Chlorine in PDB 7vrg: Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B

Protein crystallography data

The structure of Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B, PDB code: 7vrg was solved by Q.Lu, T.Liu, Y.Zhou, Q.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.03 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.908, 77.859, 81.972, 113.63, 109.9, 95
R / Rfree (%) 23.4 / 24.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B (pdb code 7vrg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B, PDB code: 7vrg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 7vrg

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Chlorine binding site 1 out of 6 in the Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:59.3
occ:0.59
 CL1 A:7U8601 0.0 59.3 0.6
C16 A:7U8601 1.8 44.8 0.6
O A:HOH715 2.6 39.2 1.0
C17 A:7U8601 2.8 43.4 0.6
C15 A:7U8601 2.8 33.7 0.6
NZ A:LYS362 3.0 31.0 1.0
O A:HOH790 3.1 37.1 1.0
CE A:LYS362 3.2 36.0 1.0
CL2 A:7U8601 3.3 53.7 0.6
CE2 A:PHE309 4.0 35.7 1.0
C18 A:7U8601 4.1 36.9 0.6
C14 A:7U8601 4.1 33.9 0.6
CZ A:PHE309 4.1 38.5 1.0
OH A:TYR411 4.5 35.6 1.0
CD A:LYS362 4.5 33.1 1.0
C22 A:7U8601 4.5 42.6 0.6
OG A:SER357 4.6 29.6 1.0
C13 A:7U8601 4.6 32.5 0.6
CE2 A:TYR411 4.6 28.9 1.0
O A:LYS313 4.7 33.1 1.0
N23 A:7U8601 4.8 43.7 0.6
CD2 A:PHE309 4.9 34.3 1.0
CZ A:TYR411 5.0 32.4 1.0

Chlorine binding site 2 out of 6 in 7vrg

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Chlorine binding site 2 out of 6 in the Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:53.7
occ:0.59
 CL2 A:7U8601 0.0 53.7 0.6
C15 A:7U8601 1.8 33.7 0.6
C14 A:7U8601 2.7 33.9 0.6
C16 A:7U8601 2.8 44.8 0.6
CE2 A:TYR411 3.1 28.9 1.0
CZ A:TYR411 3.1 32.4 1.0
OG A:SER357 3.2 29.6 1.0
OH A:TYR411 3.2 35.6 1.0
N A:GLY359 3.2 32.4 1.0
CA A:GLY359 3.3 32.7 1.0
CL1 A:7U8601 3.3 59.3 0.6
NZ A:LYS362 3.8 31.0 1.0
CD2 A:TYR411 3.9 34.2 1.0
CE1 A:TYR411 3.9 28.9 1.0
C13 A:7U8601 4.0 32.5 0.6
C17 A:7U8601 4.1 43.4 0.6
O A:HOH790 4.1 37.1 1.0
C A:ALA358 4.3 30.7 1.0
CB A:SER357 4.5 29.5 1.0
N A:ALA358 4.5 33.1 1.0
CD1 A:TYR411 4.5 28.7 1.0
C A:GLY359 4.5 33.2 1.0
CG A:TYR411 4.5 32.3 1.0
CE A:LYS362 4.5 36.0 1.0
C18 A:7U8601 4.5 36.9 0.6
CD1 A:PHE385 4.6 34.1 1.0
CE1 A:PHE385 4.6 30.4 1.0
OD1 A:ASP361 4.7 26.1 1.0
O A:GLY359 4.8 36.1 1.0
CA A:ALA358 4.9 36.3 1.0

Chlorine binding site 3 out of 6 in 7vrg

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Chlorine binding site 3 out of 6 in the Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:60.5
occ:0.59
 CL3 A:7U8601 0.0 60.5 0.6
C27 A:7U8601 1.8 46.9 0.6
O A:HOH872 2.4 41.8 1.0
O A:HOH782 2.5 44.9 1.0
C28 A:7U8601 2.8 44.9 0.6
C26 A:7U8601 2.8 41.7 0.6
NH2 A:ARG439 2.8 41.2 1.0
O A:HOH890 3.0 42.0 1.0
CZ A:ARG439 3.7 41.6 1.0
NH1 A:ARG439 3.8 32.5 1.0
C29 A:7U8601 4.1 42.1 0.6
C25 A:7U8601 4.1 43.1 0.6
O4 A:7U8601 4.5 50.1 0.6
C24 A:7U8601 4.6 41.5 0.6
C1 A:7U8601 4.7 39.6 0.6
O2 A:7U8601 4.8 39.8 0.6
C3 A:7U8601 4.8 47.6 0.6
NE A:ARG439 5.0 39.3 1.0
OE1 A:GLN466 5.0 64.8 1.0

