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Mercury in PDB 1rsv: Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase

Enzymatic activity of Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase

All present enzymatic activity of Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase:
1.17.4.1;

Protein crystallography data

The structure of Azide Complex of the Diferrous E238A Mutant R2 Subunit of Ribonucleotide Reductase, PDB code: 1rsv was solved by M.Assarsson, M.E.Andersson, M.Hogbom, B.O.Persson, M.Sahlin, A.L.Barra, B.M.Sjoberg, P.Nordlund, A.Graslund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.893, 84.501, 113.963, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1rsv:

The structure of Azide Complex of the Diferrous E238A 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 E238A Mutant R2 Subunit of Ribonucleotide Reductase (pdb code 1rsv). 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 E238A Mutant R2 Subunit of Ribonucleotide Reductase, PDB code: 1rsv:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 12 in 1rsv

Go back to Mercury Binding Sites List in 1rsv
Mercury binding site 1 out of 12 in the Azide Complex of the Diferrous E238A 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 E238A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2001

b:24.6
occ:0.82
 SG A:CYS196 2.2 19.8 1.0
O A:HOH2110 2.4 23.0 1.0
HG A:HG2008 2.8 37.5 0.3
O A:CYS196 3.1 16.2 1.0
CD1 A:TYR157 3.4 17.2 1.0
CA A:CYS196 3.4 15.2 1.0
CB A:CYS196 3.4 15.7 1.0
CB A:TYR156 3.5 32.3 1.0
CE1 A:TYR157 3.5 17.5 1.0
C A:CYS196 3.5 16.8 1.0
CG2 A:VAL200 3.5 19.7 1.0
CG A:TYR157 3.7 16.2 1.0
CZ A:TYR157 3.9 22.9 1.0
N A:TYR157 4.0 19.9 1.0
CD2 A:TYR157 4.0 16.1 1.0
CE2 A:TYR157 4.1 15.9 1.0
CG A:TYR156 4.3 38.5 1.0
CA A:TYR157 4.4 17.9 1.0
CB A:SER199 4.4 18.2 1.0
C A:TYR156 4.5 26.9 1.0
CB A:TYR157 4.5 17.2 1.0
OH A:TYR157 4.6 22.2 1.0
N A:LEU197 4.7 12.9 1.0
N A:VAL200 4.7 15.2 1.0
CA A:TYR156 4.7 28.4 1.0
CD2 A:TYR156 4.8 40.6 1.0
O A:ILE153 4.8 24.9 1.0
N A:CYS196 4.8 15.8 1.0
CB A:VAL200 4.9 19.7 1.0
OG A:SER199 4.9 31.7 1.0

Mercury binding site 2 out of 12 in 1rsv

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Mercury binding site 2 out of 12 in the Azide Complex of the Diferrous E238A 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 E238A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2007

b:24.6
occ:0.80
 O A:HOH2127 1.4 3.6 1.0
SG A:CYS272 2.2 20.6 1.0
OH A:TYR194 2.8 22.7 1.0
CB A:CYS272 3.1 16.9 1.0
O A:HOH2160 3.3 27.7 1.0
O A:ALA265 3.6 29.2 1.0
CE A:MET198 3.6 18.3 1.0
CZ A:TYR194 3.8 24.9 1.0
CE2 A:TYR194 3.8 19.3 1.0
CA A:LYS269 3.8 26.2 1.0
CD2 A:LEU321 4.1 26.4 1.0
N A:LYS269 4.2 27.3 1.0
CG A:LYS269 4.4 50.1 1.0
C A:ALA265 4.5 29.7 1.0
CB A:LYS269 4.5 29.4 1.0
CA A:CYS272 4.6 16.7 1.0
C A:CYS268 4.6 33.5 1.0
CA A:ALA265 4.7 24.8 1.0
O A:HOH2131 4.7 23.4 1.0
O A:CYS268 4.7 33.9 1.0
O A:LYS269 4.7 27.3 1.0
C A:LYS269 4.7 26.6 1.0
CB A:ALA265 4.8 25.7 1.0
CG A:LEU321 4.9 24.5 1.0
SD A:MET198 5.0 21.8 1.0

Mercury binding site 3 out of 12 in 1rsv

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Mercury binding site 3 out of 12 in the Azide Complex of the Diferrous E238A 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 E238A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2008

b:37.5
occ:0.30
 SG A:CYS196 1.8 19.8 1.0
HG A:HG2001 2.8 24.6 0.8
CB A:CYS196 3.0 15.7 1.0
CE1 A:TYR157 3.1 17.5 1.0
CG2 A:VAL200 3.2 19.7 1.0
C A:CYS196 3.3 16.8 1.0
O A:CYS196 3.3 16.2 1.0
CD1 A:TYR157 3.5 17.2 1.0
CA A:CYS196 3.7 15.2 1.0
N A:LEU197 3.7 12.9 1.0
CZ A:TYR157 3.9 22.9 1.0
CA A:LEU197 4.2 13.1 1.0
CD2 A:LEU95 4.2 24.0 1.0
OH A:TYR157 4.3 22.2 1.0
CD2 A:LEU160 4.4 20.6 1.0
CB A:VAL200 4.4 19.7 1.0
CD2 A:LEU197 4.6 19.8 1.0
CG A:TYR157 4.7 16.2 1.0
O A:HOH2110 4.8 23.0 1.0
CE2 A:TYR157 4.9 15.9 1.0
CG A:LEU95 4.9 22.4 1.0
N A:CYS196 4.9 15.8 1.0

Mercury binding site 4 out of 12 in 1rsv

Go back to Mercury Binding Sites List in 1rsv
Mercury binding site 4 out of 12 in the Azide Complex of the Diferrous E238A 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 E238A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2009

b:24.9
occ:0.70
 O A:HOH2165 1.3 17.7 1.0
SG A:CYS214 2.2 23.0 1.0
O A:HOH2149 2.3 73.7 1.0
O A:VAL210 2.9 18.1 1.0
O A:HOH2147 3.0 27.4 1.0
CD2 A:LEU304 3.0 30.7 1.0
N A:CYS214 3.2 19.8 1.0
CB A:CYS214 3.3 19.4 1.0
CA A:CYS214 3.5 19.2 1.0
CG1 A:VAL210 3.7 20.6 1.0
CD1 A:LEU299 3.9 31.4 1.0
CB A:ALA213 3.9 21.7 1.0
C A:VAL210 4.0 19.8 1.0
C A:ALA213 4.0 23.6 1.0
CG A:LEU304 4.1 29.4 1.0
CA A:ALA213 4.4 20.8 1.0
CA A:VAL210 4.5 16.6 1.0
O A:ALA213 4.8 23.4 1.0
CB A:VAL210 4.8 20.5 1.0
O A:HOH2153 4.8 33.1 1.0
N A:ALA213 4.8 21.5 1.0

Mercury binding site 5 out of 12 in 1rsv

Go back to Mercury Binding Sites List in 1rsv
Mercury binding site 5 out of 12 in the Azide Complex of the Diferrous E238A 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 E238A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2011

b:40.1
occ:0.10
 O A:HOH2140 2.5 57.7 1.0
SG A:CYS268 2.6 38.1 1.0
CB A:CYS268 3.7 33.8 1.0
CD A:LYS191 3.8 36.8 1.0
CA A:CYS268 3.9 32.6 1.0
NZ A:LYS191 4.2 52.2 1.0
O A:GLU267 4.2 35.9 1.0
CG A:GLU271 4.2 33.6 1.0
N A:CYS268 4.3 32.8 1.0
CE A:LYS191 4.4 44.1 1.0
C A:GLU267 4.5 35.8 1.0
OE1 A:GLU271 5.0 67.1 1.0

