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Cobalt in PDB 2i2x: Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri

Enzymatic activity of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri

All present enzymatic activity of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri:
2.1.1.90;

Protein crystallography data

The structure of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri, PDB code: 2i2x was solved by C.H.Hagemeier, M.Kruer, R.K.Thauer, E.Warkentin, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.750, 172.850, 190.540, 90.00, 98.86, 90.00
R / Rfree (%) 18.2 / 23.1

Other elements in 2i2x:

The structure of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri also contains other interesting chemical elements:

Potassium (K) 8 atoms
Zinc (Zn) 12 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri (pdb code 2i2x). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri, PDB code: 2i2x:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 2i2x

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Cobalt binding site 1 out of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


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 Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co500

b:19.2
occ:1.00
CO B:B13500 0.0 19.2 1.0
N24 B:B13500 1.8 17.7 1.0
N21 B:B13500 1.8 20.0 1.0
N22 B:B13500 1.9 20.5 1.0
N23 B:B13500 1.9 17.4 1.0
NE2 B:HIS136 2.5 39.9 1.0
C19 B:B13500 2.8 18.9 1.0
C1 B:B13500 2.8 20.1 1.0
C9 B:B13500 2.8 22.1 1.0
C11 B:B13500 2.9 16.2 1.0
C4 B:B13500 2.9 19.8 1.0
C16 B:B13500 2.9 18.4 1.0
C14 B:B13500 3.0 16.1 1.0
C6 B:B13500 3.0 23.2 1.0
C10 B:B13500 3.2 19.8 1.0
O B:HOH501 3.2 42.7 1.0
C20 B:B13500 3.3 16.1 1.0
C5 B:B13500 3.4 22.9 1.0
C15 B:B13500 3.4 15.0 1.0
CD2 B:HIS136 3.4 40.1 1.0
CE1 B:HIS136 3.5 40.1 1.0
C18 B:B13500 4.1 20.1 1.0
C2 B:B13500 4.1 20.9 1.0
C8 B:B13500 4.2 24.1 1.0
C3 B:B13500 4.2 20.7 1.0
C17 B:B13500 4.2 20.6 1.0
C13 B:B13500 4.3 16.2 1.0
C12 B:B13500 4.3 16.5 1.0
C7 B:B13500 4.3 25.2 1.0
C26 B:B13500 4.6 22.4 1.0
ND1 B:HIS136 4.6 41.7 1.0
CG B:HIS136 4.6 41.8 1.0
C37 B:B13500 4.8 28.1 1.0
C41 B:B13500 4.8 27.1 1.0
C53 B:B13500 4.9 16.5 1.0
C35 B:B13500 4.9 21.9 1.0
C54 B:B13500 5.0 19.6 1.0

Cobalt binding site 2 out of 8 in 2i2x

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Cobalt binding site 2 out of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


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 Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co500

b:27.6
occ:1.00
CO D:B13500 0.0 27.6 1.0
N24 D:B13500 1.8 26.9 1.0
N21 D:B13500 1.8 28.1 1.0
N22 D:B13500 1.9 31.7 1.0
N23 D:B13500 1.9 29.5 1.0
NE2 D:HIS136 2.4 43.2 1.0
C19 D:B13500 2.7 26.7 1.0
C9 D:B13500 2.8 32.9 1.0
C1 D:B13500 2.8 26.4 1.0
C11 D:B13500 2.9 29.2 1.0
C4 D:B13500 2.9 28.3 1.0
C16 D:B13500 2.9 26.0 1.0
C6 D:B13500 3.0 33.3 1.0
C14 D:B13500 3.0 27.3 1.0
C10 D:B13500 3.2 30.7 1.0
O D:HOH501 3.3 20.5 1.0
CE1 D:HIS136 3.3 43.6 1.0
CD2 D:HIS136 3.4 44.9 1.0
C5 D:B13500 3.4 31.3 1.0
C15 D:B13500 3.5 25.7 1.0
C20 D:B13500 3.5 22.9 1.0
C18 D:B13500 4.1 27.8 1.0
C2 D:B13500 4.1 27.8 1.0
C8 D:B13500 4.2 34.6 1.0
C3 D:B13500 4.2 27.3 1.0
C17 D:B13500 4.2 25.2 1.0
C12 D:B13500 4.3 29.4 1.0
C13 D:B13500 4.3 28.4 1.0
C7 D:B13500 4.3 34.8 1.0
C26 D:B13500 4.4 25.9 1.0
ND1 D:HIS136 4.4 45.2 1.0
CG D:HIS136 4.5 46.0 1.0
C37 D:B13500 4.9 36.2 1.0
C46 D:B13500 4.9 27.5 1.0
C41 D:B13500 4.9 37.2 1.0
C54 D:B13500 4.9 23.8 1.0
C35 D:B13500 4.9 29.3 1.0

