Cobalt in PDB 3h7j: Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Monoclinic Form
Protein crystallography data
The structure of Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Monoclinic Form, PDB code: 3h7j
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)
|
26.21 /
1.87
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.990,
118.493,
46.926,
90.00,
97.92,
90.00
|
R / Rfree (%)
|
18.5 /
22.7
|
Other elements in 3h7j:
The structure of Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Monoclinic 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 Monoclinic Form
(pdb code 3h7j). 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 Monoclinic Form, PDB code: 3h7j:
Jump to Cobalt binding site number:
1;
2;
3;
4;
Cobalt binding site 1 out
of 4 in 3h7j
Go back to
Cobalt Binding Sites List in 3h7j
Cobalt binding site 1 out
of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Monoclinic 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 Monoclinic Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co244
b:22.2
occ:1.00
|
NE2
|
A:HIS91
|
2.1
|
11.6
|
1.0
|
O
|
A:HOH291
|
2.1
|
17.2
|
1.0
|
OE1
|
A:GLN56
|
2.1
|
15.9
|
1.0
|
NE2
|
A:HIS52
|
2.2
|
13.5
|
1.0
|
NE2
|
A:HIS50
|
2.2
|
20.4
|
1.0
|
O
|
A:HOH251
|
2.2
|
19.9
|
1.0
|
CE1
|
A:HIS91
|
3.0
|
13.1
|
1.0
|
CD
|
A:GLN56
|
3.1
|
14.8
|
1.0
|
CE1
|
A:HIS50
|
3.1
|
20.6
|
1.0
|
CE1
|
A:HIS52
|
3.1
|
13.6
|
1.0
|
CD2
|
A:HIS52
|
3.2
|
10.4
|
1.0
|
CD2
|
A:HIS91
|
3.2
|
11.0
|
1.0
|
CD2
|
A:HIS50
|
3.2
|
17.0
|
1.0
|
NE2
|
A:GLN56
|
3.4
|
12.3
|
1.0
|
ND1
|
A:HIS91
|
4.1
|
13.4
|
1.0
|
ND1
|
A:HIS50
|
4.2
|
19.7
|
1.0
|
ND1
|
A:HIS52
|
4.2
|
9.4
|
1.0
|
CG
|
A:HIS91
|
4.3
|
12.3
|
1.0
|
CG
|
A:HIS50
|
4.3
|
18.1
|
1.0
|
CG
|
A:HIS52
|
4.3
|
11.8
|
1.0
|
CG
|
A:GLN56
|
4.4
|
12.5
|
1.0
|
O
|
A:HOH274
|
4.4
|
24.2
|
1.0
|
CB
|
A:GLN56
|
4.6
|
8.9
|
1.0
|
O
|
A:HOH340
|
4.9
|
25.0
|
1.0
|
|
Cobalt binding site 2 out
of 4 in 3h7j
Go back to
Cobalt Binding Sites List in 3h7j
Cobalt binding site 2 out
of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Monoclinic 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 Monoclinic Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co245
b:17.3
occ:1.00
|
O2
|
A:PPY246
|
1.8
|
14.1
|
1.0
|
NE2
|
A:HIS202
|
2.1
|
9.6
|
1.0
|
O3
|
A:PPY246
|
2.1
|
16.6
|
1.0
|
NE2
|
A:HIS164
|
2.2
|
8.3
|
1.0
|
OE1
|
A:GLN168
|
2.2
|
9.8
|
1.0
|
NE2
|
A:HIS162
|
2.3
|
12.9
|
1.0
|
C1
|
A:PPY246
|
2.7
|
20.6
|
1.0
|
C2
|
A:PPY246
|
2.7
|
12.3
|
1.0
|
CE1
|
A:HIS202
|
3.0
|
13.5
|
1.0
|
CD2
|
A:HIS202
|
3.1
|
7.4
|
1.0
|
CE1
|
A:HIS162
|
3.1
|
12.2
|
1.0
|
CD2
|
A:HIS164
|
3.2
|
10.7
|
1.0
|
CD
|
A:GLN168
|
3.2
|
7.9
|
1.0
|
CE1
|
A:HIS164
|
3.2
|
5.2
|
1.0
|
CD2
|
A:HIS162
|
3.3
|
8.6
|
1.0
|
NE2
|
A:GLN168
|
3.5
|
8.3
|
1.0
|
O1
|
A:PPY246
|
4.0
|
20.4
|
1.0
|
CE1
|
A:PHE218
|
4.1
|
8.1
|
1.0
|
ND1
|
A:HIS202
|
4.1
|
11.4
|
1.0
|
C3
|
A:PPY246
|
4.2
|
14.8
|
1.0
|
CG
|
A:HIS202
|
4.2
|
11.6
|
1.0
|
ND1
|
A:HIS162
|
4.3
|
10.6
|
1.0
|
ND1
|
A:HIS164
|
4.3
|
6.9
|
1.0
|
CG
