Cobalt in PDB 9cbo: Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on)
Enzymatic activity of Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on)
All present enzymatic activity of Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on):
2.1.1.13;
Protein crystallography data
The structure of Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on), PDB code: 9cbo
was solved by
K.Yamada,
J.Mendoza,
M.Koutmos,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
163.18 /
3.34
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
187.769,
187.769,
325.547,
90,
90,
90
|
R / Rfree (%)
|
17.3 /
21.6
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on)
(pdb code 9cbo). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the
Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on), PDB code: 9cbo:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
Cobalt binding site 1 out
of 6 in 9cbo
Go back to
Cobalt Binding Sites List in 9cbo
Cobalt binding site 1 out
of 6 in the Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on)
 Mono view
 Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co901
b:136.0
occ:1.00
|
CO
|
A:COB901
|
0.0
|
136.0
|
1.0
|
N23
|
A:COB901
|
1.8
|
154.2
|
1.0
|
N24
|
A:COB901
|
1.9
|
147.4
|
1.0
|
N22
|
A:COB901
|
1.9
|
167.3
|
1.0
|
N21
|
A:COB901
|
1.9
|
166.1
|
1.0
|
C1A
|
A:COB901
|
2.0
|
163.1
|
1.0
|
NE2
|
A:HIS761
|
2.6
|
136.1
|
1.0
|
C19
|
A:COB901
|
2.7
|
151.9
|
1.0
|
C11
|
A:COB901
|
2.8
|
166.3
|
1.0
|
C9
|
A:COB901
|
2.8
|
152.5
|
1.0
|
C14
|
A:COB901
|
2.9
|
160.2
|
1.0
|
C4
|
A:COB901
|
2.9
|
138.3
|
1.0
|
C16
|
A:COB901
|
2.9
|
160.7
|
1.0
|
C1
|
A:COB901
|
2.9
|
162.6
|
1.0
|
C6
|
A:COB901
|
3.0
|
162.5
|
1.0
|
C10
|
A:COB901
|
3.2
|
160.1
|
1.0
|
C5
|
A:COB901
|
3.3
|
147.4
|
1.0
|
C15
|
A:COB901
|
3.3
|
176.6
|
1.0
|
CD2
|
A:HIS761
|
3.5
|
148.8
|
1.0
|
C20
|
A:COB901
|
3.7
|
176.5
|
1.0
|
CE1
|
A:HIS761
|
3.7
|
147.7
|
1.0
|
C18
|
A:COB901
|
4.1
|
130.0
|
1.0
|
C2
|
A:COB901
|
4.2
|
133.6
|
1.0
|
C13
|
A:COB901
|
4.2
|
141.9
|
1.0
|
C8
|
A:COB901
|
4.2
|
138.4
|
1.0
|
C12
|
A:COB901
|
4.2
|
130.4
|
1.0
|
C3
|
A:COB901
|
4.2
|
118.5
|
1.0
|
C7
|
A:COB901
|
4.2
|
132.1
|
1.0
|
C17
|
A:COB901
|
4.3
|
126.8
|
1.0
|
C26
|
A:COB901
|
4.6
|
128.6