Cobalt binding site 3 out of 8 in 2i2x

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Cobalt binding site 3 out of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


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Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Co500

b:65.9
occ:1.00
CO F:B13500 0.0 65.9 1.0
N24 F:B13500 1.8 64.9 1.0
N21 F:B13500 1.8 64.7 1.0
N22 F:B13500 1.9 66.5 1.0
N23 F:B13500 1.9 65.5 1.0
NE2 F:HIS136 2.7 57.9 1.0
C19 F:B13500 2.8 64.2 1.0
C1 F:B13500 2.8 64.2 1.0
C9 F:B13500 2.9 66.7 1.0
C4 F:B13500 2.9 64.7 1.0
C11 F:B13500 2.9 65.8 1.0
C16 F:B13500 2.9 64.5 1.0
C14 F:B13500 3.0 65.5 1.0
C6 F:B13500 3.0 67.6 1.0
C10 F:B13500 3.2 65.7 1.0
O F:HOH501 3.2 17.7 0.5
C5 F:B13500 3.4 66.3 1.0
C15 F:B13500 3.4 64.7 1.0
C20 F:B13500 3.4 63.8 1.0
CE1 F:HIS136 3.5 57.2 1.0
CD2 F:HIS136 3.7 58.1 1.0
C18 F:B13500 4.1 63.5 1.0
C2 F:B13500 4.1 63.9 1.0
C3 F:B13500 4.2 63.8 1.0
C17 F:B13500 4.2 63.5 1.0
C8 F:B13500 4.2 68.0 1.0
C12 F:B13500 4.3 66.3 1.0
C13 F:B13500 4.3 66.0 1.0
C7 F:B13500 4.3 68.6 1.0
C26 F:B13500 4.6 63.3 1.0
ND1 F:HIS136 4.7 58.2 1.0
C37 F:B13500 4.7 69.7 1.0
CG F:HIS136 4.8 58.7 1.0
C54 F:B13500 4.9 64.2 1.0
C35 F:B13500 4.9 66.2 1.0
C53 F:B13500 4.9 64.5 1.0
C46 F:B13500 5.0 66.7 1.0

Cobalt binding site 4 out of 8 in 2i2x

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Cobalt binding site 4 out of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


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 Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Co500

b:54.1
occ:1.00
CO H:B13500 0.0 54.1 1.0
N24 H:B13500 1.8 54.4 1.0
N21 H:B13500 1.8 53.3 1.0
N22 H:B13500 1.9 55.4 1.0
N23 H:B13500 1.9 54.4 1.0
NE2 H:HIS136 2.6 57.5 1.0
C19 H:B13500 2.8 54.2 1.0
C1 H:B13500 2.8 53.4 1.0
C9 H:B13500 2.8 56.2 1.0
C11 H:B13500 2.9 55.4 1.0
C4 H:B13500 2.9 53.3 1.0
C16 H:B13500 2.9 54.9 1.0
C14 H:B13500 3.0 55.2 1.0
C6 H:B13500 3.0 56.4 1.0
C10 H:B13500 3.2 55.6 1.0
CE1 H:HIS136 3.4 57.0 1.0
C5 H:B13500 3.4 55.2 1.0
C20 H:B13500 3.4 53.0 1.0
C15 H:B13500 3.4 54.4 1.0
O H:HOH501 3.6 18.1 0.5
CD2 H:HIS136 3.7 57.8 1.0
C18 H:B13500 4.1 55.1 1.0
C2 H:B13500 4.1 52.7 1.0
C3 H:B13500 4.2 51.8 1.0
C8 H:B13500 4.2 58.2 1.0
C17 H:B13500 4.2 55.0 1.0
C12 H:B13500 4.2 56.1 1.0
C13 H:B13500 4.3 56.5 1.0
C7 H:B13500 4.3 58.4 1.0
ND1 H:HIS136 4.6 57.9 1.0
C26 H:B13500 4.6 53.0 1.0
CG H:HIS136 4.8 58.5 1.0
C37 H:B13500 4.9 59.3 1.0
C46 H:B13500 4.9 56.0 1.0
C35 H:B13500 4.9 56.1 1.0
C54 H:B13500 4.9 55.5 1.0
C41 H:B13500 4.9 59.8 1.0
C53 H:B13500 4.9 52.2 1.0

Cobalt binding site 5 out of 8 in 2i2x

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Cobalt binding site 5 out of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


