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Iron in PDB 7pd1: Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans

Protein crystallography data

The structure of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans, PDB code: 7pd1 was solved by P.Amara, C.Saragaglia, J.-M.Mouesca, L.Martin, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.03 / 1.27
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.09, 48.85, 85.41, 90, 97.02, 90
R / Rfree (%) 15 / 17

Other elements in 7pd1:

The structure of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans also contains other interesting chemical elements:

Potassium (K) 1 atom
Bromine (Br) 12 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans (pdb code 7pd1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans, PDB code: 7pd1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 7pd1

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Iron binding site 1 out of 8 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:14.5
occ:1.00
 FE1 A:SF4401 0.0 14.5 1.0
O A:MET403 2.2 14.6 1.0
N A:MET403 2.2 14.5 1.0
S3 A:SF4401 2.3 14.6 1.0
S2 A:SF4401 2.4 14.7 1.0
S4 A:SF4401 2.4 15.0 1.0
SD A:MET403 2.6 14.5 1.0
FE4 A:SF4401 2.9 14.5 1.0
FE2 A:SF4401 2.9 14.8 1.0
FE3 A:SF4401 3.0 15.1 1.0
C A:MET403 3.0 14.5 1.0
CA A:MET403 3.1 14.4 1.0
CG A:MET403 3.6 14.6 1.0
CE A:MET403 3.7 13.8 1.0
CB A:MET403 3.8 14.7 1.0
NZ A:LYS199 4.1 14.3 1.0
S1 A:SF4401 4.2 15.4 1.0
OXT A:MET403 4.2 15.0 1.0
O A:HOH725 4.4 18.1 1.0
NE2 A:GLN336 4.6 16.5 1.0
SG A:CYS85 4.8 15.7 1.0
O A:THR129 4.9 15.2 1.0
SG A:CYS92 4.9 14.3 1.0
CD A:LYS199 5.0 14.3 1.0

Iron binding site 2 out of 8 in 7pd1

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Iron binding site 2 out of 8 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:14.8
occ:1.00
 FE2 A:SF4401 0.0 14.8 1.0
S4 A:SF4401 2.3 15.0 1.0
SG A:CYS89 2.3 16.1 1.0
S1 A:SF4401 2.3 15.4 1.0
S3 A:SF4401 2.3 14.6 1.0
FE4 A:SF4401 2.6 14.5 1.0
FE3 A:SF4401 2.7 15.1 1.0
FE1 A:SF4401 2.9 14.5 1.0
CB A:CYS89 3.2 17.5 1.0
NZ A:LYS199 3.8 14.3 1.0
S2 A:SF4401 3.9 14.7 1.0
O A:MET403 4.0 14.6 1.0
CD A:LYS199 4.0 14.3 1.0
CB A:ASN87 4.1 16.9 1.0
CB A:CYS92 4.4 13.8 1.0
CE A:LYS199 4.5 14.5 1.0
CA A:CYS89 4.5 17.9 1.0
N A:CYS89 4.5 18.6 1.0
SG A:CYS92 4.5 14.3 1.0
SG A:CYS85 4.6 15.7 1.0
OH A:TYR91 4.8 15.5 1.0
ND2 A:ASN87 4.8 16.0 1.0
N A:MET403 4.9 14.5 1.0
CG A:ASN87 4.9 17.6 1.0

Iron binding site 3 out of 8 in 7pd1

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Iron binding site 3 out of 8 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:15.1
occ:1.00
 FE3 A:SF4401 0.0 15.1 1.0
SG A:CYS85 2.3 15.7 1.0
S1 A:SF4401 2.3 15.4 1.0
S2 A:SF4401 2.3 14.7 1.0
S4 A:SF4401 2.3 15.0 1.0
FE4 A:SF4401 2.7 14.5 1.0
FE2 A:SF4401 2.7 14.8 1.0
FE1 A:SF4401 3.0 14.5 1.0
CB A:CYS85 3.3 15.9 1.0
S3 A:SF4401 3.9 14.6 1.0
N A:MET403 4.1 14.5 1.0
CB A:ASN87 4.2 16.9 1.0
N A:GLU131 4.3 16.6 1.0
ND2 A:ASN87 4.5 16.0 1.0
CA A:GLY130 4.5 14.0 1.0
O A:PHE94 4.6 15.7 1.0
SG A:CYS89 4.7 16.1 1.0
CA A:CYS85 4.7 15.0 1.0
CB A:PHE94 4.7 15.1 1.0
SG A:CYS92 4.8 14.3 1.0
O A:MET403 4.8 14.6 1.0
C A:PHE94 4.8 15.1 1.0
O A:ASN87 4.9 19.5 1.0
N A:ASN87 4.9 16.1 1.0
CG A:ASN87 4.9 17.6 1.0
CA A:ASN87 5.0 17.0 1.0
C A:GLY130 5.0 17.7 1.0

