Mercury in PDB 1pj0: Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Enzymatic activity of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
All present enzymatic activity of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH:
1.17.4.1;
Protein crystallography data
The structure of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH, PDB code: 1pj0
was solved by
W.C.Voegtli,
M.Sommerhalter,
L.Saleh,
J.Baldwin,
J.M.Bollinger Jr.,
A.C.Rosenzweig,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.32 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.000,
84.400,
114.600,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.4 /
23.6
|
Other elements in 1pj0:
The structure of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH also contains other interesting chemical elements:
Mercury Binding Sites:
The binding sites of Mercury atom in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
(pdb code 1pj0). This binding sites where shown within
5.0 Angstroms radius around Mercury atom.
In total 9 binding sites of Mercury where determined in the
Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH, PDB code: 1pj0:
Jump to Mercury binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Mercury binding site 1 out
of 9 in 1pj0
Go back to
Mercury Binding Sites List in 1pj0
Mercury binding site 1 out
of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 1 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg378
b:26.1
occ:1.00
|
SG
|
A:CYS272
|
2.4
|
18.6
|
1.0
|
OH
|
A:TYR194
|
2.8
|
20.5
|
1.0
|
CB
|
A:CYS272
|
3.3
|
17.6
|
1.0
|
O
|
A:ALA265
|
3.5
|
24.5
|
1.0
|
CZ
|
A:TYR194
|
3.8
|
19.3
|
1.0
|
CA
|
A:LYS269
|
3.8
|
24.9
|
1.0
|
CE2
|
A:TYR194
|
3.8
|
19.2
|
1.0
|
CE
|
A:MET198
|
4.0
|
18.5
|
1.0
|
CD2
|
A:LEU321
|
4.1
|
16.5
|
1.0
|
SG
|
A:CYS268
|
4.1
|
30.3
|
1.0
|
N
|
A:LYS269
|
4.1
|
25.6
|
1.0
|
C
|
A:ALA265
|
4.4
|
24.1
|
1.0
|
O
|
A:HOH426
|
4.4
|
23.5
|
1.0
|
CB
|
A:LYS269
|
4.5
|
26.4
|
1.0
|
C
|
A:CYS268
|
4.5
|
26.2
|
1.0
|
O
|
A:LYS269
|
4.6
|
23.2
|
1.0
|
CA
|
A:ALA265
|
4.6
|
23.4
|
1.0
|
O
|
A:CYS268
|
4.7
|
25.9
|
1.0
|
CA
|
A:CYS272
|
4.7
|
17.3
|
1.0
|
C
|
A:LYS269
|
4.7
|
24.1
|
1.0
|
CB
|
A:ALA265
|
4.8
|
22.4
|
1.0
|
CG
|
A:LEU321
