Cobalt in PDB 7xcn: Crystal Structure of the Mttb-Mttc Complex at 2.7 A Resolution
Enzymatic activity of Crystal Structure of the Mttb-Mttc Complex at 2.7 A Resolution
All present enzymatic activity of Crystal Structure of the Mttb-Mttc Complex at 2.7 A Resolution:
2.1.1.250;
Protein crystallography data
The structure of Crystal Structure of the Mttb-Mttc Complex at 2.7 A Resolution, PDB code: 7xcn
was solved by
J.Li,
M.K.Chan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
20.00 /
2.70
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
120.434,
188.138,
123.952,
90,
119.25,
90
|
|
R / Rfree (%)
|
19.2 /
23.8
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of the Mttb-Mttc Complex at 2.7 A Resolution
(pdb code 7xcn). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the
Crystal Structure of the Mttb-Mttc Complex at 2.7 A Resolution, PDB code: 7xcn:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
Cobalt binding site 1 out
of 6 in 7xcn
Go back to
Cobalt Binding Sites List in 7xcn
Cobalt binding site 1 out
of 6 in the Crystal Structure of the Mttb-Mttc Complex at 2.7 A Resolution
 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 the Mttb-Mttc Complex at 2.7 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Co301
b:47.8
occ:1.00
|
CO
|
M:HCB301
|
0.0
|
47.8
|
1.0
|
|
N21
|
M:HCB301
|
1.9
|
48.9
|
1.0
|
|
N24
|
M:HCB301
|
1.9
|
46.0
|
1.0
|
|
N23
|
M:HCB301
|
1.9
|
53.6
|
1.0
|
|
N22
|
M:HCB301
|
1.9
|
51.1
|
1.0
|
|
NE2
|
M:HIS107
|
2.3
|
43.7
|
1.0
|
|
C19
|
M:HCB301
|
2.9
|
44.3
|
1.0
|
|
C9
|
M:HCB301
|
2.9
|
53.4
|
1.0
|
|
C1
|
M:HCB301
|
2.9
|
45.2
|
1.0
|
|
C11
|
M:HCB301
|
2.9
|
50.7
|
1.0
|
|
C4
|
M:HCB301
|
2.9
|
47.5
|
1.0
|
|
C16
|
M:HCB301
|
3.0
|
52.4
|
1.0
|
|
C14
|
M:HCB301
|
3.0
|
54.0
|
1.0
|
|
C6
|
M:HCB301
|
3.0
|
44.3
|
1.0
|
|
C10
|
M:HCB301
|
3.2
|
47.2
|
1.0
|
|
CE1
|
M:HIS107
|
3.3
|
49.1
|
1.0
|
|
CD2
|
M:HIS107
|
3.3
|
51.0
|
1.0
|
|
C5
|
M:HCB301
|
3.4
|
40.1
|
1.0
|
|
C15
|
M:HCB301
|
3.4
|
56.6
|
1.0
|
|
C20
|
M:HCB301
|
3.5
|
30.1
|
1.0
|
|
O3
|
A:GOL601
|
4.0
|
64.7
|
1.0
|
|
C18
|
M:HCB301
|
4.1
|
50.7
|
1.0
|
|
C2
|
M:HCB301
|
4.2
|
43.3
|
1.0
|
|
C8
|
M:HCB301
|
4.2
|
51.2
|
1.0
|
|
C17
|
M:HCB301
|
4.2
|
50.2
|
1.0
|
|
C3
|
M:HCB301
|
4.2
|
45.8
|
1.0
|
|
C12
|
M:HCB301
|
4.3
|
51.6
|
1.0
|
|
C13
|
M:HCB301
|
4.3
|
53.8
|
1.0
|
|
C7
|
M:HCB301
|
4.3
|
54.1
|
1.0
|
|
ND1
|
M:HIS107