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 Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Co500

b:32.8
occ:1.00
CO J:B13500 0.0 32.8 1.0
N24 J:B13500 1.8 33.0 1.0
N21 J:B13500 1.9 34.1 1.0
N22 J:B13500 1.9 38.3 1.0
N23 J:B13500 1.9 34.7 1.0
NE2 J:HIS136 2.4 43.0 1.0
C19 J:B13500 2.8 33.9 1.0
C9 J:B13500 2.8 40.1 1.0
C1 J:B13500 2.9 34.4 1.0
C11 J:B13500 2.9 35.8 1.0
C4 J:B13500 2.9 35.4 1.0
C16 J:B13500 2.9 33.7 1.0
C6 J:B13500 3.0 40.6 1.0
C14 J:B13500 3.0 34.2 1.0
O J:HOH501 3.1 2.8 0.5
C10 J:B13500 3.2 36.9 1.0
CE1 J:HIS136 3.3 43.3 1.0
C5 J:B13500 3.4 38.1 1.0
CD2 J:HIS136 3.4 44.2 1.0
C15 J:B13500 3.4 32.9 1.0
C20 J:B13500 3.5 32.3 1.0
C18 J:B13500 4.1 34.8 1.0
C2 J:B13500 4.1 35.8 1.0
C8 J:B13500 4.1 44.1 1.0
C17 J:B13500 4.2 34.0 1.0
C3 J:B13500 4.2 35.9 1.0
C12 J:B13500 4.3 35.9 1.0
C13 J:B13500 4.3 35.9 1.0
C7 J:B13500 4.3 44.1 1.0
ND1 J:HIS136 4.5 45.5 1.0
C26 J:B13500 4.5 35.5 1.0
CG J:HIS136 4.5 46.4 1.0
C41 J:B13500 4.7 48.7 1.0
C37 J:B13500 4.8 46.6 1.0
C54 J:B13500 4.8 32.9 1.0
C46 J:B13500 4.9 34.2 1.0
C35 J:B13500 4.9 36.8 1.0
C53 J:B13500 4.9 32.2 1.0
C48 J:B13500 5.0 38.2 1.0

Cobalt binding site 6 out of 8 in 2i2x

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Cobalt binding site 6 out of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


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 Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Co500

b:43.5
occ:1.00
CO L:B13500 0.0 43.5 1.0
N24 L:B13500 1.8 45.5 1.0
N21 L:B13500 1.9 45.5 1.0
N22 L:B13500 1.9 47.3 1.0
N23 L:B13500 1.9 46.7 1.0
NE2 L:HIS136 2.6 53.2 1.0
C19 L:B13500 2.8 45.2 1.0
C9 L:B13500 2.8 48.4 1.0
O L:HOH501 2.8 18.9 0.5
C1 L:B13500 2.9 44.2 1.0
C11 L:B13500 2.9 47.2 1.0
C4 L:B13500 2.9 45.4 1.0
C16 L:B13500 2.9 46.2 1.0
C6 L:B13500 3.0 48.6 1.0
C14 L:B13500 3.0 46.5 1.0
C10 L:B13500 3.2 47.3 1.0
C5 L:B13500 3.4 47.8 1.0
CD2 L:HIS136 3.4 54.4 1.0
C15 L:B13500 3.5 46.0 1.0
C20 L:B13500 3.5 42.2 1.0
CE1 L:HIS136 3.6 53.8 1.0
C18 L:B13500 4.1 46.2 1.0
C2 L:B13500 4.1 43.9 1.0
C8 L:B13500 4.2 49.7 1.0
C3 L:B13500 4.2 44.9 1.0
C17 L:B13500 4.2 46.9 1.0
C12 L:B13500 4.3 47.0 1.0
C7 L:B13500 4.3 49.7 1.0
C13 L:B13500 4.3 47.5 1.0
C26 L:B13500 4.4 43.2 1.0
CG L:HIS136 4.6 55.2 1.0
ND1 L:HIS136 4.7 54.7 1.0
C41 L:B13500 4.8 50.8 1.0
C54 L:B13500 4.9 46.7 1.0
C35 L:B13500 4.9 47.6 1.0
C37 L:B13500 4.9 52.1 1.0
C46 L:B13500 4.9 46.1 1.0
C53 L:B13500 5.0 44.7 1.0