|
4.9
|
16.3
|
1.0
|
CG
|
A:MET198
|
5.0
|
18.1
|
1.0
|
|
Mercury binding site 2 out
of 9 in 1pj0
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Mercury Binding Sites List in 1pj0
Mercury binding site 2 out
of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 2 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg379
b:22.8
occ:1.00
|
SG
|
A:CYS196
|
2.3
|
18.3
|
1.0
|
O
|
A:CYS196
|
3.1
|
15.1
|
1.0
|
CB
|
A:CYS196
|
3.3
|
16.1
|
1.0
|
CA
|
A:CYS196
|
3.4
|
15.7
|
1.0
|
CD1
|
A:TYR157
|
3.6
|
14.1
|
1.0
|
CE1
|
A:TYR157
|
3.6
|
14.7
|
1.0
|
C
|
A:CYS196
|
3.6
|
15.5
|
1.0
|
CG2
|
A:VAL200
|
3.7
|
12.9
|
1.0
|
CG
|
A:TYR157
|
3.9
|
14.4
|
1.0
|
CZ
|
A:TYR157
|
3.9
|
14.5
|
1.0
|
CD2
|
A:TYR157
|
4.1
|
14.1
|
1.0
|
CB
|
A:TYR156
|
4.2
|
23.8
|
1.0
|
CE2
|
A:TYR157
|
4.2
|
13.9
|
1.0
|
CD1
|
A:TYR156
|
4.2
|
27.4
|
1.0
|
N
|
A:TYR157
|
4.2
|
18.1
|
1.0
|
CB
|
A:SER199
|
4.3
|
14.4
|
1.0
|
CA
|
A:TYR157
|
4.5
|
16.6
|
1.0
|
CG
|
A:TYR156
|
4.5
|
26.7
|
1.0
|
C
|
A:TYR156
|
4.6
|
19.9
|
1.0
|
OH
|
A:TYR157
|
4.7
|
15.7
|
1.0
|
N
|
A:VAL200
|
4.7
|
11.8
|
1.0
|
CB
|
A:TYR157
|
4.7
|
15.4
|
1.0
|
O
|
A:ILE153
|
4.7
|
20.5
|
1.0
|
N
|
A:CYS196
|
4.8
|
15.4
|
1.0
|
N
|
A:LEU197
|
4.8
|
14.9
|
1.0
|
OG
|
A:SER199
|
4.9
|
15.4
|
1.0
|
|
Mercury binding site 3 out
of 9 in 1pj0
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Mercury Binding Sites List in 1pj0
Mercury binding site 3 out
of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 3 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg380
b:34.6
occ:1.00
|
SG
|
A:CYS214
|
2.3
|
24.6
|
1.0
|
O
|
A:VAL210
|
2.8
|
18.5
|
1.0
|
N
|
A:CYS214
|
3.2
|
20.8
|
1.0
|
CB
|
A:CYS214
|
3.5
|
21.8
|
1.0
|
CA
|
A:CYS214
|
3.6
|
21.2
|
1.0
|
CB
|
A:ALA213
|
3.7
|
20.4
|
1.0
|
CD1
|
A:LEU299
|
4.0
|
24.1
|
1.0
|
C
|
A:ALA213
|
4.0
|
20.7
|
1.0
|
C
|
A:VAL210
|
4.0
|
19.4
|
1.0
|
CG1
|
A:VAL210
|
4.1
|
20.0
|
1.0
|
CD1
|
A:LEU304
|
4.1
|
21.1
|
1.0
|
CA
|
A:ALA213
|
4.4
|
20.3
|
1.0
|
O
|
A:HOH452
|
4.5
|
37.1
|
1.0
|
CG
|
A:LEU304
|
4.5
|
21.1
|
1.0
|
CA
|
A:VAL210
|
4.7
|
18.9
|
1.0
|
O
|
A:ALA213
|
4.8
|
20.4
|
1.0
|
CB
|
A:LEU304
|
4.8
|
20.7
|
1.0
|
N
|
A:ALA213
|
4.9
|
20.3
|
1.0
|
N
|
A:SER211
|
5.0
|
19.2
|
1.0
|
|