|
1.0
|
CG
|
A:HIS761
|
4.7
|
133.7
|
1.0
|
C37
|
A:COB901
|
4.7
|
116.8
|
1.0
|
ND1
|
A:HIS761
|
4.8
|
114.4
|
1.0
|
C35
|
A:COB901
|
4.8
|
128.9
|
1.0
|
C47
|
A:COB901
|
4.8
|
130.3
|
1.0
|
C53
|
A:COB901
|
4.8
|
164.0
|
1.0
|
C41
|
A:COB901
|
4.9
|
147.3
|
1.0
|
|
Cobalt binding site 2 out
of 6 in 9cbo
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Cobalt Binding Sites List in 9cbo
Cobalt binding site 2 out
of 6 in the Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on)
 Mono view
 Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co901
b:105.0
occ:1.00
|
CO
|
B:COB901
|
0.0
|
105.0
|
1.0
|
N23
|
B:COB901
|
1.8
|
111.0
|
1.0
|
N22
|
B:COB901
|
1.8
|
104.6
|
1.0
|
N21
|
B:COB901
|
1.9
|
119.3
|
1.0
|
N24
|
B:COB901
|
1.9
|
101.5
|
1.0
|
C1A
|
B:COB901
|
2.0
|
105.5
|
1.0
|
NE2
|
B:HIS761
|
2.5
|
114.9
|
1.0
|
C9
|
B:COB901
|
2.8
|
102.5
|
1.0
|
C11
|
B:COB901
|
2.8
|
108.0
|
1.0
|
C19
|
B:COB901
|
2.8
|
98.9
|
1.0
|
C4
|
B:COB901
|
2.8
|
121.8
|
1.0
|
C14
|
B:COB901
|
2.9
|
120.1
|
1.0
|
C6
|
B:COB901
|
2.9
|
119.9
|
1.0
|
C1
|
B:COB901
|
2.9
|
107.8
|
1.0
|
C16
|
B:COB901
|
3.0
|
117.7
|
1.0
|
C10
|
B:COB901
|
3.1
|
106.3
|
1.0
|
C5
|
B:COB901
|
3.2
|
131.0
|
1.0
|
C15
|
B:COB901
|
3.3
|
129.2
|
1.0
|
CD2
|
B:HIS761
|
3.4
|
126.2
|
1.0
|
CE1
|
B:HIS761
|
3.6
|
115.3
|
1.0
|
C20
|
B:COB901
|
3.6
|
123.6
|
1.0
|
C8
|
B:COB901
|
4.1
|
105.0
|
1.0
|
C12
|
B:COB901
|
4.1
|
101.6
|
1.0
|
C2
|
B:COB901
|
4.1
|
109.3
|
1.0
|
C18
|
B:COB901
|
4.2
|
105.5
|
1.0
|
C3
|
B:COB901
|
4.2
|
109.5
|
1.0
|
C7
|
B:COB901
|
4.2
|
117.7
|
1.0
|
C13
|
B:COB901
|
4.2
|
112.1
|
1.0
|
C17
|
B:COB901
|
4.3
|
110.8
|
1.0
|
C26
|
B:COB901
|
4.5
|
118.3
|
1.0
|
CG
|
B:HIS761
|
4.6
|
119.4
|
1.0
|
C47
|
B:COB901
|
4.7
|
95.6
|
1.0
|
C37
|
B:COB901
|
4.7
|
123.4
|
1.0
|
ND1
|
B:HIS761
|
4.7
|
105.2
|
1.0
|
C35
|
B:COB901
|
4.7
|
138.1
|
1.0
|
C41
|
B:COB901
|
4.8
|
113.0
|
1.0
|
C53
|
B:COB901
|
4.9
|
126.5
|
1.0
|
C48
|
B:COB901
|
4.9
|
115.2
|
1.0
|
C54
|
B:COB901
|
5.0
|
96.3
|
1.0
|
|
Cobalt binding site 3 out
of 6 in 9cbo
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Cobalt Binding Sites List in 9cbo
Cobalt binding site 3 out
of 6 in the Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on)
