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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 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 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 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

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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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