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Chlorine in PDB 4dj4: X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato)

Protein crystallography data

The structure of X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato), PDB code: 4dj4 was solved by T.Koval, A.Stepankova, P.Lipovova, T.Podzimek, J.Matousek, J.Duskova, T.Skalova, J.Hasek, J.Dohnalek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 2.35
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 113.322, 113.322, 138.322, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 20.7

Other elements in 4dj4:

The structure of X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) also contains other interesting chemical elements:

Zinc (Zn) 6 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) (pdb code 4dj4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato), PDB code: 4dj4:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4dj4

Go back to Chlorine Binding Sites List in 4dj4
Chlorine binding site 1 out of 2 in the X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:48.5
occ:0.50
O A:HOH728 2.8 46.0 1.0
NE1 A:TRP68 3.1 35.6 1.0
N2 A:NAG512 3.5 41.4 1.0
CE2 A:TRP68 3.8 36.3 1.0
CZ2 A:TRP68 3.9 35.5 1.0
C3 A:NAG512 4.0 44.0 1.0
CD1 A:TRP68 4.1 37.8 1.0
C2 A:NAG512 4.2 40.5 1.0
CZ3 A:TRP75 4.2 47.8 1.0
CH2 A:TRP75 4.3 43.7 1.0
O6 A:NAG511 4.3 42.5 1.0
C1 A:NAG512 4.3 40.5 1.0
C6 A:NAG511 4.4 42.4 1.0
C7 A:NAG512 4.5 39.8 1.0
C8 A:NAG512 4.5 37.4 1.0
O3 A:NAG512 4.6 39.7 1.0

Chlorine binding site 2 out of 2 in 4dj4

Go back to Chlorine Binding Sites List in 4dj4
Chlorine binding site 2 out of 2 in the X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:41.8
occ:0.50
N2 B:NAG512 3.1 56.2 1.0
NE1 B:TRP68 3.2 43.6 1.0
C3 B:NAG512 3.7 62.4 1.0
C2 B:NAG512 3.8 57.1 1.0
CH2 B:TRP75 4.0 43.3 1.0
CD1 B:TRP68 4.0 40.1 1.0
C7 B:NAG512 4.1 59.9 1.0
C8 B:NAG512 4.1 55.5 1.0
CE2 B:TRP68 4.2 40.9 1.0
C1 B:NAG512 4.2 54.1 1.0
O3 B:NAG512 4.3 63.3 1.0
C6 B:NAG511 4.3 46.2 1.0
CZ3 B:TRP75 4.4 43.3 1.0
O6 B:NAG511 4.5 40.4 1.0
CZ2 B:TRP68 4.5 42.4 1.0
C4 B:NAG512 4.8 64.2 1.0

Reference:

T.Koval, P.Lipovova, T.Podzimek, J.Matousek, J.Duskova, T.Skalova, A.Stepankova, J.Hasek, J.Dohnalek. Plant Multifunctional Nuclease TBN1 with Unexpected Phospholipase Activity: Structural Study and Reaction-Mechanism Analysis. Acta Crystallogr.,Sect.D V. 69 213 2013.
ISSN: ISSN 0907-4449
PubMed: 23385457
DOI: 10.1107/S0907444912043697
Page generated: Sat Dec 12 10:32:18 2020

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