 Mono view
 Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co901
b:72.3
occ:1.00
|
CO
|
C:COB901
|
0.0
|
72.3
|
1.0
|
N22
|
C:COB901
|
1.8
|
68.9
|
1.0
|
N23
|
C:COB901
|
1.8
|
63.7
|
1.0
|
N21
|
C:COB901
|
1.8
|
73.1
|
1.0
|
N24
|
C:COB901
|
1.9
|
70.9
|
1.0
|
C1A
|
C:COB901
|
2.1
|
61.5
|
1.0
|
CE1
|
C:HIS761
|
2.3
|
73.6
|
1.0
|
C9
|
C:COB901
|
2.7
|
69.8
|
1.0
|
C19
|
C:COB901
|
2.7
|
69.8
|
1.0
|
C11
|
C:COB901
|
2.7
|
60.5
|
1.0
|
C4
|
C:COB901
|
2.8
|
68.9
|
1.0
|
C14
|
C:COB901
|
2.8
|
69.0
|
1.0
|
C6
|
C:COB901
|
2.8
|
68.1
|
1.0
|
C1
|
C:COB901
|
2.9
|
68.3
|
1.0
|
C16
|
C:COB901
|
3.0
|
65.7
|
1.0
|
C10
|
C:COB901
|
3.0
|
60.1
|
1.0
|
ND1
|
C:HIS761
|
3.2
|
76.3
|
1.0
|
C5
|
C:COB901
|
3.2
|
63.8
|
1.0
|
C20
|
C:COB901
|
3.3
|
75.9
|
1.0
|
C15
|
C:COB901
|
3.3
|
66.4
|
1.0
|
NE2
|
C:HIS761
|
3.4
|
85.4
|
1.0
|
C18
|
C:COB901
|
4.0
|
69.3
|
1.0
|
C12
|
C:COB901
|
4.1
|
70.6
|
1.0
|
C2
|
C:COB901
|
4.1
|
67.1
|
1.0
|
C8
|
C:COB901
|
4.1
|
72.9
|
1.0
|
C13
|
C:COB901
|
4.1
|
77.5
|
1.0
|
C7
|
C:COB901
|
4.1
|
71.0
|
1.0
|
C3
|
C:COB901
|
4.2
|
64.9
|
1.0
|
C17
|
C:COB901
|
4.2
|
67.2
|
1.0
|
CG
|
C:HIS761
|
4.4
|
88.4
|
1.0
|
CD2
|
C:HIS761
|
4.5
|
77.8
|
1.0
|
C26
|
C:COB901
|
4.6
|
69.5
|
1.0
|
C35
|
C:COB901
|
4.7
|
67.0
|
1.0
|
C37
|
C:COB901
|
4.7
|
74.1
|
1.0
|
C47
|
C:COB901
|
4.7
|
75.7
|
1.0
|
C48
|
C:COB901
|
4.8
|
79.5
|
1.0
|
C53
|
C:COB901
|
4.8
|
76.1
|
1.0
|
C54
|
C:COB901
|
5.0
|
69.0
|
1.0
|
|
Cobalt binding site 4 out
of 6 in 9cbo
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Cobalt Binding Sites List in 9cbo
Cobalt binding site 4 out
of 6 in the Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on)
 Mono view
 Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co901
b:81.9
occ:1.00
|
CO
|
D:COB901
|
0.0
|
81.9
|
1.0
|
N22
|
D:COB901
|
1.8
|
78.4
|
1.0
|
N21
|
D:COB901
|
1.8
|
98.0
|
1.0
|
N23
|
D:COB901
|
1.8
|
84.1
|
1.0
|
N24
|
D:COB901
|
1.9
|
73.2
|
1.0
|
C1A
|
D:COB901
|
2.1
|
78.7
|
1.0
|
CE1
|
D:HIS761
|
2.5
|
67.7
|
1.0
|
C9
|
D:COB901
|
2.7
|
75.3
|
1.0
|
C19
|
D:COB901
|
2.8
|
73.8
|
1.0
|
C11
|
D:COB901
|
2.8
|
81.1
|
1.0
|
C4
|
D:COB901
|
2.8
|
87.3
|
1.0
|
C6
|
D:COB901
|
2.8
|
88.5
|
1.0
|
C1
|
D:COB901
|
2.9
|
85.5
|
1.0
|
C14
