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Iron 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:

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 Tryptophan Substrate and Sam Analog (Aza-Sam) Bound (pdb code 6wtf). 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 Tryptophan Substrate and Sam Analog (Aza-Sam) Bound, PDB code: 6wtf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6wtf

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Iron binding site 1 out of 8 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 Iron with other atoms in the Fe 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:Fe801

b:18.5
occ:1.00
 FE1 A:SF4801 0.0 18.5 1.0
S4 A:SF4801 2.3 16.0 1.0
S2 A:SF4801 2.3 18.5 1.0
S3 A:SF4801 2.3 19.1 1.0
SG A:CYS231 2.4 15.2 1.0
FE3 A:SF4801 2.7 23.2 1.0
FE2 A:SF4801 2.7 18.9 1.0
FE4 A:SF4801 2.7 18.9 1.0
CB A:CYS231 3.2 17.3 1.0
S1 A:SF4801 3.9 22.5 1.0
OH A:TYR354 3.9 19.1 1.0
N A:CYS231 4.3 21.8 1.0
CA A:CYS231 4.4 19.9 1.0
CE A:LYS346 4.4 18.4 1.0
CB A:TYR229 4.5 18.9 1.0
OE2 A:GLU273 4.7 20.7 1.0
CB A:CYS234 4.7 17.3 1.0
SG A:CYS227 4.7 20.2 1.0
CE1 A:HIS233 4.7 18.3 1.0
SG A:CYS234 4.8 14.9 1.0
CD A:GLN310 4.9 18.9 1.0
OE1 A:GLN310 5.0 21.4 1.0
NE2 A:GLN310 5.0 16.7 1.0

Iron binding site 2 out of 8 in 6wtf

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

b:18.9
occ:1.00
 FE2 A:SF4801 0.0 18.9 1.0
SG A:CYS227 2.2 20.2 1.0
S1 A:SF4801 2.3 22.5 1.0
S3 A:SF4801 2.3 19.1 1.0
S4 A:SF4801 2.3 16.0 1.0
FE4 A:SF4801 2.7 18.9 1.0
FE3 A:SF4801 2.7 23.2 1.0
FE1 A:SF4801 2.7 18.5 1.0
CB A:CYS227 3.4 20.5 1.0
S2 A:SF4801 3.9 18.5 1.0
CG A:GLU273 4.3 16.4 1.0
CB A:TYR229 4.4 18.9 1.0
OE2 A:GLU273 4.5 20.7 1.0
CG A:PRO237 4.7 17.6 1.0
CB A:SER272 4.7 18.4 1.0
CA A:CYS227 4.8 20.1 1.0
CD1 A:LEU276 4.8 20.9 1.0
SG A:CYS234 4.8 14.9 1.0
CD A:PRO237 4.8 19.7 1.0
SG A:CYS231 4.9 15.2 1.0
CD A:GLU273 4.9 16.4 1.0
N A:TYR229 5.0 20.8 1.0

Iron binding site 3 out of 8 in 6wtf

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

b:23.2
occ:1.00
 FE3 A:SF4801 0.0 23.2 1.0
OE2 A:GLU273 2.1 20.7 1.0
S2 A:SF4801 2.3 18.5 1.0
S4 A:SF4801 2.3 16.0 1.0
S1 A:SF4801 2.3 22.5 1.0
FE4 A:SF4801 2.7 18.9 1.0
FE1 A:SF4801 2.7 18.5 1.0
FE2 A:SF4801 2.7 18.9 1.0
CD A:GLU273 3.0 16.4 1.0
CG A:GLU273 3.2 16.4 1.0
S3 A:SF4801 3.9 19.1 1.0
NE2 A:GLN310 3.9 16.7 1.0
OE1 A:GLU273 4.1 18.9 1.0
CD A:GLN310 4.3 18.9 1.0
O A:HOH993 4.4 18.3 1.0
O A:SER272 4.4 20.4 1.0
CG A:GLN310 4.4 18.1 1.0
CA A:SA8803 4.5 20.8 1.0
N A:SA8803 4.5 20.4 1.0
SG A:CYS227 4.6 20.2 1.0
CG A:SA8803 4.7 17.8 1.0
CB A:SA8803 4.7 20.9 1.0
CB A:GLU273 4.7 17.5 1.0
SG A:CYS234 4.8 14.9 1.0
C A:SER272 5.0 17.3 1.0
SG A:CYS231 5.0 15.2 1.0

