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Chlorine in PDB 6p3h: Crystal Structure of Ligu(K66M) Bound to Substrate

Protein crystallography data

The structure of Crystal Structure of Ligu(K66M) Bound to Substrate, PDB code: 6p3h was solved by S.A.Cory, T.N.Hogancamp, F.M.Raushel, D.P.Barondeau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.46 / 1.62
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.880, 134.000, 168.370, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Ligu(K66M) Bound to Substrate (pdb code 6p3h). 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 Ligu(K66M) Bound to Substrate, PDB code: 6p3h:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6p3h

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Chlorine binding site 1 out of 6 in the Crystal Structure of Ligu(K66M) Bound to Substrate


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 Ligu(K66M) Bound to Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:33.0
occ:1.00
 O A:HOH796 3.0 39.3 1.0
O A:HOH696 3.0 32.1 1.0
O A:HOH738 3.1 36.0 1.0
N A:ALA29 3.2 20.5 1.0
N A:ARG28 3.4 19.8 1.0
CB A:ALA29 3.6 25.3 1.0
CB A:SER71 3.8 24.3 1.0
CB A:LEU27 3.9 20.9 1.0
CB A:ARG28 3.9 22.2 1.0
CA A:ALA29 4.0 22.7 1.0
CA A:ARG28 4.0 20.6 1.0
O A:VAL70 4.0 21.5 1.0
C A:ARG28 4.1 22.6 1.0
C A:LEU27 4.1 19.5 1.0
CA A:SER71 4.1 21.8 1.0
CA A:LEU27 4.3 19.2 1.0
CD2 A:LEU27 4.6 26.7 1.0
CG A:LEU27 4.7 23.2 1.0
O A:LEU27 4.9 21.9 1.0
O A:HOH797 4.9 48.4 1.0
O A:HOH758 5.0 44.9 1.0
C A:VAL70 5.0 22.1 1.0

Chlorine binding site 2 out of 6 in 6p3h

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Chlorine binding site 2 out of 6 in the Crystal Structure of Ligu(K66M) Bound to Substrate


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 Ligu(K66M) Bound to Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:49.1
occ:1.00
 N A:VAL148 3.1 26.4 1.0
O A:HOH663 3.1 34.1 1.0
O A:HOH753 3.6 55.3 1.0
CA A:SER147 3.7 30.9 1.0
CG2 A:VAL148 3.8 22.9 1.0
CB A:VAL148 3.8 25.5 1.0
C A:SER147 3.9 28.1 1.0
CB A:SER147 4.0 41.1 1.0
CA A:GLU113 4.0 22.5 1.0
CG A:GLU113 4.0 22.4 1.0
CA A:VAL148 4.1 28.4 1.0
CG2 A:ILE112 4.3 21.1 1.0
N A:GLU113 4.3 19.8 1.0
OG A:SER147 4.4 44.6 1.0
O A:ILE112 4.5 23.7 1.0
O A:HOH640 4.5 44.2 1.0
C A:ILE112 4.5 24.4 1.0
CB A:GLU113 4.6 21.1 1.0
O A:GLY146 4.6 38.5 1.0
CD A:GLU113 4.9 28.2 1.0
O A:VAL148 4.9 29.7 1.0
N A:SER147 4.9 30.3 1.0
O A:HOH719 5.0 36.2 1.0

Chlorine binding site 3 out of 6 in 6p3h

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Chlorine binding site 3 out of 6 in the Crystal Structure of Ligu(K66M) Bound to Substrate


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 Ligu(K66M) Bound to Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:33.6
occ:1.00
 O D:HOH785 3.0 41.8 1.0
O D:HOH524 3.0 35.6 1.0
O D:HOH660 3.0 27.7 1.0
N D:ALA29 3.2 20.3 1.0
N D:ARG28 3.4 21.4 0.5
N D:ARG28 3.4 21.4 0.5
CB D:ALA29 3.7 25.9 1.0
CB D:SER71 3.7 25.4 1.0
CB D:ARG28 3.9 20.9 0.5
CB D:ARG28 3.9 21.1 0.5
CB D:LEU27 3.9 18.6 1.0
O D:VAL70 4.0 22.0 1.0
CA D:ARG28 4.0 20.1 0.5
CA D:ARG28 4.0 20.2 0.5
C D:ARG28 4.1 19.8 0.5
C D:ARG28 4.1 20.0 0.5
CA D:ALA29 4.1 22.5 1.0
C D:LEU27 4.1 22.7 1.0
CA D:SER71 4.1 22.3 1.0
CA D:LEU27 4.3 18.6 1.0
CD2 D:LEU27 4.6 21.4 1.0
NE D:ARG28 4.7 33.1 0.5
CG D:LEU27 4.8 23.2 1.0
C D:VAL70 4.9 23.6 1.0
O D:HOH737 4.9 44.6 1.0
O D:LEU27 5.0 22.9 1.0
O D:HOH782 5.0 45.1 1.0