|
A:HIS164
|
4.3
|
6.9
|
1.0
|
CG
|
A:HIS162
|
4.4
|
10.3
|
1.0
|
CZ
|
A:PHE218
|
4.6
|
8.8
|
1.0
|
CG
|
A:GLN168
|
4.6
|
8.9
|
1.0
|
CB
|
A:GLN168
|
4.9
|
10.8
|
1.0
|
C2'
|
A:PPY246
|
4.9
|
15.1
|
1.0
|
|
Cobalt binding site 3 out
of 4 in 3h7j
Go back to
Cobalt Binding Sites List in 3h7j
Cobalt binding site 3 out
of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Monoclinic 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 Monoclinic Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co244
b:29.5
occ:1.00
|
O3
|
B:PPY246
|
1.8
|
28.3
|
1.0
|
NE2
|
B:HIS164
|
2.2
|
11.7
|
1.0
|
OE1
|
B:GLN168
|
2.2
|
16.8
|
1.0
|
NE2
|
B:HIS202
|
2.2
|
14.5
|
1.0
|
O2
|
B:PPY246
|
2.2
|
25.7
|
1.0
|
NE2
|
B:HIS162
|
2.3
|
13.8
|
1.0
|
C2
|
B:PPY246
|
2.6
|
33.4
|
1.0
|
C1
|
B:PPY246
|
2.8
|
27.6
|
1.0
|
CD2
|
B:HIS164
|
3.1
|
12.5
|
1.0
|
CE1
|
B:HIS202
|
3.1
|
19.7
|
1.0
|
CD
|
B:GLN168
|
3.2
|
19.5
|
1.0
|
CE1
|
B:HIS162
|
3.2
|
13.7
|
1.0
|
CD2
|
B:HIS202
|
3.2
|
15.1
|
1.0
|
CE1
|
B:HIS164
|
3.2
|
10.9
|
1.0
|
CD2
|
B:HIS162
|
3.3
|
15.5
|
1.0
|
NE2
|
B:GLN168
|
3.6
|
14.9
|
1.0
|
C3
|
B:PPY246
|
4.0
|
29.4
|
1.0
|
O1
|
B:PPY246
|
4.1
|
29.0
|
1.0
|
CE1
|
B:PHE218
|
4.2
|
19.8
|
1.0
|
ND1
|
B:HIS202
|
4.2
|
12.6
|
1.0
|
CG
|
B:HIS164
|
4.3
|
14.6
|
1.0
|
ND1
|
B:HIS164
|
4.3
|
11.2
|
1.0
|
CG
|
B:HIS202
|
4.3
|
14.5
|
1.0
|
ND1
|
B:HIS162
|
4.3
|
11.2
|
1.0
|
CG
|
B:HIS162
|
4.4
|
14.8
|
1.0
|
CG
|
B:GLN168
|
4.6
|
15.1
|
1.0
|
CZ
|
B:PHE218
|
4.6
|
15.7
|
1.0
|
C2'
|
B:PPY246
|
4.7
|
34.6
|
1.0
|
C1'
|
B:PPY246
|
4.8
|
34.3
|
1.0
|
CB
|
B:GLN168
|
4.9
|
17.4
|
1.0
|
|
Cobalt binding site 4 out
of 4 in 3h7j
Go back to
Cobalt Binding Sites List in 3h7j
Cobalt binding site 4 out
of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Monoclinic 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 Monoclinic Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co245
b:32.7
occ:1.00
|
OE1
|
B:GLN56
|
2.1
|
20.7
|
1.0
|
NE2
|
B:HIS52
|
2.1
|
18.6
|
1.0
|
NE2
|
B:HIS50
|
2.1
|
27.3
|
1.0
|
O
|
B:HOH296
|
2.1
|
29.1
|
1.0
|
O
|
B:HOH295
|
2.2
|
29.0
|
1.0
|
NE2
|
B:HIS91
|
2.3
|
22.9
|
1.0
|
CD
|
B:GLN56
|
3.0
|
24.1
|
1.0
|
CD2
|
B:HIS52
|
3.0
|
18.6
|
1.0
|
CE1
|
B:HIS50
|
3.1
|
28.1
|
1.0
|
CD2
|
B:HIS50
|
3.1
|
28.7
|
1.0
|
CE1
|
B:HIS52
|
3.1
|
19.7
|
1.0
|
CE1
|
B:HIS91
|
3.2
|
19.4
|
1.0
|
CD2
|
B:HIS91
|
3.3
|
17.9
|
1.0
|
NE2
|
B:GLN56
|
3.3
|
24.9
|
1.0
|
ND1
|
B:HIS50
|
4.2
|
29.1
|
1.0
|
CG
|
B:HIS52
|
4.2
|
19.0
|
1.0
|
ND1
|
B:HIS52
|
4.2
|
20.0
|
1.0
|
CG
|
B:HIS50
|
4.3
|
27.2
|
1.0
|
CG
|
B:GLN56
|
4.3
|
22.3
|
1.0
|
ND1
|
B:HIS91
|
4.3
|
19.2
|
1.0
|
CG
|
B:HIS91
|
4.4
|
18.5
|
1.0
|
CB
|
B:GLN56
|
4.6
|
16.9
|
1.0
|
NZ
|
B:LYS107
|
4.7
|
33.6
|
1.0
|
O
|
B:HOH269
|
4.8
|
45.9
|
1.0
|
CD
|
B:LYS107
|
4.9
|
29.2
|
1.0
|
|
Reference:
M.Rajavel,
A.Mitra,
B.Gopal.
Role of Bacillus Subtilis Bacb in the Synthesis of Bacilysin J.Biol.Chem. V. 284 31882 2009.
ISSN: ISSN 0021-9258
PubMed: 19776011
DOI: 10.1074/JBC.M109.014522
Page generated: Tue Jul 30 16:07:18 2024
|