|
4.4
|
47.7
|
1.0
|
|
CG
|
M:HIS107
|
4.5
|
50.2
|
1.0
|
|
C26
|
M:HCB301
|
4.6
|
37.2
|
1.0
|
|
C1
|
A:GOL601
|
4.6
|
82.0
|
1.0
|
|
C54
|
M:HCB301
|
4.9
|
55.2
|
1.0
|
|
C35
|
M:HCB301
|
4.9
|
43.2
|
1.0
|
|
C53
|
M:HCB301
|
4.9
|
58.5
|
1.0
|
|
C37
|
M:HCB301
|
5.0
|
58.8
|
1.0
|
|
Cobalt binding site 2 out
of 6 in 7xcn
Go back to
Cobalt Binding Sites List in 7xcn
Cobalt binding site 2 out
of 6 in the Crystal Structure of the Mttb-Mttc Complex at 2.7 A Resolution
 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 the Mttb-Mttc Complex at 2.7 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Co301
b:47.6
occ:1.00
|
CO
|
N:HCB301
|
0.0
|
47.6
|
1.0
|
|
N24
|
N:HCB301
|
1.9
|
56.2
|
1.0
|
|
N21
|
N:HCB301
|
1.9
|
57.2
|
1.0
|
|
N23
|
N:HCB301
|
1.9
|
56.0
|
1.0
|
|
N22
|
N:HCB301
|
2.0
|
59.6
|
1.0
|
|
NE2
|
N:HIS107
|
2.4
|
59.4
|
1.0
|
|
C19
|
N:HCB301
|
2.8
|
57.8
|
1.0
|
|
C9
|
N:HCB301
|
2.9
|
54.9
|
1.0
|
|
C1
|
N:HCB301
|
2.9
|
57.8
|
1.0
|
|
C11
|
N:HCB301
|
2.9
|
51.7
|
1.0
|
|
C4
|
N:HCB301
|
3.0
|
60.8
|
1.0
|
|
C16
|
N:HCB301
|
3.0
|
58.9
|
1.0
|
|
C14
|
N:HCB301
|
3.0
|
54.0
|
1.0
|
|
C6
|
N:HCB301
|
3.1
|
60.2
|
1.0
|
|
C10
|
N:HCB301
|
3.2
|
54.6
|
1.0
|
|
CE1
|
N:HIS107
|
3.3
|
52.6
|
1.0
|
|
CD2
|
N:HIS107
|
3.3
|
61.8
|
1.0
|
|
C5
|
N:HCB301
|
3.4
|
61.1
|
1.0
|
|
C15
|
N:HCB301
|
3.4
|
58.3
|
1.0
|
|
C20
|
N:HCB301
|
3.6
|
49.3
|
1.0
|
|
O
|
N:HOH413
|
4.0
|
31.3
|
1.0
|
|
C18
|
N:HCB301
|
4.1
|
52.0
|
1.0
|
|
C2
|
N:HCB301
|
4.2
|
61.2
|
1.0
|
|
C17
|
N:HCB301
|
4.2
|
52.9
|
1.0
|
|
C3
|
N:HCB301
|
4.2
|
58.8
|
1.0
|
|
C8
|
N:HCB301
|
4.2
|
54.4
|
1.0
|
|
C12
|
N:HCB301
|
4.3
|
52.8
|
1.0
|
|
C13
|
N:HCB301
|
4.3
|
48.7
|
1.0
|
|
C7
|
N:HCB301
|
4.4
|
58.1
|
1.0
|
|
ND1
|
N:HIS107
|
4.4
|
57.6
|
1.0
|
|
CG
|
N:HIS107
|
4.5
|
62.8
|
1.0
|
|
C26
|
N:HCB301
|
4.6
|
57.1
|
1.0
|
|
C54
|
N:HCB301
|
4.9
|
52.5
|
1.0
|
|
C53
|
N:HCB301
|
4.9
|
62.2
|
1.0
|
|
C35
|
N:HCB301
|
5.0
|
64.7
|
1.0
|
|
C42
|
N:HCB301
|
5.0
|
51.5
|
1.0
|
|
Cobalt binding site 3 out
of 6 in 7xcn
Go back to
Cobalt Binding Sites List in 7xcn
Cobalt binding site 3 out
of 6 in the Crystal Structure of the Mttb-Mttc Complex at 2.7 A Resolution
 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 the Mttb-Mttc Complex at 2.7 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Co301
b:39.0
occ:1.00
|
CO
|
O:HCB301
|
0.0
|
39.0
|
1.0
|
|
N21
|
