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Sodium 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
Iron (Fe) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of the Tryptophan Lyase Nosl with Tryptophan, 5'- Deoxyadenosine and Methionine Bound, PDB code: 4r34:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4r34

Go back to Sodium Binding Sites List in 4r34
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na510

b:37.4
occ:1.00
O A:PHE389 2.4 26.8 1.0
OE2 A:GLU380 2.5 28.5 1.0
O A:VAL386 2.5 24.1 1.0
O A:HOH635 3.0 40.0 1.0
O A:HOH629 3.1 41.5 1.0
C A:VAL386 3.5 21.3 1.0
C A:PHE389 3.5 23.5 1.0
CD A:GLU380 3.6 28.2 1.0
O A:HOH699 3.9 49.5 1.0
N A:VAL386 3.9 25.8 1.0
OE1 A:GLU380 3.9 30.2 1.0
CB A:PHE389 4.0 20.2 1.0
CA A:PHE389 4.1 22.4 1.0
N A:PHE389 4.2 21.2 1.0
CA A:VAL386 4.2 26.3 1.0
CD2 A:PHE389 4.2 22.1 1.0
N A:ASP387 4.4 21.7 1.0
O A:HOH751 4.4 52.2 1.0
CG A:PHE389 4.5 24.4 1.0
CA A:ASP387 4.6 22.4 1.0
N A:VAL390 4.7 23.5 1.0
CB A:VAL386 4.7 27.9 1.0
CG A:GLU380 4.8 24.5 1.0
C A:PRO385 4.9 29.4 1.0
C A:ASP387 5.0 26.9 1.0
CA A:VAL390 5.0 22.2 1.0

Sodium binding site 2 out of 2 in 4r34

Go back to Sodium Binding Sites List in 4r34
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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
B:Na512

b:37.5
occ:1.00
O B:PHE389 2.5 23.0 1.0
OE2 B:GLU380 2.6 27.8 1.0
O B:VAL386 2.7 22.5 1.0
O B:HOH654 3.0 43.9 1.0
O B:HOH668 3.2 26.3 1.0
O B:HOH764 3.4 39.0 1.0
CD B:GLU380 3.6 30.0 1.0
C B:PHE389 3.6 23.1 1.0
C B:VAL386 3.7 22.7 1.0
OE1 B:GLU380 3.9 27.8 1.0
N B:VAL386 4.1 22.6 1.0
N B:PHE389 4.3 20.1 1.0
CA B:PHE389 4.3 21.3 1.0
CB B:PHE389 4.3 18.9 1.0
CD2 B:PHE389 4.3 21.5 1.0
CA B:VAL386 4.4 21.3 1.0
O B:HOH935 4.5 50.7 1.0
N B:ASP387 4.6 23.8 1.0
N B:VAL390 4.7 20.0 1.0
O B:HOH778 4.7 46.0 1.0
CA B:ASP387 4.8 23.4 1.0
CG B:PHE389 4.8 20.3 1.0
O B:HOH860 4.8 61.6 1.0
CB B:VAL386 4.9 21.6 1.0
CG B:GLU380 4.9 25.8 1.0
CA B:VAL390 4.9 22.3 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: Tue Dec 15 07:09:16 2020

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