Cobalt binding site 7 out of 8 in 2i2x

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Cobalt binding site 7 out of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Co500

b:65.7
occ:1.00
CO N:B13500 0.0 65.7 1.0
N21 N:B13500 1.8 65.7 1.0
N24 N:B13500 1.8 65.5 1.0
N22 N:B13500 1.9 67.5 1.0
N23 N:B13500 1.9 66.3 1.0
NE2 N:HIS136 2.5 57.2 1.0
C19 N:B13500 2.8 64.6 1.0
C9 N:B13500 2.8 67.8 1.0
C1 N:B13500 2.8 64.8 1.0
C11 N:B13500 2.9 66.9 1.0
C4 N:B13500 2.9 65.8 1.0
C16 N:B13500 3.0 64.5 1.0
C6 N:B13500 3.0 68.3 1.0
C14 N:B13500 3.0 65.6 1.0
C10 N:B13500 3.2 67.0 1.0
O N:HOH501 3.3 10.9 0.5
C5 N:B13500 3.4 67.1 1.0
CD2 N:HIS136 3.4 57.9 1.0
C20 N:B13500 3.4 63.6 1.0
C15 N:B13500 3.5 64.8 1.0
CE1 N:HIS136 3.5 57.4 1.0
C18 N:B13500 4.1 64.0 1.0
C2 N:B13500 4.1 64.6 1.0
C8 N:B13500 4.2 69.2 1.0
C3 N:B13500 4.2 65.1 1.0
C12 N:B13500 4.2 66.6 1.0
C17 N:B13500 4.2 63.7 1.0
C13 N:B13500 4.3 66.1 1.0
C7 N:B13500 4.3 69.4 1.0
C26 N:B13500 4.6 64.3 1.0
ND1 N:HIS136 4.6 57.9 1.0
CG N:HIS136 4.6 58.9 1.0
C46 N:B13500 4.6 66.3 1.0
C37 N:B13500 4.9 70.8 1.0
C35 N:B13500 4.9 66.4 1.0
C54 N:B13500 4.9 63.7 1.0
C41 N:B13500 4.9 70.2 1.0
C48 N:B13500 5.0 65.7 1.0
C53 N:B13500 5.0 63.8 1.0

Cobalt binding site 8 out of 8 in 2i2x

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Cobalt binding site 8 out of 8 in the Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of Methanol:Cobalamin Methyltransferase Complex Mtabc From Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Co500

b:37.6
occ:1.00
CO P:B13500 0.0 37.6 1.0
N24 P:B13500 1.8 36.0 1.0
N21 P:B13500 1.8 36.8 1.0
N22 P:B13500 1.9 37.0 1.0
N23 P:B13500 1.9 36.1 1.0
NE2 P:HIS136 2.5 46.1 1.0
C19 P:B13500 2.8 36.9 1.0
C9 P:B13500 2.8 38.4 1.0
C1 P:B13500 2.8 37.0 1.0
C11 P:B13500 2.9 35.9 1.0
C4 P:B13500 2.9 36.5 1.0
C16 P:B13500 2.9 36.9 1.0
C6 P:B13500 3.0 39.5 1.0
C14 P:B13500 3.0 35.9 1.0
C10 P:B13500 3.2 36.3 1.0
CD2 P:HIS136 3.3 46.1 1.0
C5 P:B13500 3.4 38.2 1.0
C20 P:B13500 3.4 35.3 1.0
C15 P:B13500 3.4 35.3 1.0
O P:HOH501 3.5 2.0 0.5
CE1 P:HIS136 3.6 45.9 1.0
C18 P:B13500 4.1 37.9 1.0
C2 P:B13500 4.1 37.0 1.0
C8 P:B13500 4.2 40.9 1.0
C3 P:B13500 4.2 36.0 1.0
C17 P:B13500 4.2 37.3 1.0
C12 P:B13500 4.3 36.6 1.0
C13 P:B13500 4.3 37.9 1.0
C7 P:B13500 4.3 41.8 1.0
CG P:HIS136 4.5 47.8 1.0
C26 P:B13500 4.6 37.4 1.0
ND1 P:HIS136 4.6 47.0 1.0
C35 P:B13500 4.9 37.7 1.0
C37 P:B13500 4.9 45.5 1.0
C41 P:B13500 4.9 43.2 1.0
C53 P:B13500 5.0 33.5 1.0
C46 P:B13500 5.0 35.7 1.0

Reference:

C.H.Hagemeier, M.Krer, R.K.Thauer, E.Warkentin, U.Ermler. Insight Into the Mechanism of Biological Methanol Activation Based on the Crystal Structure of the Methanol-Cobalamin Methyltransferase Complex Proc.Natl.Acad.Sci.Usa V. 103 18917 2006.
ISSN: ISSN 0027-8424
PubMed: 17142327
DOI: 10.1073/PNAS.0603650103
Page generated: Tue Jul 30 15:15:49 2024

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