Mercury in PDB 1qd9: Bacillus Subtilis Yabj
Protein crystallography data
The structure of Bacillus Subtilis Yabj, PDB code: 1qd9
was solved by
J.L.Smith,
S.Sinha,
P.Rappu,
S.C.Lange,
P.Mantsala,
H.Zalkin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
1.70
|
Space group
|
P 65
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.350,
53.350,
204.960,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.6 /
19.7
|
Mercury Binding Sites:
The binding sites of Mercury atom in the Bacillus Subtilis Yabj
(pdb code 1qd9). This binding sites where shown within
5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the
Bacillus Subtilis Yabj, PDB code: 1qd9:
Jump to Mercury binding site number:
1;
2;
3;
4;
5;
6;
Mercury binding site 1 out
of 6 in 1qd9
Go back to
Mercury Binding Sites List in 1qd9
Mercury binding site 1 out
of 6 in the Bacillus Subtilis Yabj
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 1 of Bacillus Subtilis Yabj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg126
b:23.3
occ:0.60
|
HG
|
A:HG126
|
0.0
|
23.3
|
0.6
|
SG
|
A:CYS104
|
2.2
|
23.4
|
0.8
|
SD
|
A:MET81
|
3.1
|
34.3
|
0.8
|
CB
|
A:CYS104
|
3.2
|
17.9
|
1.0
|
CE
|
A:MET81
|
3.2
|
13.7
|
0.8
|
CD1
|
A:PHE84
|
3.2
|
42.0
|
1.0
|
HG
|
A:HG126
|
3.2
|
22.5
|
0.3
|
C
|
A:CYS104
|
3.4
|
13.2
|
1.0
|
CE1
|
A:PHE84
|
3.4
|
33.2
|
1.0
|
CD1
|
A:ILE78
|
3.4
|
22.3
|
1.0
|
O
|
A:CYS104
|
3.5
|
14.4
|
1.0
|
N
|
A:VAL105
|
3.6
|
12.0
|
1.0
|
CG1
|
A:ILE78
|
3.8
|
12.8
|
1.0
|
CA
|
A:CYS104
|
3.8
|
12.1
|
1.0
|
CA
|
A:VAL105
|
4.0
|
11.2
|
1.0
|
C
|
A:VAL105
|
4.2
|
12.4
|
1.0
|
CG
|
A:PHE84
|
4.3
|
33.9
|
1.0
|
O
|
A:VAL105
|
4.3
|
12.3
|
1.0
|
CZ
|
A:PHE84
|
4.5
|
43.2
|
1.0
|
N
|
A:GLU106
|
4.8
|
13.7
|
1.0
|
CB
|
A:PHE84
|
4.9
|
29.2
|
1.0
|
CG2
|
A:ILE78
|
4.9
|
18.8
|
1.0
|
CG
|
A:MET81
|
4.9
|
25.5
|
0.8
|
CB
|
A:ILE78
|
5.0
|
17.1
|
1.0
|
|
Mercury binding site 2 out
of 6 in 1qd9
Go back to
Mercury Binding Sites List in 1qd9
Mercury binding site 2 out
of 6 in the Bacillus Subtilis Yabj
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 2 of Bacillus Subtilis Yabj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg126
b:22.5
occ:0.26
|
HG
|
A:HG126
|
0.0
|
22.5
|
0.3
|
SG
|
A:CYS104
|
2.2
|
23.4
|
0.8
|
CB
|
A:CYS104
|
3.2
|
17.9
|
1.0
|
HG
|
A:HG126
|
3.2
|
23.3
|
0.6
|
CE1
|
A:PHE84
|
3.5
|
33.2
|
1.0
|
CZ
|
A:PHE84
|
3.6
|
43.2
|
1.0
|
CD1
|
A:PHE84
|
3.7
|
42.0
|
1.0
|
CE2
|
A:PHE84
|
3.9
|
41.9
|
1.0
|
CG1
|
A:VAL76
|
4.0
|
14.1
|
1.0
|
CG
|
A:PHE84
|
4.0
|
33.9
|
1.0
|
CD2
|
A:PHE84
|
4.1
|
41.2
|
1.0
|
CB
|
A:VAL76
|
4.3
|
12.7
|
1.0
|
CZ
|
A:ARG102
|
4.5
|