|
D:COB901
|
2.9
|
70.5
|
1.0
|
C16
|
D:COB901
|
3.0
|
76.4
|
1.0
|
C10
|
D:COB901
|
3.1
|
69.9
|
1.0
|
C5
|
D:COB901
|
3.2
|
85.1
|
1.0
|
NE2
|
D:HIS761
|
3.2
|
74.1
|
1.0
|
C15
|
D:COB901
|
3.4
|
73.0
|
1.0
|
C20
|
D:COB901
|
3.5
|
92.4
|
1.0
|
ND1
|
D:HIS761
|
3.6
|
75.9
|
1.0
|
C8
|
D:COB901
|
4.0
|
84.8
|
1.0
|
C18
|
D:COB901
|
4.1
|
78.4
|
1.0
|
C2
|
D:COB901
|
4.1
|
84.6
|
1.0
|
C3
|
D:COB901
|
4.1
|
82.3
|
1.0
|
C12
|
D:COB901
|
4.1
|
73.3
|
1.0
|
C13
|
D:COB901
|
4.2
|
68.7
|
1.0
|
C7
|
D:COB901
|
4.2
|
84.3
|
1.0
|
C17
|
D:COB901
|
4.3
|
80.1
|
1.0
|
CD2
|
D:HIS761
|
4.5
|
83.5
|
1.0
|
C26
|
D:COB901
|
4.6
|
94.5
|
1.0
|
C47
|
D:COB901
|
4.6
|
78.4
|
1.0
|
C35
|
D:COB901
|
4.6
|
90.0
|
1.0
|
CG
|
D:HIS761
|
4.6
|
104.7
|
1.0
|
C41
|
D:COB901
|
4.6
|
78.6
|
1.0
|
C37
|
D:COB901
|
4.8
|
79.5
|
1.0
|
C48
|
D:COB901
|
4.8
|
76.0
|
1.0
|
C53
|
D:COB901
|
4.9
|
84.3
|
1.0
|
|
Cobalt binding site 5 out
of 6 in 9cbo
Go back to
Cobalt Binding Sites List in 9cbo
Cobalt binding site 5 out
of 6 in the Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on)
 Mono view
 Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 5 of Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Co901
b:94.0
occ:1.00
|
CO
|
E:COB901
|
0.0
|
94.0
|
1.0
|
N23
|
E:COB901
|
1.8
|
85.4
|
1.0
|
N21
|
E:COB901
|
1.8
|
97.8
|
1.0
|
N24
|
E:COB901
|
1.8
|
85.9
|
1.0
|
N22
|
E:COB901
|
1.9
|
96.6
|
1.0
|
C1A
|
E:COB901
|
2.0
|
97.7
|
1.0
|
NE2
|
E:HIS761
|
2.5
|
96.8
|
1.0
|
C19
|
E:COB901
|
2.7
|
92.6
|
1.0
|
C9
|
E:COB901
|
2.8
|
98.3
|
1.0
|
C11
|
E:COB901
|
2.8
|
96.6
|
1.0
|
C4
|
E:COB901
|
2.8
|
87.8
|
1.0
|
C14
|
E:COB901
|
2.8
|
93.4
|
1.0
|
C1
|
E:COB901
|
2.9
|
99.2
|
1.0
|
C6
|
E:COB901
|
2.9
|
89.9
|
1.0
|
C16
|
E:COB901
|
2.9
|
93.1
|
1.0
|
C10
|
E:COB901
|
3.1
|
95.1
|
1.0
|
C5
|
E:COB901
|
3.2
|
85.8
|
1.0
|
C15
|
E:COB901
|
3.3
|
92.1
|
1.0
|
CD2
|
E:HIS761
|
3.3
|
104.0
|
1.0
|
C20
|
E:COB901
|
3.5
|
116.7
|
1.0
|
CE1
|
E:HIS761
|
3.5
|
96.3
|
1.0
|
C18
|
E:COB901
|
4.1
|
94.0
|
1.0
|
C2
|
E:COB901
|
4.1
|
95.1
|
1.0
|
C12
|
E:COB901
|
4.1
|
100.1
|
1.0
|
C13
|
E:COB901
|
4.1
|
103.1
|
1.0
|
C3
|
E:COB901
|
4.1
|
88.4
|
1.0
|
C8
|
E:COB901
|
4.1
|
88.8
|
1.0
|
C7
|
E:COB901
|
4.2
|
85.1
|
1.0
|
C17
|
