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Cobalt in PDB 6wtf: Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Tryptophan Substrate and Sam Analog (Aza-Sam) Bound

Protein crystallography data

The structure of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Tryptophan Substrate and Sam Analog (Aza-Sam) Bound, PDB code: 6wtf 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) 46.92 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.355, 103.085, 105.757, 90.00, 94.77, 90.00
R / Rfree (%) 21.1 / 24.9

Other elements in 6wtf:

The structure of Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Tryptophan Substrate and Sam Analog (Aza-Sam) 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 Tryptophan Substrate and Sam Analog (Aza-Sam) Bound (pdb code 6wtf). 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 Tryptophan Substrate and Sam Analog (Aza-Sam) Bound, PDB code: 6wtf:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 6wtf

Go back to Cobalt Binding Sites List in 6wtf
Cobalt binding site 1 out of 2 in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Tryptophan Substrate and Sam Analog (Aza-Sam) 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 Tryptophan Substrate and Sam Analog (Aza-Sam) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co802

b:16.0
occ:1.00
CO A:B12802 0.0 16.0 1.0
N21 A:B12802 1.9 16.4 1.0
N24 A:B12802 1.9 14.6 1.0
N22 A:B12802 1.9 16.4 1.0
N23 A:B12802 1.9 15.9 1.0
O A:HOH975 2.7 22.0 1.0
C9 A:B12802 2.9 17.1 1.0
C4 A:B12802 2.9 15.4 1.0
C11 A:B12802 2.9 16.0 1.0
C19 A:B12802 2.9 15.6 1.0
C1 A:B12802 2.9 17.1 1.0
C16 A:B12802 3.0 16.8 1.0
C6 A:B12802 3.0 16.5 1.0
C14 A:B12802 3.0 15.0 1.0
C10 A:B12802 3.2 15.2 1.0
NH2 A:ARG69 3.3 16.7 1.0
C5 A:B12802 3.3 16.5 1.0
C15 A:B12802 3.4 16.1 1.0
NH1 A:ARG69 3.5 15.9 1.0
C20 A:B12802 3.7 16.5 1.0
CZ A:ARG69 3.9 17.4 1.0
C2 A:B12802 4.1 15.6 1.0
C18 A:B12802 4.1 17.5 1.0
C3 A:B12802 4.2 14.4 1.0
C8 A:B12802 4.2 17.5 1.0
C12 A:B12802 4.2 18.1 1.0
C7 A:B12802 4.2 17.4 1.0
C17 A:B12802 4.2 15.7 1.0
C13 A:B12802 4.3 17.3 1.0
C26 A:B12802 4.3 15.8 1.0
C35 A:B12802 4.8 18.0 1.0
CE3 A:TRP804 4.8 18.0 1.0
C47 A:B12802 4.8 18.4 1.0
OXT A:SA8803 4.8 22.0 1.0
C41 A:B12802 4.8 15.3 1.0
C37 A:B12802 4.9 16.5 1.0
C53 A:B12802 4.9 16.1 1.0

Cobalt binding site 2 out of 2 in 6wtf

Go back to Cobalt Binding Sites List in 6wtf
Cobalt binding site 2 out of 2 in the Structure of Radical S-Adenosylmethionine Methyltransferase, Tsrm, From Kitasatospora Setae with Tryptophan Substrate and Sam Analog (Aza-Sam) 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 Tryptophan Substrate and Sam Analog (Aza-Sam) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co802

b:18.1
occ:1.00
CO B:B12802 0.0 18.1 1.0
N21 B:B12802 1.9 18.9 1.0
N24 B:B12802 1.9 15.2 1.0
N22 B:B12802 1.9 16.2 1.0
N23 B:B12802 1.9 16.9 1.0
O B:HOH992 2.8 23.0 1.0
C9 B:B12802 2.9 18.2 1.0
C19 B:B12802 2.9 16.5 1.0
C4 B:B12802 2.9 17.2 1.0
C1 B:B12802 2.9 17.2 1.0
C11 B:B12802 2.9 15.6 1.0
C16 B:B12802 3.0 16.5 1.0
C6 B:B12802 3.0 16.8 1.0
C14 B:B12802 3.0 16.3 1.0
C10 B:B12802 3.3 16.1 1.0
C5 B:B12802 3.3 17.0 1.0
C15 B:B12802 3.4 16.1 1.0
NH1 B:ARG69 3.4 14.9 1.0
NH2 B:ARG69 3.4 16.5 1.0
C20 B:B12802 3.6 16.6 1.0
CZ B:ARG69 3.9 17.4 1.0
C2 B:B12802 4.1 17.7 1.0
C18 B:B12802 4.1 16.9 1.0
C3 B:B12802 4.2 17.6 1.0
C8 B:B12802 4.2 17.3 1.0
C12 B:B12802 4.2 18.6 1.0
C7 B:B12802 4.2 18.6 1.0
C17 B:B12802 4.2 16.1 1.0
C13 B:B12802 4.3 19.1 1.0
C26 B:B12802 4.4 18.2 1.0
CE3 B:TRP804 4.7 19.2 1.0
C35 B:B12802 4.8 17.1 1.0
C41 B:B12802 4.8 17.0 1.0
OH B:TYR308 4.9 21.6 1.0
C37 B:B12802 4.9 17.0 1.0
C47 B:B12802 4.9 18.1 1.0
C53 B:B12802 4.9 16.8 1.0
OXT B:SA8803 4.9 20.1 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 14:52:53 2021

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