34.1
|
1.0
|
CA
|
A:CYS104
|
4.6
|
12.1
|
1.0
|
NH1
|
A:ARG102
|
4.6
|
24.5
|
1.0
|
NH2
|
A:ARG102
|
4.6
|
26.4
|
1.0
|
CG1
|
A:VAL87
|
4.6
|
22.1
|
1.0
|
CG2
|
A:VAL76
|
4.8
|
13.6
|
1.0
|
NE
|
A:ARG102
|
4.9
|
23.4
|
1.0
|
CG2
|
A:ILE78
|
4.9
|
18.8
|
1.0
|
O
|
A:PHE84
|
4.9
|
19.4
|
1.0
|
CD1
|
A:ILE78
|
4.9
|
22.3
|
1.0
|
|
Mercury binding site 3 out
of 6 in 1qd9
Go back to
Mercury Binding Sites List in 1qd9
Mercury binding site 3 out
of 6 in the Bacillus Subtilis Yabj
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 3 of Bacillus Subtilis Yabj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg500
b:20.3
occ:0.73
|
HG
|
B:EMC500
|
0.0
|
20.3
|
0.7
|
HG
|
B:EMC500
|
1.2
|
32.0
|
0.1
|
C1
|
B:EMC500
|
1.9
|
27.1
|
0.1
|
C1
|
B:EMC500
|
2.1
|
19.8
|
0.7
|
C2
|
B:EMC500
|
2.1
|
27.1
|
0.1
|
SG
|
B:CYS104
|
2.3
|
17.8
|
0.8
|
C2
|
B:EMC500
|
2.9
|
15.1
|
0.7
|
SG
|
B:CYS104
|
3.0
|
36.5
|
0.2
|
CB
|
B:CYS104
|
3.1
|
18.2
|
1.0
|
CE1
|
B:PHE84
|
3.3
|
18.7
|
1.0
|
CD1
|
B:PHE84
|
3.4
|
14.2
|
1.0
|
CG1
|
B:VAL76
|
3.9
|
10.5
|
1.0
|
CZ
|
B:PHE84
|
4.1
|
24.3
|
1.0
|
CB
|
B:VAL76
|
4.2
|
9.7
|
1.0
|
CG
|
B:PHE84
|
4.3
|
17.1
|
1.0
|
CA
|
B:CYS104
|
4.4
|
14.1
|
1.0
|
CD1
|
B:ILE78
|
4.5
|
27.0
|
1.0
|
CG2
|
B:VAL76
|
4.7
|
17.2
|
1.0
|
NE
|
B:ARG102
|
4.9
|
16.0
|
1.0
|
CZ
|
B:ARG102
|
4.9
|
20.5
|
1.0
|
CE2
|
B:PHE84
|
4.9
|
20.3
|
1.0
|
CD2
|
B:PHE84
|
5.0
|
17.3
|
1.0
|
|
Mercury binding site 4 out
of 6 in 1qd9
Go back to
Mercury Binding Sites List in 1qd9
Mercury binding site 4 out
of 6 in the Bacillus Subtilis Yabj
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 4 of Bacillus Subtilis Yabj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg500
b:32.0
occ:0.15
|
HG
|
B:EMC500
|
0.0
|
32.0
|
0.1
|
HG
|
B:EMC500
|
1.2
|
20.3
|
0.7
|
C1
|
B:EMC500
|
2.0
|
19.8
|
0.7
|
C1
|
B:EMC500
|
2.1
|
27.1
|
0.1
|
SG
|
B:CYS104
|
2.4
|
36.5
|
0.2
|
C2
|
B:EMC500
|
2.4
|
15.1
|
0.7
|
C2
|
B:EMC500
|
2.9
|
27.1
|
0.1
|
SG
|
B:CYS104
|
3.0
|
17.8
|
0.8
|
CB
|
B:CYS104
|
3.1
|
18.2
|
1.0
|
CE1
|
B:PHE84
|
3.6
|
18.7
|
1.0
|
NE
|
B:ARG102
|
3.7
|
16.0
|
1.0
|
CZ
|
B:ARG102
|
3.8
|
20.5
|
1.0
|
CB
|
B:VAL76
|
4.0
|
9.7
|
1.0
|
CG1
|
B:VAL76
|
4.1
|
10.5
|
1.0
|
CD
|
B:ARG102
|
4.1
|
15.2
|
1.0
|
NH2
|
B:ARG102
|
4.1
|
23.2
|
1.0
|
CZ
|
B:PHE84
|
4.1
|
24.3
|
1.0
|
CD1
|
B:PHE84
|
4.1
|
14.2
|
1.0
|
NH1
|
B:ARG102
|
4.1
|
16.4
|
1.0
|
CG2
|
B:VAL76
|
4.2
|
17.2
|
1.0
|
CA
|
B:CYS104
|
4.4
|
14.1
|
1.0
|
O
|
B:HOH540
|
4.6
|
22.3
|
1.0
|
O
|
B:HOH635
|
4.6
|
34.3
|
1.0
|
CG
|
B:ARG102
|
4.8
|
14.7
|
1.0
|
CE2
|
B:PHE84
|
5.0
|
20.3
|
1.0
|
|
