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Cobalt in PDB 6wte: Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound

Protein crystallography data

The structure of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound, PDB code: 6wte was solved by H.L.Knox, P.Y.-T.Chen, C.L.Drennan, S.J.Booker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.14 / 1.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.368, 103.759, 105.970, 90.00, 95.08, 90.00
R / Rfree (%) 19 / 21.5

Other elements in 6wte:

The structure of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound (pdb code 6wte). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound, PDB code: 6wte:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 6wte

Go back to Cobalt Binding Sites List in 6wte
Cobalt binding site 1 out of 2 in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co802

b:14.5
occ:1.00
CO A:B12802 0.0 14.5 1.0
N21 A:B12802 1.9 15.5 1.0
N24 A:B12802 1.9 9.2 1.0
N22 A:B12802 1.9 13.9 1.0
N23 A:B12802 1.9 14.3 1.0
O A:HOH1209 2.7 28.9 1.0
C11 A:B12802 2.9 14.5 1.0
C9 A:B12802 2.9 17.6 1.0
C4 A:B12802 2.9 13.4 1.0
C19 A:B12802 2.9 12.5 1.0
C1 A:B12802 2.9 12.3 1.0
C16 A:B12802 3.0 11.0 1.0
C14 A:B12802 3.0 11.4 1.0
C6 A:B12802 3.0 18.0 1.0
C10 A:B12802 3.2 13.7 1.0
C5 A:B12802 3.3 15.2 1.0
C15 A:B12802 3.4 12.0 1.0
NH2 A:ARG69 3.5 13.4 1.0
C20 A:B12802 3.6 13.8 1.0
NH1 A:ARG69 3.6 15.1 1.0
CZ A:ARG69 4.0 16.3 1.0
C2 A:B12802 4.1 12.3 1.0
C18 A:B12802 4.1 11.6 1.0
C12 A:B12802 4.2 14.1 1.0
C3 A:B12802 4.2 11.4 1.0
C8 A:B12802 4.2 16.8 1.0
C17 A:B12802 4.3 11.7 1.0
C7 A:B12802 4.3 16.7 1.0
C13 A:B12802 4.3 14.9 1.0
C26 A:B12802 4.4 12.8 1.0
C47 A:B12802 4.7 16.1 1.0
C35 A:B12802 4.8 19.1 1.0
C53 A:B12802 4.9 14.5 1.0
C41 A:B12802 4.9 16.6 1.0
C37 A:B12802 4.9 17.7 1.0
O A:HOH1323 4.9 41.5 1.0

Cobalt binding site 2 out of 2 in 6wte

Go back to Cobalt Binding Sites List in 6wte
Cobalt binding site 2 out of 2 in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Cobalamin and [4FE-4S] Cluster Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co802

b:15.8
occ:1.00
CO B:B12802 0.0 15.8 1.0
N21 B:B12802 1.9 15.5 1.0
N24 B:B12802 1.9 10.3 1.0
N22 B:B12802 1.9 14.7 1.0
N23 B:B12802 1.9 13.1 1.0
O B:HOH1128 2.5 26.3 1.0
C9 B:B12802 2.9 20.1 1.0
C11 B:B12802 2.9 14.9 1.0
C4 B:B12802 2.9 12.9 1.0
C19 B:B12802 2.9 12.8 1.0
C1 B:B12802 2.9 15.1 1.0
C16 B:B12802 3.0 13.2 1.0
C14 B:B12802 3.0 12.4 1.0
C6 B:B12802 3.0 18.3 1.0
C10 B:B12802 3.2 14.4 1.0
C5 B:B12802 3.3 16.3 1.0
C15 B:B12802 3.4 12.0 1.0
NH2 B:ARG69 3.5 16.6 1.0
NH1 B:ARG69 3.6 15.3 1.0
C20 B:B12802 3.6 15.8 1.0
CZ B:ARG69 4.0 16.2 1.0
C2 B:B12802 4.1 13.7 1.0
C18 B:B12802 4.1 12.1 1.0
C3 B:B12802 4.2 12.8 1.0
C12 B:B12802 4.2 12.9 1.0
C8 B:B12802 4.2 15.9 1.0
C17 B:B12802 4.3 13.2 1.0
C7 B:B12802 4.3 17.8 1.0
C13 B:B12802 4.3 15.7 1.0
C26 B:B12802 4.4 13.6 1.0
C47 B:B12802 4.8 14.1 1.0
C35 B:B12802 4.8 19.2 1.0
C41 B:B12802 4.9 17.6 1.0
C53 B:B12802 4.9 15.0 1.0
C37 B:B12802 4.9 18.6 1.0

Reference:

H.L.Knox, P.Y.-T.Chen, A.J.Blaszczyk, A.Mukherjee, T.L.Grove, E.L.Schwalm, B.Wang, C.L.Drennan, S.J.Booker. Structural Basis For Non-Radical Catalysis By Tsrm, A Radical Sam Methylase Nat.Chem.Biol..
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-020-00717-Y
Page generated: Sun Jan 24 14:52:52 2021

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