Iron binding site 4 out of 8 in 7pd1

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Iron binding site 4 out of 8 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:14.5
occ:1.00
 FE4 A:SF4401 0.0 14.5 1.0
S2 A:SF4401 2.3 14.7 1.0
SG A:CYS92 2.3 14.3 1.0
S1 A:SF4401 2.3 15.4 1.0
S3 A:SF4401 2.3 14.6 1.0
FE2 A:SF4401 2.6 14.8 1.0
FE3 A:SF4401 2.7 15.1 1.0
FE1 A:SF4401 2.9 14.5 1.0
CB A:CYS92 3.1 13.8 1.0
S4 A:SF4401 3.8 15.0 1.0
NE2 A:GLN336 3.9 16.5 1.0
CB A:PHE94 4.2 15.1 1.0
SD A:MET403 4.2 14.5 1.0
CA A:CYS92 4.6 13.7 1.0
C A:PHE94 4.6 15.1 1.0
N A:GLN95 4.6 14.8 1.0
N A:PHE94 4.7 13.6 1.0
SG A:CYS89 4.7 16.1 1.0
CA A:PHE94 4.7 15.2 1.0
CB A:CYS89 4.8 17.5 1.0
CE A:MET403 4.8 13.8 1.0
CD A:GLN336 4.8 15.1 1.0
O A:MET403 4.8 14.6 1.0
SG A:CYS85 4.8 15.7 1.0
N A:MET403 4.9 14.5 1.0
CG A:GLN336 4.9 16.2 1.0
CD2 A:PHE94 5.0 15.6 1.0

Iron binding site 5 out of 8 in 7pd1

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Iron binding site 5 out of 8 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:14.8
occ:1.00
 FE1 B:SF4401 0.0 14.8 1.0
OXT B:MET403 2.2 14.6 1.0
N B:MET403 2.3 14.8 1.0
S3 B:SF4401 2.3 14.8 1.0
S2 B:SF4401 2.4 15.3 1.0
S4 B:SF4401 2.4 15.5 1.0
SD B:MET403 2.7 14.9 1.0
FE4 B:SF4401 2.9 15.1 1.0
FE2 B:SF4401 2.9 15.6 1.0
FE3 B:SF4401 3.0 15.9 1.0
C B:MET403 3.0 13.7 1.0
CA B:MET403 3.1 14.3 1.0
CG B:MET403 3.6 13.7 1.0
CE B:MET403 3.7 15.1 1.0
CB B:MET403 3.8 14.8 1.0
NZ B:LYS199 4.1 16.2 1.0
S1 B:SF4401 4.2 16.1 1.0
O B:MET403 4.3 15.3 1.0
O B:HOH718 4.3 18.2 1.0
NE2 B:GLN336 4.6 16.4 1.0
SG B:CYS85 4.8 16.4 1.0
O B:THR129 4.9 15.6 1.0
SG B:CYS92 4.9 15.1 1.0

Iron binding site 6 out of 8 in 7pd1

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Iron binding site 6 out of 8 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:15.6
occ:1.00
 FE2 B:SF4401 0.0 15.6 1.0
S4 B:SF4401 2.2 15.5 1.0
SG B:CYS89 2.3 17.3 1.0
S3 B:SF4401 2.3 14.8 1.0
S1 B:SF4401 2.3 16.1 1.0
FE4 B:SF4401 2.6 15.1 1.0
FE3 B:SF4401 2.7 15.9 1.0
FE1 B:SF4401 2.9 14.8 1.0
CB B:CYS89 3.2 16.5 1.0
NZ B:LYS199 3.8 16.2 1.0
S2 B:SF4401 3.8 15.3 1.0
OXT B:MET403 4.0 14.6 1.0
CD B:LYS199 4.1 15.5 1.0
CB B:ASN87 4.1 18.9 1.0
CB B:CYS92 4.4 14.4 1.0
CA B:CYS89 4.5 17.9 1.0
N B:CYS89 4.5 17.9 1.0
CE B:LYS199 4.5 14.6 1.0
SG B:CYS92 4.5 15.1 1.0
SG B:CYS85 4.6 16.4 1.0
ND2 B:ASN87 4.8 17.8 1.0
OH B:TYR91 4.8 16.0 1.0
N B:MET403 4.9 14.8 1.0
CG B:ASN87 4.9 19.3 1.0

Iron binding site 7 out of 8 in 7pd1

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Iron binding site 7 out of 8 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:15.9
occ:1.00
 FE3 B:SF4401 0.0 15.9 1.0
SG B:CYS85 2.3 16.4 1.0
S1 B:SF4401 2.3 16.1 1.0
S2 B:SF4401 2.3 15.3 1.0
S4 B:SF4401 2.3 15.5 1.0
FE4 B:SF4401 2.7 15.1 1.0
FE2 B:SF4401 2.7 15.6 1.0
FE1 B:SF4401 3.0 14.8 1.0
CB B:CYS85 3.4 16.3 1.0
S3 B:SF4401 3.9 14.8 1.0
N B:MET403 4.0 14.8 1.0
CB B:ASN87 4.2 18.9 1.0
N B:GLU131 4.3 17.4 1.0
CA B:GLY130 4.5 14.2 1.0
ND2 B:ASN87 4.5 17.8 1.0
O B:PHE94 4.7 17.7 1.0
SG B:CYS89 4.7 17.3 1.0
CA B:CYS85 4.7 17.4 1.0
CB B:PHE94 4.8 16.3 1.0
SG B:CYS92 4.8 15.1 1.0
OXT B:MET403 4.8 14.6 1.0
N B:ASN87 4.9 17.3 1.0
O B:ASN87 4.9 20.4 1.0
C B:PHE94 4.9 18.7 1.0
CG B:ASN87 4.9 19.3 1.0
C B:GLY130 5.0 16.9 1.0
CA B:ASN87 5.0 19.3 1.0

Iron binding site 8 out of 8 in 7pd1

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Iron binding site 8 out of 8 in the Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the L-Tyrosine-Bound Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:15.1
occ:1.00
 FE4 B:SF4401 0.0 15.1 1.0
S2 B:SF4401 2.3 15.3 1.0
S3 B:SF4401 2.3 14.8 1.0
S1 B:SF4401 2.3 16.1 1.0
SG B:CYS92 2.3 15.1 1.0
FE2 B:SF4401 2.6 15.6 1.0
FE3 B:SF4401 2.7 15.9 1.0
FE1 B:SF4401 2.9 14.8 1.0
CB B:CYS92 3.1 14.4 1.0
S4 B:SF4401 3.8 15.5 1.0
NE2 B:GLN336 3.8 16.4 1.0
CB B:PHE94 4.2 16.3 1.0
SD B:MET403 4.2 14.9 1.0
CA B:CYS92 4.6 14.7 1.0
SG B:CYS89 4.6 17.3 1.0
N B:GLN95 4.7 17.3 1.0
C B:PHE94 4.7 18.7 1.0
CB B:CYS89 4.7 16.5 1.0
N B:PHE94 4.7 15.2 1.0
CE B:MET403 4.8 15.1 1.0
CA B:PHE94 4.8 16.5 1.0
OXT B:MET403 4.8 14.6 1.0
SG B:CYS85 4.8 16.4 1.0
CD B:GLN336 4.8 15.7 1.0
N B:MET403 4.9 14.8 1.0
CD2 B:PHE94 4.9 15.6 1.0

Reference:

P.Amara, C.Saragaglia, J.M.Mouesca, L.Martin, Y.Nicolet. L-Tyrosine-Bound Thih Structure Reveals C-C Bond Break Differences Within Radical Sam Aromatic Amino Acid Lyases. Nat Commun V. 13 2284 2022.
ISSN: ESSN 2041-1723
PubMed: 35477710
DOI: 10.1038/S41467-022-29980-4
Page generated: Thu Aug 8 16:36:23 2024

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