O:HCB301
|
1.9
|
43.6
|
1.0
|
|
N24
|
O:HCB301
|
1.9
|
46.8
|
1.0
|
|
N23
|
O:HCB301
|
1.9
|
46.0
|
1.0
|
|
N22
|
O:HCB301
|
1.9
|
48.1
|
1.0
|
|
NE2
|
O:HIS107
|
2.3
|
45.6
|
1.0
|
|
C19
|
O:HCB301
|
2.9
|
40.8
|
1.0
|
|
C9
|
O:HCB301
|
2.9
|
48.9
|
1.0
|
|
C1
|
O:HCB301
|
2.9
|
46.3
|
1.0
|
|
C11
|
O:HCB301
|
2.9
|
50.2
|
1.0
|
|
C4
|
O:HCB301
|
2.9
|
43.9
|
1.0
|
|
C16
|
O:HCB301
|
3.0
|
47.6
|
1.0
|
|
C14
|
O:HCB301
|
3.0
|
43.4
|
1.0
|
|
C6
|
O:HCB301
|
3.1
|
48.4
|
1.0
|
|
O1
|
C:GOL601
|
3.2
|
59.7
|
1.0
|
|
C10
|
O:HCB301
|
3.2
|
45.8
|
1.0
|
|
CE1
|
O:HIS107
|
3.3
|
45.1
|
1.0
|
|
CD2
|
O:HIS107
|
3.3
|
44.2
|
1.0
|
|
C5
|
O:HCB301
|
3.4
|
43.7
|
1.0
|
|
C15
|
O:HCB301
|
3.4
|
52.4
|
1.0
|
|
C20
|
O:HCB301
|
3.5
|
27.9
|
1.0
|
|
C18
|
O:HCB301
|
4.1
|
42.9
|
1.0
|
|
C2
|
O:HCB301
|
4.2
|
45.8
|
1.0
|
|
C8
|
O:HCB301
|
4.2
|
58.6
|
1.0
|
|
C17
|
O:HCB301
|
4.2
|
46.2
|
1.0
|
|
C3
|
O:HCB301
|
4.2
|
46.5
|
1.0
|
|
C12
|
O:HCB301
|
4.3
|
47.3
|
1.0
|
|
C13
|
O:HCB301
|
4.3
|
40.2
|
1.0
|
|
C7
|
O:HCB301
|
4.3
|
46.9
|
1.0
|
|
ND1
|
O:HIS107
|
4.4
|
47.9
|
1.0
|
|
CG
|
O:HIS107
|
4.5
|
41.2
|
1.0
|
|
C1
|
C:GOL601
|
4.6
|
73.5
|
1.0
|
|
C26
|
O:HCB301
|
4.6
|
36.6
|
1.0
|
|
C3
|
C:GOL601
|
4.8
|
74.7
|
1.0
|
|
C54
|
O:HCB301
|
4.9
|
53.0
|
1.0
|
|
C35
|
O:HCB301
|
4.9
|
38.7
|
1.0
|
|
C53
|
O:HCB301
|
5.0
|
59.7
|
1.0
|
|
C37
|
O:HCB301
|
5.0
|
44.9
|
1.0
|
|
Cobalt binding site 4 out
of 6 in 7xcn
Go back to
Cobalt Binding Sites List in 7xcn
Cobalt binding site 4 out
of 6 in the Crystal Structure of the Mttb-Mttc Complex at 2.7 A Resolution
 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 the Mttb-Mttc Complex at 2.7 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Co301
b:41.4
occ:1.00
|
CO
|
P:HCB301
|
0.0
|
41.4
|
1.0
|
|
N24
|
P:HCB301
|
1.9
|
49.5
|
1.0
|
|
N21
|
P:HCB301
|
1.9
|
42.9
|
1.0
|
|
N23
|
P:HCB301
|
1.9
|
44.8
|
1.0
|
|
N22
|
P:HCB301
|
1.9
|
47.0
|
1.0
|
|
NE2
|
P:HIS107
|
2.3
|
40.0
|
1.0
|
|
C9
|
P:HCB301
|
2.9
|
47.4
|
1.0
|
|
C19
|
P:HCB301
|
2.9
|
43.6
|
1.0
|
|
C11
|
P:HCB301
|
2.9
|
41.0
|
1.0
|
|
C1
|
P:HCB301
|
2.9
|
40.9
|
1.0
|
|
C4
|
P:HCB301
|
3.0
|
39.1
|
1.0
|
|
C16
|
P:HCB301
|
3.0
|
47.9
|
1.0
|
|
C14
|
P:HCB301
|
3.0
|
46.7
|
1.0
|
|
C6
|
P:HCB301
|
3.0
|
43.1
|
1.0
|
|
C10
|
P:HCB301
|
3.2
|
49.2
|
1.0
|
|
CE1
|
P:HIS107
|
3.3
|
52.7
|
1.0
|
|
CD2
|
P:HIS107
|
3.3
|
53.9
|
1.0
|
|
C5
|
P:HCB301
|
3.4
|
36.2
|
1.0
|
|
C15
|
P:HCB301
|
3.4
|
48.9
|
1.0
|
|
C20
|
P:HCB301
|
3.5
|
27.5
|
1.0
|
|
O
|
P:HOH406
|
3.8
|
40.5
|
1.0
|
|
C18
|
P:HCB301
|
4.1
|
42.3
|
1.0
|
|
C8
|
P:HCB301
|
4.2
|
47.1
|
1.0
|
|
C2
|
P:HCB301
|
4.2
|
41.3
|
1.0
|
|
C17
|
P:HCB301
|
4.3
|
46.1
|
1.0
|
|
C3
|
P:HCB301
|
4.3
|
39.4
|
1.0
|
|
C12
|
P:HCB301
|
4.3
|
38.6
|
1.0
|
|
C13
|
P:HCB301
|
4.3
|
41.9
|
1.0
|
|
C7
|
P:HCB301
|
4.3
|
44.7
|
1.0
|
|
ND1
|
P:HIS107
|
4.4
|
51.9
|
1.0
|
|
CG
|
P:HIS107
|
4.5
|
50.6
|
1.0
|
|
C26
|
P:HCB301
|
4.6
|
28.2
|
1.0
|
|
C35
|
P:HCB301
|
4.9
|
41.9
|
1.0
|
|
C54
|
P:HCB301
|
4.9
|
50.5
|
1.0
|
|
C53
|
P:HCB301
|
4.9
|
52.1
|
1.0
|
|
C37
|
P:HCB301
|
5.0
|
55.6
|
1.0
|
|
C42
|
P:HCB301
|
5.0
|
52.5
|
1.0
|
|
Cobalt binding site 5 out
of 6 in 7xcn
Go back to
Cobalt Binding Sites List in 7xcn
Cobalt binding site 5 out
of 6 in the Crystal Structure of the Mttb-Mttc Complex at 2.7 A Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Cobalt with other atoms in the Co binding
site number 5 of Crystal Structure of the Mttb-Mttc Complex at 2.7 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Co301
b:68.4
occ:1.00
|
CO
|
Q:HCB301
|
0.0
|
68.4
|
1.0
|
|
N24
|
Q:HCB301
|
1.9
|
74.6
|
1.0
|
|
N21
|
Q:HCB301
|
1.9
|
68.1
|
1.0
|
|
N23
|
Q:HCB301
|
1.9
|
68.0
|
1.0
|
|
N22
|
Q:HCB301
|
2.0
|
66.0
|
1.0
|
|
NE2
|
Q:HIS107
|
2.3
|
80.6
|
1.0
|
|
C19
|
Q:HCB301
|
2.9
|
72.2
|
1.0
|
|
C9
|
Q:HCB301
|
2.9
|
65.9
|
1.0
|
|
C11
|
Q:HCB301
|
2.9
|
62.4
|
1.0
|
|
C1
|
Q:HCB301
|
2.9
|
66.8
|
1.0
|
|
C4
|
Q:HCB301
|
3.0
|
61.4
|
1.0
|
|
C16
|
Q:HCB301
|
3.0
|
78.3
|
1.0
|
|
C14
|
Q:HCB301
|
3.0
|
67.3
|
1.0
|
|
C6
|
Q:HCB301
|
3.1
|
63.2
|
1.0
|
|
C10
|
Q:HCB301
|
3.2
|
67.1
|
1.0
|
|
CE1
|
Q:HIS107
|
3.3
|
79.2
|
1.0
|
|
O2
|
E:GOL601
|
3.3
|
59.9
|
1.0
|
|
CD2
|
Q:HIS107
|
3.3
|
87.5
|
1.0
|
|
C5
|
Q:HCB301
|
3.4
|
65.3
|
1.0
|
|
C15
|
Q:HCB301
|
3.4
|
76.3
|
1.0
|
|
C20
|
Q:HCB301
|
3.6
|
53.7
|
1.0
|
|
C18
|
Q:HCB301
|
4.2
|
73.4
|
1.0
|
|
C2
|
Q:HCB301
|
4.2
|
66.2
|
1.0
|
|
C3
|
Q:HCB301
|
4.3
|
60.1
|
1.0
|
|
C17
|
Q:HCB301
|
4.3
|
75.5
|
1.0
|
|
C8
|
Q:HCB301
|
4.3
|
62.8
|
1.0
|
|
C12
|
Q:HCB301
|
4.3
|
59.6
|
1.0
|
|
C13
|
Q:HCB301
|
4.3
|
63.4
|
1.0
|
|
C7
|
Q:HCB301
|
4.4
|
58.7
|
1.0
|
|
C2
|
E:GOL601
|
4.4
|
70.4
|
1.0
|
|
ND1
|
Q:HIS107
|
4.4
|
86.1
|
1.0
|
|
CG
|
Q:HIS107
|
4.5
|
90.9
|
1.0
|
|
C26
|
Q:HCB301
|
4.6
|
68.6
|
1.0
|
|
C1
|
E:GOL601
|
4.7
|
74.4
|
1.0
|
|
C54
|
Q:HCB301
|
4.9
|
75.4
|
1.0
|
|
C53
|
Q:HCB301
|
5.0
|
74.2
|
1.0
|
|
C35
|
Q:HCB301
|
5.0
|
61.1
|
1.0
|
|
C37
|
Q:HCB301
|
5.0
|
54.4
|
1.0
|
|
Cobalt binding site 6 out
of 6 in 7xcn
Go back to
Cobalt Binding Sites List in 7xcn
Cobalt binding site 6 out
of 6 in the Crystal Structure of the Mttb-Mttc Complex at 2.7 A Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Cobalt with other atoms in the Co binding
site number 6 of Crystal Structure of the Mttb-Mttc Complex at 2.7 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Co301
b:47.9
occ:1.00
|
CO
|
R:HCB301
|
0.0
|
47.9
|
1.0
|
|
N24
|
R:HCB301
|
1.9
|
48.7
|
1.0
|
|
N21
|
R:HCB301
|
1.9
|
51.2
|
1.0
|
|
N23
|
R:HCB301
|
1.9
|
51.1
|
1.0
|
|
N22
|
R:HCB301
|
1.9
|
52.6
|
1.0
|
|
NE2
|
R:HIS107
|
2.3
|
51.5
|
1.0
|
|
C19
|
R:HCB301
|
2.9
|
42.0
|
1.0
|
|
C9
|
R:HCB301
|
2.9
|
54.0
|
1.0
|
|
C11
|
R:HCB301
|
2.9
|
50.7
|
1.0
|
|
C1
|
R:HCB301
|
2.9
|
46.4
|
1.0
|
|
C4
|
R:HCB301
|
3.0
|
46.0
|
1.0
|
|
C16
|
R:HCB301
|
3.0
|
51.3
|
1.0
|
|
C14
|
R:HCB301
|
3.0
|
48.8
|
1.0
|
|
C6
|
R:HCB301
|
3.1
|
49.9
|
1.0
|
|
O3
|
F:GOL601
|
3.1
|
59.5
|
1.0
|
|
C10
|
R:HCB301
|
3.2
|
48.8
|
1.0
|
|
CE1
|
R:HIS107
|
3.3
|
52.5
|
1.0
|
|
CD2
|
R:HIS107
|
3.3
|
49.3
|
1.0
|
|
C5
|
R:HCB301
|
3.4
|
47.5
|
1.0
|
|
C15
|
R:HCB301
|
3.4
|
56.4
|
1.0
|
|
C20
|
R:HCB301
|
3.5
|
30.1
|
1.0
|
|
C18
|
R:HCB301
|
4.1
|
47.5
|
1.0
|
|
C2
|
R:HCB301
|
4.2
|
45.4
|
1.0
|
|
C8
|
R:HCB301
|
4.2
|
59.7
|
1.0
|
|
C17
|
R:HCB301
|
4.2
|
54.8
|
1.0
|
|
C3
|
R:HCB301
|
4.3
|
42.8
|
1.0
|
|
C12
|
R:HCB301
|
4.3
|
47.8
|
1.0
|
|
C13
|
R:HCB301
|
4.3
|
41.7
|
1.0
|
|
C7
|
R:HCB301
|
4.3
|
53.1
|
1.0
|
|
ND1
|
R:HIS107
|
4.4
|
51.5
|
1.0
|
|
C3
|
F:GOL601
|
4.4
|
66.6
|
1.0
|
|
CG
|
R:HIS107
|
4.5
|
52.4
|
1.0
|
|
C26
|
R:HCB301
|
4.6
|
35.5
|
1.0
|
|
C54
|
R:HCB301
|
4.9
|
55.5
|
1.0
|
|
C35
|
R:HCB301
|
4.9
|
40.1
|
1.0
|
|
C53
|
R:HCB301
|
4.9
|
60.7
|
1.0
|
|
C37
|
R:HCB301
|
5.0
|
50.4
|
1.0
|
|
C42
|
R:HCB301
|
5.0
|
60.9
|
1.0
|
|
Reference:
J.Li,
P.T.Kang,
R.Jiang,
J.Y.Lee,
J.A.Soares,
J.A.Krzycki,
M.K.Chan.
Insights Into Pyrrolysine Function From Structures of A Trimethylamine Methyltransferase and Its Corrinoid Protein Complex Commun Biol 2023.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-022-04397-3
Page generated: Tue Jul 30 19:36:45 2024
|