E:COB901
|
4.3
|
94.7
|
1.0
|
C26
|
E:COB901
|
4.5
|
106.2
|
1.0
|
CG
|
E:HIS761
|
4.5
|
116.3
|
1.0
|
ND1
|
E:HIS761
|
4.6
|
102.9
|
1.0
|
C47
|
E:COB901
|
4.7
|
105.1
|
1.0
|
C35
|
E:COB901
|
4.7
|
89.8
|
1.0
|
C37
|
E:COB901
|
4.7
|
101.8
|
1.0
|
C53
|
E:COB901
|
4.8
|
95.7
|
1.0
|
C48
|
E:COB901
|
4.9
|
102.2
|
1.0
|
|
Cobalt binding site 6 out
of 6 in 9cbo
Go back to
Cobalt Binding Sites List in 9cbo
Cobalt binding site 6 out
of 6 in the Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on)
 Mono view
 Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 6 of Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Co901
b:87.6
occ:1.00
|
CO
|
F:COB901
|
0.0
|
87.6
|
1.0
|
N23
|
F:COB901
|
1.8
|
86.7
|
1.0
|
N22
|
F:COB901
|
1.8
|
84.8
|
1.0
|
N21
|
F:COB901
|
1.8
|
88.2
|
1.0
|
N24
|
F:COB901
|
1.9
|
78.5
|
1.0
|
C1A
|
F:COB901
|
2.0
|
81.8
|
1.0
|
NE2
|
F:HIS761
|
2.5
|
87.7
|
1.0
|
C9
|
F:COB901
|
2.7
|
93.8
|
1.0
|
C11
|
F:COB901
|
2.7
|
96.7
|
1.0
|
C19
|
F:COB901
|
2.8
|
78.3
|
1.0
|
C4
|
F:COB901
|
2.8
|
89.7
|
1.0
|
C6
|
F:COB901
|
2.8
|
80.7
|
1.0
|
C14
|
F:COB901
|
2.8
|
80.8
|
1.0
|
C1
|
F:COB901
|
2.9
|
87.8
|
1.0
|
C16
|
F:COB901
|
2.9
|
81.8
|
1.0
|
C10
|
F:COB901
|
3.1
|
96.9
|
1.0
|
C5
|
F:COB901
|
3.2
|
85.7
|
1.0
|
C15
|
F:COB901
|
3.3
|
83.2
|
1.0
|
CD2
|
F:HIS761
|
3.4
|
93.4
|
1.0
|
C20
|
F:COB901
|
3.5
|
109.4
|
1.0
|
CE1
|
F:HIS761
|
3.6
|
106.2
|
1.0
|
C12
|
F:COB901
|
4.1
|
86.1
|
1.0
|
C18
|
F:COB901
|
4.1
|
89.8
|
1.0
|
C2
|
F:COB901
|
4.1
|
92.1
|
1.0
|
C7
|
F:COB901
|
4.1
|
82.8
|
1.0
|
C13
|
F:COB901
|
4.1
|
84.7
|
1.0
|
C8
|
F:COB901
|
4.1
|
94.1
|
1.0
|
C3
|
F:COB901
|
4.2
|
89.0
|
1.0
|
C17
|
F:COB901
|
4.2
|
88.8
|
1.0
|
C47
|
F:COB901
|
4.4
|
79.8
|
1.0
|
C26
|
F:COB901
|
4.5
|
100.2
|
1.0
|
CG
|
F:HIS761
|
4.6
|
112.0
|
1.0
|
C37
|
F:COB901
|
4.6
|
82.7
|
1.0
|
C35
|
F:COB901
|
4.6
|
89.0
|
1.0
|
ND1
|
F:HIS761
|
4.7
|
108.3
|
1.0
|
C53
|
F:COB901
|
4.8
|
107.2
|
1.0
|
C54
|
F:COB901
|
4.9
|
106.8
|
1.0
|
|
Reference:
J.Mendoza,
K.Yamada,
M.Koutmos.
Methionine Synthase From Thermus Thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on) To Be Published.
Page generated: Sun Jul 13 22:11:56 2025
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