Mercury binding site 6 out of 12 in 1rsv

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Mercury binding site 6 out of 12 in the Azide Complex of the Diferrous E238A 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 E238A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg2012

b:31.6
occ:0.30
 O A:HOH2151 1.3 15.1 1.0
OE2 A:GLU309 3.3 25.2 1.0
NZ A:LYS284 3.5 34.1 1.0
CD A:GLU309 3.6 36.9 1.0
CB A:CYS305 3.6 30.4 1.0
C A:CYS305 3.7 29.7 1.0
N A:GLN306 3.7 23.1 1.0
O A:CYS305 3.8 29.9 1.0
CG A:GLU309 3.9 25.8 1.0
CA A:GLN306 3.9 22.1 1.0
CG A:GLN306 4.1 39.9 1.0
OE1 A:GLU309 4.2 22.3 1.0
NH2 A:ARG328 4.2 61.0 1.0
CA A:CYS305 4.3 29.0 1.0
CB A:GLN306 4.6 23.3 1.0
CZ A:ARG328 4.7 68.2 1.0
CE A:LYS284 4.8 28.2 1.0
O A:ASP302 4.9 30.5 1.0
NH1 A:ARG328 4.9 40.2 1.0

Mercury binding site 7 out of 12 in 1rsv

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Mercury binding site 7 out of 12 in the Azide Complex of the Diferrous E238A 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 E238A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg2002

b:39.2
occ:0.40
 SG B:CYS196 2.0 21.7 1.0
O B:HOH2175 2.7 7.6 1.0
HG B:HG2004 2.8 23.7 0.6
CE1 B:TYR157 3.0 17.3 1.0
CB B:CYS196 3.2 18.5 1.0
O B:CYS196 3.2 18.0 1.0
CG2 B:VAL200 3.3 19.6 1.0
C B:CYS196 3.3 19.6 1.0
CD1 B:TYR157 3.4 17.8 1.0
CA B:CYS196 3.8 18.7 1.0
N B:LEU197 3.8 15.5 1.0
CZ B:TYR157 3.9 21.3 1.0
CA B:LEU197 4.3 16.1 1.0
CD2 B:LEU160 4.3 21.8 1.0
OH B:TYR157 4.4 21.9 1.0
CG B:TYR157 4.5 16.0 1.0
CB B:VAL200 4.5 20.0 1.0
CD2 B:LEU95 4.6 21.8 1.0
CD2 B:LEU197 4.8 21.4 1.0
O B:HOH2138 4.8 15.5 1.0
CE2 B:TYR157 4.9 16.6 1.0
O B:LEU193 5.0 24.7 1.0
CG B:LEU197 5.0 19.4 1.0

Mercury binding site 8 out of 12 in 1rsv

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Mercury binding site 8 out of 12 in the Azide Complex of the Diferrous E238A 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 E238A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg2003

b:49.3
occ:0.40
 O B:HOH2030 2.6 56.4 1.0
CD2 B:LEU195 2.8 31.9 1.0
SG B:CYS268 2.8 48.9 1.0
SG B:CYS272 2.9 44.0 1.0
O B:HOH2171 2.9 42.8 1.0
O B:CYS268 3.0 45.1 1.0
CB B:CYS268 3.1 44.9 1.0
C B:CYS268 3.5 46.6 1.0
CD1 B:TYR194 3.7 28.5 1.0
CB B:CYS272 3.7 39.2 1.0
CA B:CYS268 3.7 44.4 1.0
CE1 B:TYR194 3.8 30.4 1.0
N B:CYS272 3.9 38.7 1.0
CG B:LEU195 4.1 28.4 1.0
CA B:CYS272 4.2 38.1 1.0
N B:LYS269 4.4 42.7 1.0
CB B:GLU271 4.4 42.2 1.0
N B:CYS268 4.7 44.6 1.0
C B:GLU271 4.7 43.3 1.0
O B:ALA265 4.8 48.4 1.0
O B:HOH2137 4.9 13.4 1.0
CD2 B:LEU275 4.9 41.6 1.0
CG B:TYR194 4.9 26.1 1.0
CA B:LEU195 5.0 22.8 1.0