Mercury binding site 4 out
of 9 in 1pj0
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Mercury Binding Sites List in 1pj0
Mercury binding site 4 out
of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 4 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg381
b:44.5
occ:0.50
|
OE2
|
A:GLU309
|
3.1
|
19.7
|
1.0
|
CB
|
A:CYS305
|
3.4
|
23.2
|
1.0
|
CD
|
A:GLU309
|
3.4
|
18.7
|
1.0
|
NZ
|
A:LYS284
|
3.4
|
24.4
|
1.0
|
C
|
A:CYS305
|
3.5
|
21.0
|
1.0
|
O
|
A:CYS305
|
3.6
|
20.9
|
1.0
|
N
|
A:GLN306
|
3.7
|
19.8
|
1.0
|
OE1
|
A:GLU309
|
3.9
|
19.2
|
1.0
|
CG
|
A:GLU309
|
4.0
|
17.4
|
1.0
|
CA
|
A:GLN306
|
4.0
|
19.3
|
1.0
|
CA
|
A:CYS305
|
4.1
|
21.8
|
1.0
|
CG
|
A:GLN306
|
4.3
|
22.5
|
1.0
|
NH2
|
A:ARG328
|
4.5
|
36.9
|
1.0
|
CE
|
A:LYS284
|
4.7
|
25.1
|
1.0
|
SG
|
A:CYS305
|
4.8
|
29.9
|
1.0
|
CB
|
A:GLN306
|
4.8
|
20.4
|
1.0
|
O
|
A:ASP302
|
4.9
|
23.8
|
1.0
|
CZ
|
A:ARG328
|
4.9
|
36.5
|
1.0
|
CB
|
A:GLU309
|
4.9
|
16.4
|
1.0
|
|
Mercury binding site 5 out
of 9 in 1pj0
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Mercury Binding Sites List in 1pj0
Mercury binding site 5 out
of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 5 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg382
b:0.1
occ:0.50
|
CB
|
A:CYS268
|
2.7
|
28.0
|
1.0
|
CA
|
A:CYS268
|
3.0
|
27.4
|
1.0
|
N
|
A:CYS268
|
3.1
|
27.5
|
1.0
|
O
|
A:ILE264
|
3.5
|
22.0
|
1.0
|
C
|
A:GLU267
|
3.7
|
28.2
|
1.0
|
CG2
|
A:ILE264
|
3.8
|
21.4
|
1.0
|
CD
|
A:LYS191
|
4.0
|
24.5
|
1.0
|
CG
|
A:LYS191
|
4.1
|
22.7
|
1.0
|
O
|
A:GLU267
|
4.2
|
28.1
|
1.0
|
CB
|
A:GLU267
|
4.2
|
29.9
|
1.0
|
SG
|
A:CYS268
|
4.3
|
30.3
|
1.0
|
C
|
A:ILE264
|
4.4
|
21.9
|
1.0
|
CB
|
A:LYS191
|
4.5
|
19.5
|
1.0
|
C
|
A:CYS268
|
4.5
|
26.2
|
1.0
|
CE
|
A:LYS191
|
4.5
|
26.6
|
1.0
|
CA
|
A:GLU267
|
4.6
|
28.5
|
1.0
|
CA
|
A:ILE264
|
4.7
|
21.5
|
1.0
|
CB
|
A:ILE264
|
4.8
|
21.4
|
1.0
|
OE1
|
A:GLU267
|
5.0
|
34.8
|
1.0
|
|
Mercury binding site 6 out
of 9 in 1pj0
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Mercury Binding Sites List in 1pj0
Mercury binding site 6 out
of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 6 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg378
b:32.3
occ:1.00
|
CB
|
B:CYS196
