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Iron in PDB 4r34: X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound

Protein crystallography data

The structure of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound, PDB code: 4r34 was solved by Y.Nicolet, L.Zeppieri, P.Amara, J.-C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.97 / 1.80
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.150, 47.070, 113.920, 90.00, 108.99, 90.00
R / Rfree (%) 17.2 / 19.9

Other elements in 4r34:

The structure of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Bromine (Br) 7 atoms
Sodium (Na) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound (pdb code 4r34). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound, PDB code: 4r34:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4r34

Go back to Iron Binding Sites List in 4r34
Iron binding site 1 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe504

b:31.5
occ:1.00
 FE1 A:SF4504 0.0 31.5 1.0
S4 A:SF4504 2.3 30.9 1.0
S3 A:SF4504 2.3 29.0 1.0
S2 A:SF4504 2.3 32.1 1.0
SG A:CYS95 2.3 33.3 1.0
FE3 A:SF4504 2.7 32.1 1.0
FE2 A:SF4504 2.7 30.2 1.0
FE4 A:SF4504 2.8 29.4 1.0
CB A:CYS95 3.4 32.8 1.0
N A:MET501 3.9 33.2 0.7
S1 A:SF4504 3.9 31.2 1.0
N A:SAH503 4.0 33.1 0.3
CB A:SER97 4.1 42.9 1.0
N A:GLU143 4.3 27.6 1.0
CA A:GLY142 4.4 25.0 1.0
O A:MET104 4.7 30.4 1.0
O A:MET501 4.7 33.4 0.7
CB A:MET104 4.7 27.6 1.0
N A:SER97 4.7 33.1 1.0
SG A:CYS99 4.8 34.4 1.0
CA A:SER97 4.8 33.5 1.0
CA A:CYS95 4.8 33.3 1.0
C A:MET104 4.8 29.6 1.0
C A:SER97 4.8 37.0 1.0
O A:SAH503 4.8 33.9 0.3
C A:GLY142 4.9 26.0 1.0
O A:SER97 4.9 35.0 1.0
SG A:CYS102 4.9 31.3 1.0
N A:ARG105 5.0 39.3 1.0

Iron binding site 2 out of 8 in 4r34

Go back to Iron Binding Sites List in 4r34
Iron binding site 2 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe504

b:30.2
occ:1.00
 FE2 A:SF4504 0.0 30.2 1.0
S4 A:SF4504 2.3 30.9 1.0
S3 A:SF4504 2.3 29.0 1.0
S1 A:SF4504 2.3 31.2 1.0
SG A:CYS102 2.5 31.3 1.0
FE3 A:SF4504 2.7 32.1 1.0
FE1 A:SF4504 2.7 31.5 1.0
FE4 A:SF4504 2.8 29.4 1.0
CB A:CYS102 3.2 41.2 1.0
S2 A:SF4504 3.8 32.1 1.0
NE2 A:GLN363 3.9 35.2 1.0
CB A:MET104 4.1 27.6 1.0
SD A:MET501 4.3 29.3 0.7
CB A:CYS99 4.4 34.7 1.0
SG A:CYS99 4.6 34.4 1.0
CA A:CYS102 4.7 28.5 1.0
N A:ARG105 4.7 39.3 1.0
C A:MET104 4.7 29.6 1.0
N A:SAH503 4.7 33.1 0.3
CG A:SAH503 4.8 29.0 0.3
CA A:MET104 4.8 28.4 1.0
CD A:GLN363 4.8 32.0 1.0
CE A:MET501 4.8 41.5 0.7
N A:MET104 4.8 28.2 1.0
O A:MET501 4.8 33.4 0.7
N A:MET501 4.8 33.2 0.7
CG A:GLN363 4.8 31.9 1.0
O A:SAH503 4.9 33.9 0.3
SG A:CYS95 4.9 33.3 1.0

Iron binding site 3 out of 8 in 4r34

Go back to Iron Binding Sites List in 4r34
Iron binding site 3 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe504

b:32.1
occ:1.00
 FE3 A:SF4504 0.0 32.1 1.0
SG A:CYS99 2.3 34.4 1.0
S2 A:SF4504 2.3 32.1 1.0
S1 A:SF4504 2.3 31.2 1.0
S4 A:SF4504 2.3 30.9 1.0
FE2 A:SF4504 2.7 30.2 1.0
FE1 A:SF4504 2.7 31.5 1.0
FE4 A:SF4504 2.8 29.4 1.0
CB A:CYS99 3.0 34.7 1.0
NZ A:LYS224 3.7 28.4 1.0
CD A:LYS224 3.9 34.9 1.0
S3 A:SF4504 3.9 29.0 1.0
O A:MET501 4.0 33.4 0.7
O A:SAH503 4.0 33.9 0.3
N A:CYS99 4.0 32.5 1.0
CA A:CYS99 4.1 38.0 1.0
CE A:LYS224 4.2 29.6 1.0
CB A:SER97 4.4 42.9 1.0
CB A:CYS102 4.7 41.2 1.0
O A:HOH672 4.7 29.7 1.0
SG A:CYS95 4.8 33.3 1.0
SG A:CYS102 4.8 31.3 1.0
N A:MET501 4.8 33.2 0.7
N A:SAH503 4.9 33.1 0.3

Iron binding site 4 out of 8 in 4r34

Go back to Iron Binding Sites List in 4r34
Iron binding site 4 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe504

b:29.4
occ:1.00
 FE4 A:SF4504 0.0 29.4 1.0
O A:MET501 2.2 33.4 0.7
N A:SAH503 2.3 33.1 0.3
S1 A:SF4504 2.3 31.2 1.0
S2 A:SF4504 2.3 32.1 1.0
S3 A:SF4504 2.3 29.0 1.0
N A:MET501 2.3 33.2 0.7
O A:SAH503 2.4 33.9 0.3
FE2 A:SF4504 2.8 30.2 1.0
SD A:MET501 2.8 29.3 0.7
FE1 A:SF4504 2.8 31.5 1.0
FE3 A:SF4504 2.8 32.1 1.0
CA A:SAH503 3.0 31.5 0.3
C A:MET501 3.0 33.2 0.7
C A:SAH503 3.0 32.3 0.3
CG A:SAH503 3.1 29.0 0.3
CA A:MET501 3.1 33.0 0.7
CB A:SAH503 3.5 28.8 0.3
CG A:MET501 3.8 28.7 0.7
CE A:MET501 3.8 41.5 0.7
CB A:MET501 3.9 29.4 0.7
S4 A:SF4504 4.0 30.9 1.0
NZ A:LYS224 4.0 28.4 1.0
OXT A:MET501 4.2 30.7 0.7
OXT A:SAH503 4.2 30.7 0.3
SD A:SAH503 4.6 29.0 0.3
NE2 A:GLN363 4.7 35.2 1.0
CD A:LYS224 4.7 34.9 1.0
SG A:CYS95 4.7 33.3 1.0
CA A:GLY142 4.9 25.0 1.0
SG A:CYS99 4.9 34.4 1.0
O A:THR141 4.9 25.9 1.0
N A:GLU143 4.9 27.6 1.0
CE A:LYS224 5.0 29.6 1.0

Iron binding site 5 out of 8 in 4r34

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Iron binding site 5 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe504

b:18.2
occ:1.00
 FE1 B:SF4504 0.0 18.2 1.0
SG B:CYS95 2.2 16.9 1.0
S3 B:SF4504 2.3 23.5 1.0
S4 B:SF4504 2.3 25.3 1.0
S2 B:SF4504 2.3 15.8 1.0
FE2 B:SF4504 2.7 20.8 1.0
FE3 B:SF4504 2.7 21.0 1.0
FE4 B:SF4504 2.8 18.8 1.0
CB B:CYS95 3.3 17.0 1.0
N B:MET501 3.8 22.3 0.6
S1 B:SF4504 3.9 23.2 1.0
N B:SAH503 4.2 21.3 0.4
CB B:SER97 4.3 26.2 1.0
N B:GLU143 4.3 16.2 1.0
CA B:GLY142 4.5 16.4 1.0
CB B:MET104 4.7 20.6 1.0
CA B:CYS95 4.7 17.4 1.0
O B:MET501 4.7 20.7 0.6
N B:SER97 4.8 21.3 1.0
O B:MET104 4.8 22.6 1.0
SG B:CYS102 4.8 25.0 1.0
O B:SER97 4.8 23.3 1.0
C B:MET104 4.8 21.8 1.0
O B:SAH503 4.8 20.6 0.4
C B:SER97 4.8 25.0 1.0
SG B:CYS99 4.8 20.8 1.0
CA B:SER97 4.8 23.9 1.0
C B:GLY142 4.9 17.7 1.0
N B:ARG105 4.9 23.5 1.0

Iron binding site 6 out of 8 in 4r34

Go back to Iron Binding Sites List in 4r34
Iron binding site 6 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe504