Mercury binding site 5 out
of 6 in 1qd9
Go back to
Mercury Binding Sites List in 1qd9
Mercury binding site 5 out
of 6 in the Bacillus Subtilis Yabj
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 5 of Bacillus Subtilis Yabj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Hg501
b:27.0
occ:0.68
|
HG
|
C:EMC501
|
0.0
|
27.0
|
0.7
|
HG
|
C:EMC501
|
2.0
|
46.4
|
0.2
|
C1
|
C:EMC501
|
2.1
|
24.4
|
0.7
|
C2
|
C:EMC501
|
2.3
|
22.6
|
0.2
|
SG
|
C:CYS104
|
2.3
|
22.0
|
0.8
|
C1
|
C:EMC501
|
2.7
|
28.4
|
0.2
|
C2
|
C:EMC501
|
2.9
|
15.8
|
0.7
|
CE1
|
C:PHE84
|
3.1
|
30.8
|
1.0
|
CB
|
C:CYS104
|
3.2
|
20.2
|
1.0
|
SG
|
C:CYS104
|
3.2
|
30.1
|
0.2
|
CD1
|
C:PHE84
|
3.3
|
28.7
|
1.0
|
CZ
|
C:PHE84
|
3.8
|
19.8
|
1.0
|
CG1
|
C:VAL76
|
4.0
|
14.8
|
1.0
|
CG
|
C:PHE84
|
4.1
|
25.7
|
1.0
|
CB
|
C:VAL76
|
4.3
|
14.8
|
1.0
|
CD1
|
C:ILE78
|
4.4
|
25.1
|
1.0
|
CA
|
C:CYS104
|
4.5
|
14.7
|
1.0
|
CE2
|
C:PHE84
|
4.6
|
26.5
|
1.0
|
CD2
|
C:PHE84
|
4.7
|
24.0
|
1.0
|
CG2
|
C:VAL76
|
4.7
|
18.1
|
1.0
|
CG2
|
C:ILE78
|
5.0
|
26.5
|
1.0
|
CA
|
C:PHE84
|
5.0
|
17.9
|
1.0
|
|
Mercury binding site 6 out
of 6 in 1qd9
Go back to
Mercury Binding Sites List in 1qd9
Mercury binding site 6 out
of 6 in the Bacillus Subtilis Yabj
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 6 of Bacillus Subtilis Yabj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Hg501
b:46.4
occ:0.18
|
HG
|
C:EMC501
|
0.0
|
46.4
|
0.2
|
HG
|
C:EMC501
|
2.0
|
27.0
|
0.7
|
C1
|
C:EMC501
|
2.1
|
28.4
|
0.2
|
C2
|
C:EMC501
|
2.1
|
15.8
|
0.7
|
C1
|
C:EMC501
|
2.3
|
24.4
|
0.7
|
SG
|
C:CYS104
|
2.4
|
30.1
|
0.2
|
C2
|
C:EMC501
|
2.8
|
22.6
|
0.2
|
NE
|
C:ARG102
|
3.4
|
19.1
|
1.0
|
CB
|
C:CYS104
|
3.4
|
20.2
|
1.0
|
CD
|
C:ARG102
|
3.5
|
14.1
|
1.0
|
CZ
|
C:ARG102
|
3.5
|
29.7
|
1.0
|
SG
|
C:CYS104
|
3.6
|
22.0
|
0.8
|
CG2
|
C:VAL76
|
3.6
|
18.1
|
1.0
|
NH1
|
C:ARG102
|
3.7
|
15.4
|
1.0
|
CB
|
C:VAL76
|
3.8
|
14.8
|
1.0
|
CG1
|
C:VAL76
|
4.1
|
14.8
|
1.0
|
NH2
|
C:ARG102
|
4.1
|
26.3
|
1.0
|
CE1
|
C:PHE84
|
4.2
|
30.8
|
1.0
|
CG
|
C:ARG102
|
4.2
|
20.2
|
1.0
|
CZ
|
C:PHE84
|
4.4
|
19.8
|
1.0
|
O
|
C:HOH579
|
4.4
|
32.2
|
1.0
|
CA
|
C:CYS104
|
4.6
|
14.7
|
1.0
|
CD1
|
C:PHE84
|
4.8
|
28.7
|
1.0
|
OD1
|
C:ASN88
|
4.9
|
17.7
|
1.0
|
O
|
C:SER103
|
5.0
|
14.8
|
1.0
|
|
Reference:
S.Sinha,
P.Rappu,
S.C.Lange,
P.Mantsala,
H.Zalkin,
J.L.Smith.
Crystal Structure of Bacillus Subtilis Yabj, A Purine Regulatory Protein and Member of the Highly Conserved Yjgf Family. Proc.Natl.Acad.Sci.Usa V. 96 13074 1999.
ISSN: ISSN 0027-8424
PubMed: 10557275
DOI: 10.1073/PNAS.96.23.13074
Page generated: Sun Aug 11 01:13:36 2024
|