Iron 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:

Cobalt (Co) 2 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 8 binding sites of Iron 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 Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6wte

Go back to Iron Binding Sites List in 6wte
Iron binding site 1 out of 8 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 Iron with other atoms in the Fe 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:Fe801

b:12.9
occ:1.00
FE1 A:SF4801 0.0 12.9 1.0
S4 A:SF4801 2.3 13.1 1.0
SG A:CYS231 2.3 12.7 1.0
S2 A:SF4801 2.3 12.9 1.0
S3 A:SF4801 2.3 12.6 1.0
FE4 A:SF4801 2.7 12.9 1.0
FE2 A:SF4801 2.7 11.8 1.0
FE3 A:SF4801 2.8 13.0 1.0
CB A:CYS231 3.1 13.2 1.0
S1 A:SF4801 3.9 12.1 1.0
OH A:TYR354 4.0 13.9 1.0
N A:CYS231 4.1 9.8 1.0
CA A:CYS231 4.2 11.8 1.0
CE A:LYS346 4.4 14.3 1.0
CB A:TYR229 4.5 13.4 1.0
OE2 A:GLU273 4.6 14.3 1.0
CB A:CYS234 4.6 12.3 1.0
SG A:CYS227 4.7 10.8 1.0
SG A:CYS234 4.7 12.7 1.0
CE1 A:HIS233 4.8 13.5 1.0

Iron binding site 2 out of 8 in 6wte

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Iron binding site 2 out of 8 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 Iron with other atoms in the Fe 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
A:Fe801

b:11.8
occ:1.00
FE2 A:SF4801 0.0 11.8 1.0
SG A:CYS227 2.2 10.8 1.0
S3 A:SF4801 2.3 12.6 1.0
S4 A:SF4801 2.3 13.1 1.0
S1 A:SF4801 2.3 12.1 1.0
FE3 A:SF4801 2.7 13.0 1.0
FE4 A:SF4801 2.7 12.9 1.0
FE1 A:SF4801 2.7 12.9 1.0
CB A:CYS227 3.3 11.6 1.0
S2 A:SF4801 3.9 12.9 1.0
CB A:TYR229 4.2 13.4 1.0
CG A:GLU273 4.3 11.2 1.0
OE2 A:GLU273 4.3 14.3 1.0
O A:HOH992 4.5 17.3 1.0
CG A:PRO237 4.6 12.7 1.0
CD A:PRO237 4.7 12.9 1.0
CA A:CYS227 4.7 11.8 1.0
SG A:CYS234 4.7 12.7 1.0
N A:TYR229 4.8 11.5 1.0
SG A:CYS231 4.8 12.7 1.0
CD A:GLU273 4.8 13.8 1.0
CD1 A:LEU276 4.9 12.8 1.0
CA A:TYR229 4.9 12.3 1.0
C A:TYR229 5.0 14.2 1.0

Iron binding site 3 out of 8 in 6wte

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Iron binding site 3 out of 8 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 Iron with other atoms in the Fe binding site number 3 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:Fe801

b:13.0
occ:1.00
FE3 A:SF4801 0.0 13.0 1.0
OE2 A:GLU273 1.9 14.3 1.0
S2 A:SF4801 2.3 12.9 1.0
S1 A:SF4801 2.3 12.1 1.0
S4 A:SF4801 2.3 13.1 1.0
FE4 A:SF4801 2.7 12.9 1.0
FE2 A:SF4801 2.7 11.8 1.0
FE1 A:SF4801 2.8 12.9 1.0
CD A:GLU273 2.9 13.8 1.0
CG A:GLU273 3.2 11.2 1.0
O A:HOH1215 3.7 25.5 1.0
S3 A:SF4801 3.9 12.6 1.0
NE2 A:GLN310 3.9 11.4 1.0
OE1 A:GLU273 4.0 16.4 1.0
CD A:GLN310 4.3 14.6 1.0
O A:HOH1102 4.4 17.2 1.0
CG A:GLN310 4.5 13.1 1.0
SG A:CYS227 4.6 10.8 1.0
O A:SER272 4.6 15.3 1.0
CB A:GLU273 4.8 13.9 1.0
SG A:CYS234 4.8 12.7 1.0
OE1 A:GLN310 4.9 14.7 1.0
SG A:CYS231 4.9 12.7 1.0

Iron binding site 4 out of 8 in 6wte

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Iron binding site 4 out of 8 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 Iron with other atoms in the Fe binding site number 4 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:Fe801

b:12.9
occ:1.00
FE4 A:SF4801 0.0 12.9 1.0
S2 A:SF4801 2.3 12.9 1.0
S1 A:SF4801 2.3 12.1 1.0
SG A:CYS234 2.3 12.7 1.0
S3 A:SF4801 2.3 12.6 1.0
FE3 A:SF4801 2.7 13.0 1.0
FE2 A:SF4801 2.7 11.8 1.0
FE1 A:SF4801 2.7 12.9 1.0
CB A:CYS234 3.0 12.3 1.0
S4 A:SF4801 3.9 13.1 1.0
CD A:PRO237 4.3 12.9 1.0
OE2 A:GLU273 4.4 14.3 1.0
CB A:CYS231 4.5 13.2 1.0
CA A:CYS234 4.5 12.1 1.0
CB A:GLU236 4.6 11.0 1.0
O A:HOH1215 4.6 25.5 1.0
SG A:CYS231 4.6 12.7 1.0
SG A:CYS227 4.8 10.8 1.0
CG A:GLU236 4.8 13.0 1.0
CE1 A:HIS233 4.9 13.5 1.0
CG A:PRO237 4.9 12.7 1.0
CD A:GLU236 5.0 16.2 1.0