b:20.8
occ:1.00
 FE2 B:SF4504 0.0 20.8 1.0
S3 B:SF4504 2.3 23.5 1.0
S4 B:SF4504 2.3 25.3 1.0
S1 B:SF4504 2.3 23.2 1.0
SG B:CYS102 2.4 25.0 1.0
FE3 B:SF4504 2.7 21.0 1.0
FE1 B:SF4504 2.7 18.2 1.0
FE4 B:SF4504 2.8 18.8 1.0
CB B:CYS102 3.1 17.3 1.0
S2 B:SF4504 3.9 15.8 1.0
NE2 B:GLN363 3.9 23.0 1.0
CB B:MET104 4.2 20.6 1.0
SD B:MET501 4.4 23.4 0.6
CB B:CYS99 4.4 20.4 1.0
SG B:CYS99 4.6 20.8 1.0
CA B:CYS102 4.6 21.8 1.0
N B:ARG105 4.6 23.5 1.0
N B:MET501 4.7 22.3 0.6
CG B:SAH503 4.8 20.6 0.4
N B:MET104 4.8 19.1 1.0
C B:MET104 4.8 21.8 1.0
CD B:GLN363 4.8 24.7 1.0
CA B:MET104 4.8 21.1 1.0
SG B:CYS95 4.8 16.9 1.0
O B:MET501 4.9 20.7 0.6
CG B:GLN363 4.9 21.3 1.0
O B:SAH503 5.0 20.6 0.4
CE B:MET501 5.0 22.0 0.6

Iron binding site 7 out of 8 in 4r34

Go back to Iron Binding Sites List in 4r34
Iron binding site 7 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe504

b:21.0
occ:1.00
 FE3 B:SF4504 0.0 21.0 1.0
S2 B:SF4504 2.3 15.8 1.0
S1 B:SF4504 2.3 23.2 1.0
S4 B:SF4504 2.3 25.3 1.0
SG B:CYS99 2.3 20.8 1.0
FE2 B:SF4504 2.7 20.8 1.0
FE1 B:SF4504 2.7 18.2 1.0
FE4 B:SF4504 2.8 18.8 1.0
CB B:CYS99 3.1 20.4 1.0
NZ B:LYS224 3.7 17.5 1.0
CD B:LYS224 3.8 14.6 1.0
S3 B:SF4504 3.8 23.5 1.0
O B:MET501 3.9 20.7 0.6
O B:SAH503 4.0 20.6 0.4
N B:CYS99 4.1 22.8 1.0
CA B:CYS99 4.2 19.3 1.0
CE B:LYS224 4.3 17.6 1.0
CB B:SER97 4.4 26.2 1.0
N B:MET501 4.7 22.3 0.6
SG B:CYS95 4.7 16.9 1.0
CB B:CYS102 4.7 17.3 1.0
O B:HOH670 4.7 20.8 1.0
SG B:CYS102 4.8 25.0 1.0
C B:MET501 5.0 22.1 0.6

Iron binding site 8 out of 8 in 4r34

Go back to Iron Binding Sites List in 4r34
Iron binding site 8 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe504

b:18.8
occ:1.00
 FE4 B:SF4504 0.0 18.8 1.0
N B:MET501 2.2 22.3 0.6
O B:MET501 2.2 20.7 0.6
S1 B:SF4504 2.3 23.2 1.0
S3 B:SF4504 2.3 23.5 1.0
O B:SAH503 2.3 20.6 0.4
S2 B:SF4504 2.3 15.8 1.0
N B:SAH503 2.5 21.3 0.4
FE3 B:SF4504 2.8 21.0 1.0
FE1 B:SF4504 2.8 18.2 1.0
FE2 B:SF4504 2.8 20.8 1.0
SD B:MET501 2.9 23.4 0.6
C B:MET501 3.0 22.1 0.6
C B:SAH503 3.1 20.7 0.4
CA B:MET501 3.1 20.9 0.6
CG B:SAH503 3.1 20.6 0.4
CA B:SAH503 3.1 18.9 0.4
CB B:SAH503 3.6 16.4 0.4
CG B:MET501 3.8 18.9 0.6
CB B:MET501 3.9 16.3 0.6
NZ B:LYS224 3.9 17.5 1.0
CE B:MET501 4.0 22.0 0.6
S4 B:SF4504 4.0 25.3 1.0
OXT B:MET501 4.2 21.4 0.6
OXT B:SAH503 4.2 21.8 0.4
CD B:LYS224 4.6 14.6 1.0
SG B:CYS95 4.6 16.9 1.0
SD B:SAH503 4.6 25.9 0.4
NE2 B:GLN363 4.8 23.0 1.0
SG B:CYS99 4.9 20.8 1.0
N B:GLU143 4.9 16.2 1.0
O B:THR141 4.9 14.1 1.0
CE B:LYS224 4.9 17.6 1.0
CA B:GLY142 5.0 16.4 1.0

Reference:

Y.Nicolet, L.Zeppieri, P.Amara, J.C.Fontecilla-Camps. Crystal Structure of Tryptophan Lyase (Nosl): Evidence For Radical Formation at the Amino Group of Tryptophan. Angew.Chem.Int.Ed.Engl. V. 53 11840 2014.
ISSN: ISSN 1433-7851
PubMed: 25196319
DOI: 10.1002/ANIE.201407320
Page generated: Mon Aug 5 09:09:58 2024

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