Mercury binding site 9 out of 12 in 1rsv

Go back to Mercury Binding Sites List in 1rsv
Mercury binding site 9 out of 12 in the Azide Complex of the Diferrous E238A 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 E238A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg2004

b:23.7
occ:0.59
 O B:HOH2175 1.1 7.6 1.0
SG B:CYS196 2.0 21.7 1.0
O B:HOH2138 2.3 15.5 1.0
HG B:HG2002 2.8 39.2 0.4
O B:CYS196 3.0 18.0 1.0
CB B:CYS196 3.4 18.5 1.0
CA B:CYS196 3.4 18.7 1.0
CG2 B:VAL200 3.5 19.6 1.0
CB B:TYR156 3.5 24.8 1.0
C B:CYS196 3.5 19.6 1.0
CD1 B:TYR157 3.5 17.8 1.0
CE1 B:TYR157 3.7 17.3 1.0
CG B:TYR157 3.7 16.0 1.0
N B:TYR157 3.8 17.6 1.0
CD2 B:TYR157 4.0 16.1 1.0
CZ B:TYR157 4.1 21.3 1.0
C B:TYR156 4.1 23.0 1.0
CA B:TYR157 4.2 16.1 1.0
CE2 B:TYR157 4.2 16.6 1.0
OG B:SER199 4.3 39.0 1.0
CB B:SER199 4.4 25.0 1.0
CB B:TYR157 4.4 15.7 1.0
CA B:TYR156 4.5 22.3 1.0
CG B:TYR156 4.5 28.5 1.0
N B:VAL200 4.6 17.5 1.0
O B:ILE153 4.6 22.4 1.0
O B:TYR156 4.6 21.6 1.0
N B:LEU197 4.7 15.5 1.0
CB B:VAL200 4.8 20.0 1.0
N B:CYS196 4.8 20.3 1.0
OH B:TYR157 4.9 21.9 1.0

Mercury binding site 10 out of 12 in 1rsv

Go back to Mercury Binding Sites List in 1rsv
Mercury binding site 10 out of 12 in the Azide Complex of the Diferrous E238A 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 E238A Mutant R2 Subunit of Ribonucleotide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg2006

b:35.5
occ:0.20
 CE B:MET296 2.6 73.5 1.0
O B:CYS214 3.1 21.2 1.0
CG2 B:ILE72 3.1 33.5 1.0
CB B:CYS214 3.2 10.7 1.0
CA B:CYS214 3.3 13.3 1.0
C B:CYS214 3.4 20.4 1.0
CE2 B:PHE218 3.6 31.6 1.0
SD B:MET296 4.0 77.0 1.0
CD2 B:LEU299 4.0 55.9 1.0
CD2 B:PHE218 4.2 29.7 1.0
CB B:ALA217 4.2 23.1 1.0
CZ B:PHE218 4.4 29.3 1.0
CB B:ILE72 4.5 32.9 1.0
CZ B:PHE291 4.6 71.2 1.0
N B:SER215 4.7 18.7 1.0
N B:CYS214 4.8 16.5 1.0
CG B:LEU299 4.8 53.6 1.0
SG B:CYS214 4.9 11.9 1.0
O B:ALA213 5.0 24.6 1.0

Reference:

M.Assarsson, M.E.Andersson, M.Hogbom, B.O.Persson, M.Sahlin, A.L.Barra, B.M.Sjoberg, P.Nordlund, A.Graslund. Restoring Proper Radical Generation By Azide Binding to the Iron Site of the E238A Mutant R2 Protein of Ribonucleotide Reductase From Escherichia Coli. J.Biol.Chem. V. 276 26852 2001.
ISSN: ISSN 0021-9258
PubMed: 11328804
DOI: 10.1074/JBC.M008190200
Page generated: Sun Aug 11 01:39:34 2024

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