B:CYS196 3.9 20.8 1.0
CZ B:TYR157 3.9 19.2 1.0
CA B:LEU197 4.3 16.0 1.0
OH B:TYR157 4.3 21.0 1.0
CB B:VAL200 4.4 23.1 1.0
CD2 B:LEU160 4.5 14.9 1.0
CD2 B:LEU95 4.5 23.8 1.0
CD2 B:LEU197 4.5 21.7 1.0
CG B:TYR157 4.6 18.8 1.0
CE2 B:TYR157 4.8 20.1 1.0
CG B:LEU197 4.9 17.5 1.0
CG B:LEU95 4.9 22.6 1.0

Mercury binding site 8 out of 12 in 1rsr

Go back to Mercury Binding Sites List in 1rsr
Mercury binding site 8 out of 12 in the Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg2003

b:46.2
occ:0.81
SG B:CYS272 2.5 36.9 1.0
SG B:CYS268 2.7 43.5 1.0
O B:CYS268 2.8 39.9 1.0
O B:HOH2029 2.9 43.8 1.0
CB B:CYS268 3.2 41.6 1.0
C B:CYS268 3.2 41.0 1.0
CD2 B:LEU195 3.4 27.0 1.0
CB B:CYS272 3.5 35.0 1.0
CD1 B:TYR194 3.7 29.1 1.0
CA B:CYS268 3.8 43.2 1.0
N B:CYS272 3.9 34.8 1.0
CE1 B:TYR194 3.9 30.8 1.0
N B:LYS269 4.0 41.6 1.0
CA B:CYS272 4.1 33.9 1.0
CA B:LYS269 4.4 42.5 1.0
O B:ALA265 4.4 47.1 1.0
CG B:LEU195 4.5 23.9 1.0
CB B:GLU271 4.7 38.5 1.0
N B:CYS268 4.7 43.3 1.0
CG B:TYR194 4.8 27.7 1.0
C B:GLU271 4.9 36.2 1.0
C B:LYS269 5.0 41.4 1.0

Mercury binding site 9 out of 12 in 1rsr

Go back to Mercury Binding Sites List in 1rsr
Mercury binding site 9 out of 12 in the Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg2004

b:31.9
occ:0.59
SG B:CYS196 2.2 25.0 1.0
O B:HOH2134 2.4 22.7 1.0
HG B:HG2002 2.9 33.2 0.6
O B:CYS196 2.9 17.7 1.0
CD1 B:TYR157 3.4 16.5 1.0
CG2 B:VAL200 3.4 25.2 1.0
CB B:CYS196 3.4 22.4 1.0
CA B:CYS196 3.4 20.8 1.0
C B:CYS196 3.5 19.1 1.0
CG B:TYR157 3.5 18.8 1.0
CE1 B:TYR157 3.5 19.8 1.0
CB B:TYR156 3.7 28.2 1.0
CD2 B:TYR157 3.7 17.1 1.0
N B:TYR157 3.8 24.0 1.0
CZ B:TYR157 3.8 19.2 1.0
CE2 B:TYR157 3.9 20.1 1.0
CA B:TYR157 4.1 21.7 1.0
C B:TYR156 4.2 25.2 1.0
CB B:SER199 4.2 22.0 1.0
CB B:TYR157 4.3 21.7 1.0
O B:ILE153 4.4 29.0 1.0
OG B:SER199 4.5 29.3 1.0
N B:VAL200 4.5 19.7 1.0
CA B:TYR156 4.6 25.0 1.0
OH B:TYR157 4.7 21.0 1.0
N B:LEU197 4.7 18.9 1.0
CB B:VAL200 4.7 23.1 1.0
O B:TYR156 4.8 23.6 1.0
CG B:TYR156 4.8 30.9 1.0
N B:CYS196 4.9 18.9 1.0

Mercury binding site 10 out of 12 in 1rsr

Go back to Mercury Binding Sites List in 1rsr
Mercury binding site 10 out of 12 in the Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Azide Complex of the Diferrous F208A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg2006

b:54.6
occ:0.15
O B:CYS214 2.8 31.8 1.0
CG2 B:ILE72 3.1 38.8 1.0
CA B:CYS214 3.2 30.4 1.0
C B:CYS214 3.3 31.0 1.0
SD B:MET296 3.4 69.7 1.0
CB B:CYS214 3.4 30.5 1.0
CE2 B:PHE218 3.5 31.1 1.0
CD2 B:LEU299 3.8 58.1 1.0
CD2 B:PHE218 4.1 32.1 1.0
SG B:CYS214 4.2 30.7 1.0
CZ B:PHE218 4.3 32.6 1.0
CB B:ILE72 4.4 38.2 1.0
CE B:MET296 4.4 71.5 1.0
CB B:ALA217 4.5 29.1 1.0
N B:SER215 4.6 30.6 1.0
N B:CYS214 4.6 29.9 1.0
CG B:MET296 4.9 69.7 1.0
CG B:LEU299 5.0 57.6 1.0

Reference:

M.E.Andersson, M.Hogbom, A.Rinaldo-Matthis, K.K.Andersson, B.M.Sjoberg, P.Nordlund. The Crystal Structure of An Azide Complex of the Diferrous R2 Subunit of Ribonucleotide Reductase Displays A Novel Carboxylate Shift with Important Mechanistic Implications For Diiron-Catalyzed Oxygen Activation J.Am.Chem.Soc. V. 121 2346 1999.
ISSN: ISSN 0002-7863
DOI: 10.1021/JA982280C
Page generated: Wed Oct 28 18:40:34 2020

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