|
2.6
|
13.9
|
1.0
|
CA
|
B:CYS196
|
2.8
|
16.2
|
1.0
|
SG
|
B:CYS196
|
2.9
|
6.6
|
1.0
|
O
|
B:CYS196
|
3.1
|
16.8
|
1.0
|
C
|
B:CYS196
|
3.3
|
16.1
|
1.0
|
CG2
|
B:VAL200
|
3.4
|
17.1
|
1.0
|
CB
|
B:TYR156
|
3.6
|
21.9
|
1.0
|
CD1
|
B:TYR157
|
3.6
|
16.4
|
1.0
|
CG
|
B:TYR157
|
3.7
|
15.2
|
1.0
|
CE1
|
B:TYR157
|
3.7
|
14.8
|
1.0
|
CD2
|
B:TYR157
|
3.8
|
15.0
|
1.0
|
CZ
|
B:TYR157
|
3.9
|
15.2
|
1.0
|
N
|
B:TYR157
|
3.9
|
18.1
|
1.0
|
CE2
|
B:TYR157
|
3.9
|
14.7
|
1.0
|
C
|
B:TYR156
|
4.2
|
19.4
|
1.0
|
N
|
B:CYS196
|
4.2
|
18.1
|
1.0
|
CB
|
B:SER199
|
4.3
|
18.5
|
1.0
|
CA
|
B:TYR157
|
4.3
|
16.4
|
1.0
|
CB
|
B:TYR157
|
4.5
|
15.6
|
1.0
|
N
|
B:LEU197
|
4.5
|
16.7
|
1.0
|
O
|
B:ILE153
|
4.5
|
22.8
|
1.0
|
CA
|
B:TYR156
|
4.5
|
20.5
|
1.0
|
N
|
B:VAL200
|
4.6
|
15.8
|
1.0
|
CG
|
B:TYR156
|
4.6
|
24.1
|
1.0
|
O
|
B:TYR156
|
4.7
|
18.6
|
1.0
|
OH
|
B:TYR157
|
4.7
|
14.2
|
1.0
|
CB
|
B:VAL200
|
4.8
|
16.0
|
1.0
|
O
|
B:LEU195
|
4.9
|
19.6
|
1.0
|
OG
|
B:SER199
|
5.0
|
22.5
|
1.0
|
|
Mercury binding site 7 out
of 9 in 1pj0
Go back to
Mercury Binding Sites List in 1pj0
Mercury binding site 7 out
of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 7 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg379
b:26.1
occ:0.50
|
SG
|
B:CYS272
|
2.3
|
29.9
|
1.0
|
SG
|
B:CYS268
|
2.5
|
38.5
|
1.0
|
O
|
B:CYS268
|
2.6
|
37.2
|
1.0
|
CB
|
B:CYS268
|
3.2
|
38.1
|
1.0
|
C
|
B:CYS268
|
3.3
|
37.2
|
1.0
|
CB
|
B:CYS272
|
3.4
|
27.3
|
1.0
|
CD2
|
B:TYR194
|
3.5
|
19.6
|
1.0
|
CE2
|
B:TYR194
|
3.8
|
21.0
|
1.0
|
CA
|
B:CYS268
|
3.9
|
37.7
|
1.0
|
N
|
B:CYS272
|
4.0
|
27.7
|
1.0
|
CD2
|
B:LEU195
|
4.0
|
24.6
|
1.0
|
CA
|
B:CYS272
|
4.2
|
27.0
|
1.0
|
N
|
B:LYS269
|
4.2
|
36.4
|
1.0
|
O
|
B:ALA265
|
4.5
|
36.0
|
1.0
|
CA
|
B:LYS269
|
4.5
|
35.7
|
1.0
|
N
|
B:CYS268
|
4.7
|
38.1
|
1.0
|
CG
|
B:TYR194
|
4.7
|
19.5
|
1.0
|
O
|
B:HOH388
|
4.8
|
25.5
|
1.0
|
CB
|
B:GLU271
|
4.8
|
30.5
|
1.0
|
CA
|
B:ALA265
|
4.9
|
35.7
|
1.0
|
C
|
B:GLU271
|
5.0
|
29.1
|
1.0
|
|
Mercury binding site 8 out
of 9 in 1pj0
Go back to
Mercury Binding Sites List in 1pj0
Mercury binding site 8 out
of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 8 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg380