Chlorine binding site 4 out of 6 in 7vrg

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Chlorine binding site 4 out of 6 in the Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:59.1
occ:0.55
 CL1 B:7U8601 0.0 59.1 0.6
C16 B:7U8601 1.8 40.6 0.6
O B:HOH722 2.6 41.2 1.0
C17 B:7U8601 2.8 42.1 0.6
C15 B:7U8601 2.8 29.8 0.6
CL2 B:7U8601 3.2 56.6 0.6
NZ B:LYS362 3.2 37.6 1.0
O B:HOH878 3.3 35.8 1.0
CE B:LYS362 3.4 42.4 1.0
CE2 B:PHE309 3.9 41.6 1.0
C14 B:7U8601 4.0 32.8 0.6
C18 B:7U8601 4.1 35.0 0.6
CZ B:PHE309 4.1 38.9 1.0
OG B:SER357 4.3 32.2 1.0
OH B:TYR411 4.4 29.2 1.0
C13 B:7U8601 4.6 33.6 0.6
C22 B:7U8601 4.6 43.5 0.6
CD B:LYS362 4.7 38.2 1.0
O B:LYS313 4.7 43.2 1.0
CE2 B:TYR411 4.7 30.6 1.0
CD2 B:PHE309 4.8 41.0 1.0
CZ B:TYR411 5.0 31.5 1.0
N23 B:7U8601 5.0 42.0 0.6
O B:HOH823 5.0 32.4 1.0

Chlorine binding site 5 out of 6 in 7vrg

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Chlorine binding site 5 out of 6 in the Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:56.6
occ:0.55
 CL2 B:7U8601 0.0 56.6 0.6
C15 B:7U8601 1.8 29.8 0.6
C14 B:7U8601 2.7 32.8 0.6
C16 B:7U8601 2.8 40.6 0.6
CZ B:TYR411 3.1 31.5 1.0
OH B:TYR411 3.1 29.2 1.0
OG B:SER357 3.2 32.2 1.0
CL1 B:7U8601 3.2 59.1 0.6
CE2 B:TYR411 3.2 30.6 1.0
N B:GLY359 3.3 31.7 1.0
CA B:GLY359 3.3 35.0 1.0
CE1 B:TYR411 3.8 26.9 1.0
CD2 B:TYR411 4.0 32.6 1.0
C13 B:7U8601 4.0 33.6 0.6
C17 B:7U8601 4.0 42.1 0.6
NZ B:LYS362 4.2 37.6 1.0
O B:HOH878 4.3 35.8 1.0
C B:ALA358 4.4 30.7 1.0
CD1 B:TYR411 4.4 27.5 1.0
N B:ALA358 4.5 29.7 1.0
CB B:SER357 4.6 29.4 1.0
CG B:TYR411 4.6 30.0 1.0
C18 B:7U8601 4.6 35.0 0.6
C B:GLY359 4.6 35.3 1.0
CE1 B:PHE385 4.6 29.3 1.0
CD1 B:PHE385 4.6 29.0 1.0
OD1 B:ASP361 4.8 37.4 1.0
CE B:LYS362 4.8 42.4 1.0
O B:GLY359 4.9 34.1 1.0
CG B:LYS362 5.0 34.7 1.0

Chlorine binding site 6 out of 6 in 7vrg

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Chlorine binding site 6 out of 6 in the Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Chitinase-H From O. Furnacalis in Complex with Lynamicin B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:50.4
occ:0.55
 CL3 B:7U8601 0.0 50.4 0.6
C27 B:7U8601 1.8 42.2 0.6
O B:HOH857 2.4 38.6 1.0
O B:HOH913 2.4 38.6 1.0
C26 B:7U8601 2.7 40.0 0.6
C28 B:7U8601 2.8 38.5 0.6
NH2 B:ARG439 3.0 43.7 1.0
C25 B:7U8601 4.1 40.7 0.6
C29 B:7U8601 4.1 41.4 0.6
CZ B:ARG439 4.1 38.7 1.0
O4 B:7U8601 4.3 48.5 0.6
NH1 B:ARG439 4.4 33.4 1.0
O B:HOH720 4.4 37.8 1.0
C24 B:7U8601 4.6 40.5 0.6
NE2 B:GLN466 4.6 55.8 1.0
O B:HOH923 4.7 42.4 1.0
C3 B:7U8601 4.7 47.5 0.6
O2 B:7U8601 4.7 39.7 0.6
C1 B:7U8601 4.9 36.5 0.6

Reference:

Q.Lu, L.Xu, L.Liu, Y.Zhou, T.Liu, Y.Song, J.Ju, Q.Yang. Lynamicin B Is A Potential Pesticide By Acting As A Lepidoptera-Exclusive Chitinase Inhibitor. J.Agric.Food Chem. V. 69 14086 2021.
ISSN: ESSN 1520-5118
PubMed: 34797675
DOI: 10.1021/ACS.JAFC.1C05385
Page generated: Tue Apr 4 22:09:29 2023

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