Iron binding site 4 out of 8 in 6wtf

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

b:18.9
occ:1.00
 FE4 A:SF4801 0.0 18.9 1.0
S3 A:SF4801 2.3 19.1 1.0
S1 A:SF4801 2.3 22.5 1.0
S2 A:SF4801 2.3 18.5 1.0
SG A:CYS234 2.3 14.9 1.0
FE3 A:SF4801 2.7 23.2 1.0
FE2 A:SF4801 2.7 18.9 1.0
FE1 A:SF4801 2.7 18.5 1.0
CB A:CYS234 3.0 17.3 1.0
S4 A:SF4801 3.9 16.0 1.0
O A:HOH924 4.0 18.8 1.0
CD A:PRO237 4.4 19.7 1.0
CA A:CYS234 4.4 16.6 1.0
OE2 A:GLU273 4.6 20.7 1.0
CB A:CYS231 4.6 17.3 1.0
CB A:GLU236 4.6 15.8 1.0
NE2 A:HIS233 4.7 17.0 1.0
SG A:CYS231 4.7 15.2 1.0
CG A:GLU236 4.8 14.9 1.0
SG A:CYS227 4.8 20.2 1.0
CD A:GLU236 4.8 19.8 1.0
CE1 A:HIS233 4.9 18.3 1.0
OE2 A:GLU236 4.9 20.7 1.0
CG A:PRO237 4.9 17.6 1.0
CA A:SA8803 5.0 20.8 1.0

Iron binding site 5 out of 8 in 6wtf

Go back to Iron Binding Sites List in 6wtf
Iron binding site 5 out of 8 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 Iron with other atoms in the Fe binding site number 5 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:Fe801

b:17.8
occ:1.00
 FE1 B:SF4801 0.0 17.8 1.0
S4 B:SF4801 2.3 18.6 1.0
S2 B:SF4801 2.3 22.4 1.0
S3 B:SF4801 2.3 21.6 1.0
SG B:CYS231 2.3 18.1 1.0
FE3 B:SF4801 2.7 23.9 1.0
FE4 B:SF4801 2.7 19.1 1.0
FE2 B:SF4801 2.7 19.6 1.0
CB B:CYS231 3.2 20.1 1.0
S1 B:SF4801 3.9 20.1 1.0
OH B:TYR354 4.0 19.2 1.0
N B:CYS231 4.4 21.2 1.0
CA B:CYS231 4.4 18.9 1.0
CE B:LYS346 4.5 17.2 1.0
OE2 B:GLU273 4.6 16.4 1.0
CB B:CYS234 4.6 19.0 1.0
CB B:TYR229 4.6 21.4 1.0
CE1 B:HIS233 4.6 22.7 1.0
SG B:CYS234 4.6 16.3 1.0
SG B:CYS227 4.7 19.2 1.0
CD B:GLN310 4.8 17.9 1.0
OE1 B:GLN310 4.9 20.2 1.0
NE2 B:GLN310 4.9 15.9 1.0