b:41.2
occ:0.50
|
SG
|
B:CYS214
|
2.6
|
18.4
|
1.0
|
O
|
B:VAL210
|
2.8
|
20.9
|
1.0
|
N
|
B:CYS214
|
3.1
|
22.7
|
1.0
|
CD1
|
B:LEU304
|
3.1
|
31.3
|
1.0
|
CA
|
B:CYS214
|
3.5
|
22.7
|
1.0
|
CB
|
B:CYS214
|
3.5
|
21.8
|
1.0
|
CG
|
B:LEU304
|
3.6
|
31.0
|
1.0
|
CB
|
B:ALA213
|
3.6
|
22.3
|
1.0
|
CG1
|
B:VAL210
|
3.8
|
22.0
|
1.0
|
C
|
B:VAL210
|
3.9
|
20.7
|
1.0
|
C
|
B:ALA213
|
3.9
|
22.4
|
1.0
|
CD2
|
B:LEU299
|
4.2
|
42.7
|
1.0
|
CA
|
B:ALA213
|
4.3
|
21.7
|
1.0
|
CD1
|
B:LEU299
|
4.3
|
42.6
|
1.0
|
CB
|
B:LEU304
|
4.3
|
30.1
|
1.0
|
CA
|
B:VAL210
|
4.5
|
21.1
|
1.0
|
N
|
B:ALA213
|
4.6
|
21.1
|
1.0
|
CG
|
B:LEU299
|
4.6
|
42.4
|
1.0
|
O
|
B:ALA213
|
4.7
|
22.5
|
1.0
|
CD2
|
B:LEU304
|
4.8
|
31.0
|
1.0
|
CB
|
B:VAL210
|
4.8
|
21.4
|
1.0
|
N
|
B:SER211
|
4.9
|
20.1
|
1.0
|
|
Mercury binding site 9 out
of 9 in 1pj0
Go back to
Mercury Binding Sites List in 1pj0
Mercury binding site 9 out
of 9 in the Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 9 of Ribonucleotide Reductase R2-D84E/W48F Mutant Soaked with Ferrous Ions at Neutral pH within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg381
b:61.7
occ:0.50
|
O
|
B:CYS272
|
2.8
|
24.9
|
1.0
|
CA
|
B:CYS272
|
2.9
|
27.0
|
1.0
|
CB
|
B:CYS272
|
3.0
|
27.3
|
1.0
|
CB
|
B:MET198
|
3.1
|
19.6
|
1.0
|
CG
|
B:MET198
|
3.2
|
22.8
|
1.0
|
C
|
B:CYS272
|
3.2
|
25.9
|
1.0
|
SG
|
B:CYS272
|
3.3
|
29.9
|
1.0
|
CD1
|
B:LEU275
|
3.4
|
27.0
|
1.0
|
SD
|
B:MET198
|
3.5
|
23.6
|
1.0
|
CB
|
B:LEU275
|
3.6
|
25.9
|
1.0
|
CD2
|
B:LEU275
|
3.6
|
26.7
|
1.0
|
CG
|
B:LEU275
|
3.7
|
26.6
|
1.0
|
CD2
|
B:PHE276
|
3.9
|
24.9
|
1.0
|
N
|
B:PHE276
|
4.3
|
24.8
|
1.0
|
N
|
B:CYS272
|
4.3
|
27.7
|
1.0
|
CA
|
B:MET198
|
4.4
|
18.3
|
1.0
|
N
|
B:TYR273
|
4.4
|
25.8
|
1.0
|
CD1
|
B:LEU321
|
4.5
|
28.0
|
1.0
|
C
|
B:MET198
|
4.6
|
18.0
|
1.0
|
CE2
|
B:PHE276
|
4.6
|
24.5
|
1.0
|
CA
|
B:LEU275
|
4.7
|
25.3
|
1.0
|
C
|
B:LEU275
|
4.7
|
25.2
|
1.0
|
CG
|
B:PHE276
|
4.7
|
24.2
|
1.0
|
CB
|
B:PHE276
|
4.8
|
24.1
|
1.0
|
O
|
B:GLU271
|
4.8
|
28.6
|
1.0
|
O
|
B:MET198
|
4.9
|
18.2
|
1.0
|
CE
|
B:MET198
|
4.9
|
23.8
|
1.0
|
CA
|
B:PHE276
|
4.9
|
24.2
|
1.0
|
N
|
B:SER199
|
5.0
|
18.2
|
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 01:02:47 2024
|