Cobalt in PDB 3h9a: Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form
Protein crystallography data
The structure of Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form, PDB code: 3h9a
was solved by
M.Rajavel,
B.Gopal,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.34 /
2.04
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.252,
47.198,
62.906,
89.05,
77.27,
82.28
|
R / Rfree (%)
|
20.6 /
26.2
|
Other elements in 3h9a:
The structure of Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form also contains other interesting chemical elements:
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form
(pdb code 3h9a). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the
Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form, PDB code: 3h9a:
Jump to Cobalt binding site number:
1;
2;
3;
4;
Cobalt binding site 1 out
of 4 in 3h9a
Go back to
Cobalt Binding Sites List in 3h9a
Cobalt binding site 1 out
of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co244
b:39.5
occ:1.00
|
NE2
|
A:HIS52
|
2.3
|
12.6
|
1.0
|
NE2
|
A:HIS50
|
2.3
|
19.7
|
1.0
|
O
|
A:HOH346
|
2.3
|
25.9
|
1.0
|
OE1
|
A:GLN56
|
2.4
|
10.8
|
1.0
|
NE2
|
A:HIS91
|
2.4
|
9.8
|
1.0
|
O
|
A:HOH335
|
2.9
|
40.0
|
1.0
|
CE1
|
A:HIS50
|
3.1
|
19.9
|
1.0
|
CD
|
A:GLN56
|
3.2
|
10.0
|
1.0
|
CD2
|
A:HIS52
|
3.2
|
13.3
|
1.0
|
CE1
|
A:HIS52
|
3.2
|
13.4
|
1.0
|
CE1
|
A:HIS91
|
3.3
|
8.9
|
1.0
|
CD2
|
A:HIS50
|
3.4
|
19.0
|
1.0
|
CD2
|
A:HIS91
|
3.5
|
9.1
|
1.0
|
NE2
|
A:GLN56
|
3.5
|
10.6
|
1.0
|
ND1
|
A:HIS50
|
4.3
|
19.4
|
1.0
|
ND1
|
A:HIS52
|
4.3
|
13.5
|
1.0
|
CG
|
A:HIS52
|
4.4
|
13.0
|
1.0
|
ND1
|
A:HIS91
|
4.4
|
9.1
|
1.0
|
CG
|
A:GLN56
|
4.4
|
9.5
|
1.0
|
CG
|
A:HIS50
|
4.5
|
18.3
|
1.0
|
NZ
|
A:LYS107
|
4.5
|
18.9
|
1.0
|
CG
|
A:HIS91
|
4.5
|
9.7
|
1.0
|
CB
|
A:GLN56
|
4.6
|
8.8
|
1.0
|
CD
|
A:LYS107
|
4.9
|
17.1
|
1.0
|
|
Cobalt binding site 2 out
of 4 in 3h9a
Go back to
Cobalt Binding Sites List in 3h9a
Cobalt binding site 2 out
of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co245
b:15.6
occ:1.00
|
O2
|
A:PPY246
|
2.0
|
15.7
|
1.0
|
OE1
|
A:GLN168
|
2.2
|
9.8
|
1.0
|
O3
|
A:PPY246
|
2.2
|
17.7
|
1.0
|
NE2
|
A:HIS162
|
2.2
|
11.5
|
1.0
|
NE2
|
A:HIS202
|
2.2
|
7.9
|
1.0
|
NE2
|
A:HIS164
|
2.2
|
10.2
|
1.0
|
C1
|
A:PPY246
|
2.7
|
18.4
|
1.0
|
C2
|
A:PPY246
|
2.8
|
17.5
|
1.0
|
CE1
|
A:HIS162
|
3.0
|
11.9
|
1.0
|
CE1
|
A:HIS202
|
3.0
|
7.5
|
1.0
|
CD
|
A:GLN168
|
3.2
|
10.4
|
1.0
|
CD2
|
A:HIS164
|
3.2
|
10.9
|
1.0
|
CE1
|
A:HIS164
|
3.2
|
9.6
|
1.0
|
CD2
|
A:HIS202
|
3.3
|
6.9
|
1.0
|
CD2
|
A:HIS162
|
3.3
|
11.4
|
1.0
|
NE2
|
A:GLN168
|
3.5
|
12.4
|
1.0
|
O1
|
A:PPY246
|
4.0
|
17.9
|
1.0
|
ND1
|
A:HIS162
|
4.2
|
11.3
|
1.0
|
CE1
|
A:PHE218
|
4.2
|
8.8
|
1.0
|
ND1
|
A:HIS202
|
4.2
|
6.0
|
1.0
|
C3
|
A:PPY246
|
4.3
|
19.8
|
1.0
|
ND1
|
A:HIS164
|
4.4
|
10.0
|
1.0
|
CG
|
A:HIS202
|