Iron binding site 6 out of 8 in 6wtf

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

b:19.6
occ:1.00
 FE2 B:SF4801 0.0 19.6 1.0
SG B:CYS227 2.2 19.2 1.0
S3 B:SF4801 2.3 21.6 1.0
S1 B:SF4801 2.3 20.1 1.0
S4 B:SF4801 2.3 18.6 1.0
FE4 B:SF4801 2.7 19.1 1.0
FE3 B:SF4801 2.7 23.9 1.0
FE1 B:SF4801 2.7 17.8 1.0
CB B:CYS227 3.4 19.0 1.0
S2 B:SF4801 3.9 22.4 1.0
CB B:TYR229 4.3 21.4 1.0
CG B:GLU273 4.3 16.8 1.0
OE2 B:GLU273 4.5 16.4 1.0
CG B:PRO237 4.6 18.8 1.0
SG B:CYS234 4.6 16.3 1.0
SG B:CYS231 4.7 18.1 1.0
CD B:PRO237 4.7 19.0 1.0
CA B:CYS227 4.8 20.3 1.0
CD1 B:LEU276 4.8 18.8 1.0
CB B:SER272 4.8 18.6 1.0
N B:TYR229 4.9 21.9 1.0
CD B:GLU273 5.0 15.5 1.0

Iron binding site 7 out of 8 in 6wtf

Go back to Iron Binding Sites List in 6wtf
Iron binding site 7 out of 8 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 Iron with other atoms in the Fe binding site number 7 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:Fe801

b:23.9
occ:1.00
 FE3 B:SF4801 0.0 23.9 1.0
OE2 B:GLU273 2.0 16.4 1.0
S2 B:SF4801 2.3 22.4 1.0
S4 B:SF4801 2.3 18.6 1.0
S1 B:SF4801 2.3 20.1 1.0
FE1 B:SF4801 2.7 17.8 1.0
FE4 B:SF4801 2.7 19.1 1.0
FE2 B:SF4801 2.7 19.6 1.0
CD B:GLU273 2.9 15.5 1.0
CG B:GLU273 3.2 16.8 1.0
NE2 B:GLN310 3.8 15.9 1.0
S3 B:SF4801 3.9 21.6 1.0
OE1 B:GLU273 4.1 17.0 1.0
CD B:GLN310 4.2 17.9 1.0
N B:SA8803 4.3 20.4 1.0
CA B:SA8803 4.3 21.7 1.0
O B:SER272 4.3 19.7 1.0
CG B:GLN310 4.4 17.6 1.0
CB B:SA8803 4.5 20.6 1.0
CG B:SA8803 4.6 19.1 1.0
SG B:CYS227 4.6 19.2 1.0
SG B:CYS234 4.7 16.3 1.0
CB B:GLU273 4.7 18.5 1.0
O B:HOH946 4.7 17.3 1.0
C B:SER272 4.9 18.8 1.0
OE1 B:GLN310 4.9 20.2 1.0
SG B:CYS231 5.0 18.1 1.0
O B:HOH940 5.0 19.1 1.0

Iron binding site 8 out of 8 in 6wtf

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

b:19.1
occ:1.00
 FE4 B:SF4801 0.0 19.1 1.0
SG B:CYS234 2.1 16.3 1.0
S1 B:SF4801 2.3 20.1 1.0
S3 B:SF4801 2.3 21.6 1.0
S2 B:SF4801 2.3 22.4 1.0
FE2 B:SF4801 2.7 19.6 1.0
FE1 B:SF4801 2.7 17.8 1.0
FE3 B:SF4801 2.7 23.9 1.0
CB B:CYS234 2.9 19.0 1.0
S4 B:SF4801 3.9 18.6 1.0
O B:HOH940 4.0 19.1 1.0
CA B:CYS234 4.4 17.8 1.0
CD B:PRO237 4.4 19.0 1.0
OE2 B:GLU273 4.5 16.4 1.0
CB B:GLU236 4.6 17.4 1.0
CB B:CYS231 4.6 20.1 1.0
NE2 B:HIS233 4.7 20.1 1.0
SG B:CYS231 4.7 18.1 1.0
CG B:GLU236 4.7 15.2 1.0
CD B:GLU236 4.7 19.3 1.0
SG B:CYS227 4.8 19.2 1.0
OE2 B:GLU236 4.8 19.5 1.0
CA B:SA8803 4.8 21.7 1.0
CE1 B:HIS233 4.9 22.7 1.0
N B:SA8803 4.9 20.4 1.0
CG B:PRO237 5.0 18.8 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: Wed Aug 7 14:18:18 2024

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