Iron binding site 5 out of 8 in 6wte

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Iron binding site 5 out of 8 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 Iron with other atoms in the Fe binding site number 5 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:Fe801

b:14.1
occ:1.00
FE1 B:SF4801 0.0 14.1 1.0
S4 B:SF4801 2.3 14.7 1.0
S2 B:SF4801 2.3 15.7 1.0
SG B:CYS231 2.3 14.8 1.0
S3 B:SF4801 2.3 14.4 1.0
FE4 B:SF4801 2.7 14.5 1.0
FE2 B:SF4801 2.7 13.9 1.0
FE3 B:SF4801 2.8 14.6 1.0
CB B:CYS231 3.1 14.3 1.0
S1 B:SF4801 3.9 16.0 1.0
OH B:TYR354 4.0 16.0 1.0
N B:CYS231 4.1 13.1 1.0
CA B:CYS231 4.2 14.2 1.0
CE B:LYS346 4.4 15.0 1.0
CB B:TYR229 4.4 16.2 1.0
OE2 B:GLU273 4.5 16.8 1.0
CB B:CYS234 4.6 13.7 1.0
SG B:CYS227 4.7 14.2 1.0
SG B:CYS234 4.7 14.6 1.0
CE1 B:HIS233 4.8 16.4 1.0

Iron binding site 6 out of 8 in 6wte

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Iron binding site 6 out of 8 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 Iron with other atoms in the Fe binding site number 6 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:Fe801

b:13.9
occ:1.00
FE2 B:SF4801 0.0 13.9 1.0
SG B:CYS227 2.2 14.2 1.0
S3 B:SF4801 2.3 14.4 1.0
S1 B:SF4801 2.3 16.0 1.0
S4 B:SF4801 2.3 14.7 1.0
FE3 B:SF4801 2.7 14.6 1.0
FE4 B:SF4801 2.7 14.5 1.0
FE1 B:SF4801 2.7 14.1 1.0
CB B:CYS227 3.3 12.4 1.0
S2 B:SF4801 3.9 15.7 1.0
CB B:TYR229 4.2 16.2 1.0
CG B:GLU273 4.3 11.5 1.0
OE2 B:GLU273 4.4 16.8 1.0
CG B:PRO237 4.6 16.6 1.0
O B:HOH950 4.6 20.6 1.0
CA B:CYS227 4.7 14.7 1.0
CD B:PRO237 4.7 15.1 1.0
SG B:CYS234 4.7 14.6 1.0
N B:TYR229 4.8 14.1 1.0
CD1 B:LEU276 4.8 16.3 1.0
SG B:CYS231 4.8 14.8 1.0
CD B:GLU273 4.8 14.2 1.0
CA B:TYR229 4.9 15.1 1.0
C B:TYR229 4.9 17.3 1.0
CB B:SER272 5.0 14.4 1.0

Iron binding site 7 out of 8 in 6wte

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Iron binding site 7 out of 8 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 Iron with other atoms in the Fe binding site number 7 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:Fe801

b:14.6
occ:1.00
FE3 B:SF4801 0.0 14.6 1.0
OE2 B:GLU273 1.9 16.8 1.0
S2 B:SF4801 2.3 15.7 1.0
S1 B:SF4801 2.3 16.0 1.0
S4 B:SF4801 2.3 14.7 1.0
FE4 B:SF4801 2.7 14.5 1.0
FE2 B:SF4801 2.7 13.9 1.0
FE1 B:SF4801 2.8 14.1 1.0
CD B:GLU273 2.9 14.2 1.0
CG B:GLU273 3.2 11.5 1.0
S3 B:SF4801 3.9 14.4 1.0
NE2 B:GLN310 3.9 13.8 1.0
OE1 B:GLU273 4.0 17.5 1.0
CD B:GLN310 4.2 15.4 1.0
O B:HOH1093 4.4 21.8 1.0
CG B:GLN310 4.5 16.0 1.0
SG B:CYS227 4.6 14.2 1.0
O B:SER272 4.6 15.2 1.0
CB B:GLU273 4.7 15.4 1.0
SG B:CYS234 4.8 14.6 1.0
OE1 B:GLN310 4.9 16.0 1.0
SG B:CYS231 4.9 14.8 1.0

Iron binding site 8 out of 8 in 6wte

Go back to Iron Binding Sites List in 6wte
Iron binding site 8 out of 8 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 Iron with other atoms in the Fe binding site number 8 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:Fe801

b:14.5
occ:1.00
FE4 B:SF4801 0.0 14.5 1.0
SG B:CYS234 2.3 14.6 1.0
S2 B:SF4801 2.3 15.7 1.0
S1 B:SF4801 2.3 16.0 1.0
S3 B:SF4801 2.3 14.4 1.0
FE3 B:SF4801 2.7 14.6 1.0
FE1 B:SF4801 2.7 14.1 1.0
FE2 B:SF4801 2.7 13.9 1.0
CB B:CYS234 3.0 13.7 1.0
S4 B:SF4801 3.9 14.7 1.0
O B:HOH1164 4.1 28.6 1.0
CD B:PRO237 4.3 15.1 1.0
OE2 B:GLU273 4.4 16.8 1.0
CB B:CYS231 4.4 14.3 1.0
CA B:CYS234 4.5 15.7 1.0
CB B:GLU236 4.6 13.7 1.0
SG B:CYS231 4.6 14.8 1.0
SG B:CYS227 4.8 14.2 1.0
CG B:GLU236 4.8 13.0 1.0
CG B:PRO237 4.9 16.6 1.0
CE1 B:HIS233 4.9 16.4 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 17:04:19 2021

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