Chlorine in PDB 6mry: NOD173 Plant Defensin

Protein crystallography data

The structure of NOD173 Plant Defensin, PDB code: 6mry was solved by S.Caria, M.Kvansakul, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.37 / 2.30
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.107, 69.318, 107.662, 90.00, 108.08, 90.00
R / Rfree (%) 18.9 / 23.2

Other elements in 6mry:

The structure of NOD173 Plant Defensin also contains other interesting chemical elements:

Iodine (I) 15 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the NOD173 Plant Defensin (pdb code 6mry). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the NOD173 Plant Defensin, PDB code: 6mry:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6mry

Go back to Chlorine Binding Sites List in 6mry
Chlorine binding site 1 out of 6 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of NOD173 Plant Defensin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl104

b:62.0
occ:1.00
O A:THR12 3.2 45.3 1.0
N A:THR12 3.5 31.6 1.0
CD2 A:PHE11 3.6 31.1 1.0
CE2 A:PHE11 3.7 30.8 1.0
CG A:PHE11 3.8 24.8 1.0
CZ A:PHE11 4.0 27.9 1.0
C A:THR12 4.1 33.6 1.0
CD1 A:PHE11 4.2 28.2 1.0
CG2 A:THR12 4.2 31.3 1.0
CA A:PHE11 4.2 36.4 1.0
CE1 A:PHE11 4.2 25.7 1.0
CA A:THR12 4.3 32.6 1.0
C A:PHE11 4.3 36.9 1.0
CB A:PHE11 4.5 28.3 1.0
O A:HOH207 4.7 31.2 1.0
CB A:THR12 4.8 37.5 1.0

Chlorine binding site 2 out of 6 in 6mry

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Chlorine binding site 2 out of 6 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of NOD173 Plant Defensin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl105

b:37.3
occ:1.00
CE1 B:PHE30 3.4 37.4 1.0
CZ B:PHE30 3.5 21.6 1.0
O B:HOH208 3.6 41.3 1.0
CD1 B:PHE30 3.9 35.2 1.0
O B:GLU28 4.0 37.8 1.0
CE2 B:PHE30 4.0 28.7 1.0
CD B:LYS46 4.1 53.0 1.0
O B:LYS29 4.2 33.7 1.0
CG B:PHE30 4.4 36.5 1.0
CD2 B:PHE30 4.4 27.9 1.0
CE B:LYS46 4.5 54.1 1.0
C B:LYS29 4.5 35.1 1.0
CB G:CYS48 4.6 58.3 1.0
CB B:LYS29 4.6 32.0 1.0
CG G:ARG2 4.8 26.8 1.0
N B:PHE30 5.0 33.1 1.0

Chlorine binding site 3 out of 6 in 6mry

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Chlorine binding site 3 out of 6 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of NOD173 Plant Defensin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl102

b:70.7
occ:1.00
CE1 F:PHE30 4.1 32.8 1.0
O F:GLU28 4.2 56.5 1.0
CZ F:PHE30 4.3 26.2 1.0
NZ F:LYS46 4.4 69.8 1.0
NH2 I:ARG47 4.6 92.0 1.0
O F:LYS29 4.7 38.5 1.0
CD1 F:PHE30 4.7 35.8 1.0
CB I:CYS48 4.7 77.3 1.0
O I:CYS48 4.8 57.9 1.0
CB F:LYS29 4.9 48.2 1.0
CD F:LYS46 4.9 45.0 1.0
CE2 F:PHE30 5.0 35.4 1.0

Chlorine binding site 4 out of 6 in 6mry

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Chlorine binding site 4 out of 6 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of NOD173 Plant Defensin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl102

b:67.7
occ:1.00
NZ H:LYS46 3.4 67.3 1.0
O H:LYS29 3.6 61.1 1.0
CZ H:PHE30 3.7 30.4 1.0
O K:CYS48 3.8 71.4 1.0
CE2 H:PHE30 3.9 36.7 1.0
CE H:LYS46 3.9 64.9 1.0
CE1 H:PHE30 3.9 36.0 1.0
O H:GLU28 4.1 64.3 1.0
CD2 H:PHE30 4.2 40.2 1.0
CD1 H:PHE30 4.3 41.2 1.0
C H:LYS29 4.3 58.7 1.0
CD H:LYS46 4.4 63.7 1.0
CG H:PHE30 4.4 43.2 1.0
CB H:LYS29 4.5 70.8 1.0
C K:CYS48 4.6 62.6 1.0
SG K:CYS48 4.9 86.0 1.0
N H:PHE30 4.9 42.5 1.0
CB K:ARG2 5.0 63.6 1.0
CA H:LYS29 5.0 69.2 1.0

Chlorine binding site 5 out of 6 in 6mry

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Chlorine binding site 5 out of 6 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of NOD173 Plant Defensin within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl105

b:54.7
occ:1.00
O K:GLU28 3.4 44.8 1.0
NZ K:LYS46 3.4 65.9 1.0
CZ K:PHE30 3.7 31.2 1.0
CE K:LYS46 3.8 57.5 1.0
CE1 K:PHE30 3.8 23.4 1.0
O K:LYS29 3.9 42.8 1.0
CE2 K:PHE30 4.0 32.4 1.0
O K:HOH202 4.0 53.1 1.0
CB H:CYS48 4.1 77.9 1.0
CD1 K:PHE30 4.2 22.8 1.0
CB K:LYS29 4.2 51.3 1.0
C K:LYS29 4.3 44.6 1.0
CG H:ARG2 4.4 54.1 1.0
CD2 K:PHE30 4.4 30.5 1.0
CB H:ARG2 4.4 56.4 1.0
CG K:PHE30 4.5 32.4 1.0
C K:GLU28 4.5 38.5 1.0
O H:CYS48 4.7 57.1 1.0
SG H:CYS48 4.7 84.5 1.0
CA K:LYS29 4.7 50.2 1.0
CD K:LYS29 4.8 72.8 1.0
N K:PHE30 4.9 42.0 1.0
CD K:LYS46 5.0 52.4 1.0

Chlorine binding site 6 out of 6 in 6mry

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Chlorine binding site 6 out of 6 in the NOD173 Plant Defensin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of NOD173 Plant Defensin within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl103

b:77.6
occ:1.00
NZ L:LYS46 3.1 62.3 1.0
CE1 L:PHE30 3.8 45.5 1.0
CZ L:PHE30 3.9 37.2 1.0
CE L:LYS46 4.0 54.5 1.0
O L:LYS29 4.0 36.9 1.0
CD L:LYS46 4.1 49.4 1.0
O L:GLU28 4.2 31.9 1.0
CD1 L:PHE30 4.2 32.9 1.0
CE2 L:PHE30 4.4 37.8 1.0
C L:LYS29 4.5 45.4 1.0
CB L:LYS29 4.6 49.5 1.0
CG L:PHE30 4.7 34.1 1.0
CD2 L:PHE30 4.8 38.8 1.0
N L:PHE30 5.0 35.6 1.0

Reference:

F.T.Lay, G.F.Ryan, S.Caria, T.K.Phan, P.K.Veneer, J.A.White, M.Kvansakul, M.D.Hulett. Structural and Functional Characterization of the Membrane-Permeabilizing Activity Ofnicotiana Occidentalisdefensin NOD173 and Protein Engineering to Enhance Oncolysis. Faseb J. V. 33 6470 2019.
ISSN: ESSN 1530-6860
PubMed: 30794440
DOI: 10.1096/FJ.201802540R
Page generated: Sat Dec 12 13:22:04 2020

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