4.4
|
7.6
|
1.0
|
CG
|
A:HIS164
|
4.4
|
10.6
|
1.0
|
CG
|
A:HIS162
|
4.4
|
11.3
|
1.0
|
CG
|
A:GLN168
|
4.5
|
10.3
|
1.0
|
C2'
|
A:PPY246
|
4.7
|
21.8
|
1.0
|
CZ
|
A:PHE218
|
4.8
|
9.1
|
1.0
|
CB
|
A:GLN168
|
4.8
|
9.6
|
1.0
|
NE
|
A:ARG222
|
4.9
|
17.0
|
1.0
|
|
Cobalt binding site 3 out
of 4 in 3h9a
Go back to
Cobalt Binding Sites List in 3h9a
Cobalt binding site 3 out
of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co244
b:60.7
occ:1.00
|
NE2
|
B:HIS91
|
2.2
|
19.7
|
1.0
|
NE2
|
B:HIS52
|
2.4
|
22.6
|
1.0
|
OE1
|
B:GLN56
|
2.4
|
19.1
|
1.0
|
NE2
|
B:HIS50
|
2.5
|
24.7
|
1.0
|
CE1
|
B:HIS91
|
3.0
|
19.2
|
1.0
|
CD
|
B:GLN56
|
3.3
|
18.2
|
1.0
|
CE1
|
B:HIS52
|
3.3
|
22.8
|
1.0
|
CD2
|
B:HIS50
|
3.3
|
24.3
|
1.0
|
CD2
|
B:HIS91
|
3.3
|
19.0
|
1.0
|
CD2
|
B:HIS52
|
3.4
|
22.8
|
1.0
|
CE1
|
B:HIS50
|
3.5
|
24.5
|
1.0
|
NE2
|
B:GLN56
|
3.6
|
18.3
|
1.0
|
ND1
|
B:HIS91
|
4.2
|
18.4
|
1.0
|
CG
|
B:HIS91
|
4.4
|
18.8
|
1.0
|
ND1
|
B:HIS52
|
4.4
|
22.9
|
1.0
|
CG
|
B:HIS50
|
4.5
|
23.9
|
1.0
|
CE
|
B:LYS107
|
4.5
|
28.3
|
1.0
|
CG
|
B:HIS52
|
4.5
|
22.9
|
1.0
|
ND1
|
B:HIS50
|
4.5
|
24.4
|
1.0
|
NZ
|
B:LYS107
|
4.5
|
29.5
|
1.0
|
CG
|
B:GLN56
|
4.6
|
18.1
|
1.0
|
CB
|
B:GLN56
|
4.7
|
17.8
|
1.0
|
CD
|
B:LYS107
|
4.9
|
27.5
|
1.0
|
|
Cobalt binding site 4 out
of 4 in 3h9a
Go back to
Cobalt Binding Sites List in 3h9a
Cobalt binding site 4 out
of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co245
b:23.6
occ:1.00
|
O2
|
B:PPY246
|
2.0
|
21.9
|
1.0
|
NE2
|
B:HIS202
|
2.2
|
14.9
|
1.0
|
NE2
|
B:HIS162
|
2.2
|
11.7
|
1.0
|
O3
|
B:PPY246
|
2.3
|
23.6
|
1.0
|
OE1
|
B:GLN168
|
2.3
|
13.4
|
1.0
|
NE2
|
B:HIS164
|
2.3
|
13.9
|
1.0
|
C1
|
B:PPY246
|
2.8
|
22.5
|
1.0
|
C2
|
B:PPY246
|
2.9
|
22.6
|
1.0
|
CE1
|
B:HIS162
|
3.1
|
11.4
|
1.0
|
CE1
|
B:HIS202
|
3.1
|
14.8
|
1.0
|
CD2
|
B:HIS202
|
3.1
|
13.6
|
1.0
|
CD
|
B:GLN168
|
3.2
|
14.1
|
1.0
|
CE1
|
B:HIS164
|
3.2
|
13.2
|
1.0
|
CD2
|
B:HIS164
|
3.3
|
13.9
|
1.0
|
CD2
|
B:HIS162
|
3.3
|
11.6
|
1.0
|
NE2
|
B:GLN168
|
3.4
|
14.3
|
1.0
|
O1
|
B:PPY246
|
4.0
|
21.7
|
1.0
|
ND1
|
B:HIS162
|
4.2
|
11.2
|
1.0
|
ND1
|
B:HIS202
|
4.2
|
14.0
|
1.0
|
CG
|
B:HIS202
|
4.3
|
13.9
|
1.0
|
CE1
|
B:PHE218
|
4.3
|
15.9
|
1.0
|
ND1
|
B:HIS164
|
4.4
|
13.0
|
1.0
|
C3
|
B:PPY246
|
4.4
|
23.8
|
1.0
|
CG
|
B:HIS162
|
4.4
|
12.5
|
1.0
|
CG
|
B:HIS164
|
4.4
|
13.8
|
1.0
|
CG
|
B:GLN168
|
4.6
|
14.2
|
1.0
|
CE
|
B:MSE159
|
4.6
|
21.0
|
1.0
|
C2'
|
B:PPY246
|
4.7
|
26.0
|
1.0
|
CB
|
B:GLN168
|
4.9
|
14.9
|
1.0
|
CZ
|
B:PHE218
|
4.9
|
16.1
|
1.0
|
|
Reference:
M.Rajavel,
B.Gopal.
Analysis of Multiple Crystal Forms of Bacillus Subtilis Bacb Suggests A Role For A Metal Ion As A Nucleant For Crystallization Acta Crystallogr.,Sect.D V. 66 635 2010.
ISSN: ISSN 0907-4449
PubMed: 20445239
DOI: 10.1107/S0907444910006682
Page generated: Tue Jul 30 16:07:31 2024
|