Chlorine binding site 4 out of 6 in 6p3h

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Chlorine binding site 4 out of 6 in the Crystal Structure of Ligu(K66M) Bound to Substrate


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 Ligu(K66M) Bound to Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:30.8
occ:1.00
 O C:HOH932 3.0 36.7 1.0
O C:HOH797 3.0 34.0 1.0
O C:HOH685 3.1 22.8 1.0
N C:ALA29 3.3 19.5 1.0
N C:ARG28 3.5 19.9 1.0
CB C:ALA29 3.7 29.0 1.0
CB C:SER71 3.7 19.5 1.0
CB C:ARG28 3.8 20.2 1.0
CB C:LEU27 3.9 17.7 1.0
O C:VAL70 4.0 18.6 1.0
CA C:ARG28 4.0 19.1 1.0
C C:ARG28 4.1 19.3 1.0
CA C:SER71 4.1 19.4 1.0
CA C:ALA29 4.1 23.1 1.0
C C:LEU27 4.1 19.8 1.0
CA C:LEU27 4.3 18.6 1.0
O C:HOH821 4.6 54.2 1.0
CD2 C:LEU27 4.7 21.0 1.0
CG C:LEU27 4.8 18.7 1.0
C C:VAL70 4.9 16.9 1.0
O C:LEU27 5.0 18.4 1.0
NE C:ARG28 5.0 40.8 1.0
CD1 C:LEU27 5.0 24.7 1.0
O C:HOH841 5.0 49.6 1.0

Chlorine binding site 5 out of 6 in 6p3h

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Chlorine binding site 5 out of 6 in the Crystal Structure of Ligu(K66M) Bound to Substrate


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 Ligu(K66M) Bound to Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:39.9
occ:1.00
 N B:VAL148 3.1 18.1 1.0
O B:HOH585 3.6 38.8 1.0
CA B:SER147 3.7 20.8 1.0
CG2 B:VAL148 3.7 20.5 1.0
CB B:VAL148 3.8 16.1 1.0
C B:SER147 3.9 21.8 1.0
CA B:VAL148 4.0 16.9 1.0
CG2 B:ILE112 4.1 15.0 1.0
CA B:GLU113 4.1 16.9 1.0
CB B:SER147 4.1 27.0 1.0
CG B:GLU113 4.2 20.0 1.0
N B:GLU113 4.3 16.1 1.0
O B:ILE112 4.4 20.7 1.0
O B:GLY146 4.5 23.4 1.0
C B:ILE112 4.5 17.5 1.0
OG B:SER147 4.6 31.4 1.0
O B:HOH721 4.7 43.5 1.0
CB B:GLU113 4.7 17.7 1.0
N B:SER147 4.9 19.2 1.0
O B:VAL148 4.9 20.2 1.0
CB B:ILE112 5.0 15.6 1.0
CD B:GLU113 5.0 23.8 1.0

Chlorine binding site 6 out of 6 in 6p3h

Go back to Chlorine Binding Sites List in 6p3h
Chlorine binding site 6 out of 6 in the Crystal Structure of Ligu(K66M) Bound to Substrate


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 Ligu(K66M) Bound to Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:28.2
occ:1.00
 O B:HOH762 3.0 33.6 1.0
O B:HOH776 3.0 21.6 1.0
O B:HOH963 3.2 35.7 1.0
N B:ALA29 3.3 16.2 1.0
N B:ARG28 3.5 16.8 0.7
N B:ARG28 3.5 16.8 0.3
CB B:ALA29 3.7 25.8 1.0
CB B:SER71 3.8 16.9 1.0
CB B:ARG28 3.8 18.1 0.3
CB B:ARG28 3.9 17.7 0.7
CB B:LEU27 3.9 17.7 1.0
CA B:ARG28 4.0 16.8 0.3
O B:VAL70 4.0 16.9 1.0
CA B:ARG28 4.0 16.2 0.7
C B:ARG28 4.1 17.6 0.3
C B:ARG28 4.1 18.0 0.7
C B:LEU27 4.1 18.0 1.0
CA B:SER71 4.1 16.7 1.0
CA B:ALA29 4.1 20.6 1.0
CA B:LEU27 4.3 16.1 1.0
O B:HOH844 4.4 47.8 1.0
CD2 B:LEU27 4.7 20.6 1.0
CG B:LEU27 4.7 21.6 1.0
NE B:ARG28 4.9 28.2 0.7
C B:VAL70 4.9 19.3 1.0
O B:HOH958 5.0 35.8 1.0
O B:LEU27 5.0 18.2 1.0

Reference:

T.N.Hogancamp, S.A.Cory, D.P.Barondeau, F.M.Raushel. Structure and Chemical Reaction Mechanism of Ligu, An Enzyme That Catalyzes An Allylic Isomerization in the Bacterial Degradation of Lignin. Biochemistry V. 58 3494 2019.
ISSN: ISSN 0006-2960
PubMed: 31339729
DOI: 10.1021/ACS.BIOCHEM.9B00549
Page generated: Mon Jul 29 13:04:36 2024

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