Atomistry » Iron » PDB 6wnd-6xai » 6wtf
Atomistry »
  Iron »
    PDB 6wnd-6xai »
      6wtf »

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

Go back to Iron Binding Sites List in 6wtf
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

Go back to Iron Binding Sites List in 6wtf
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

Go back to Iron Binding Sites List in 6wtf
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

Go back to Iron Binding Sites List in 6wtf
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 6 15:31:35 2025

Last articles

Mg in 6U1I
Mg in 6U1G
Mg in 6U1F
Mg in 6U1E
Mg in 6U1D
Mg in 6TXA
Mg in 6U0U
Mg in 6U0T
Mg in 6TXC
Mg in 6U0H
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy