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Chlorine in PDB 6p3j: Crystal Structure of Ligu

Protein crystallography data

The structure of Crystal Structure of Ligu, PDB code: 6p3j 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) 41.99 / 2.02
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.776, 67.364, 161.072, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.2

Other elements in 6p3j:

The structure of Crystal Structure of Ligu also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Ligu (pdb code 6p3j). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of Ligu, PDB code: 6p3j:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 6p3j

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Chlorine binding site 1 out of 9 in the Crystal Structure of Ligu


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:66.2
occ:1.00
 N A:HIS278 3.2 48.4 1.0
N A:ARG279 3.3 50.5 1.0
O A:ILE276 3.3 56.4 1.0
CD A:PRO277 3.5 50.5 1.0
C A:ILE276 3.6 51.0 1.0
CB A:HIS278 3.6 51.2 1.0
N A:PRO277 3.6 48.5 1.0
CG A:ARG279 3.7 72.6 1.0
CA A:HIS278 3.7 51.6 1.0
C A:HIS278 4.0 50.6 1.0
ND1 A:HIS278 4.0 52.4 1.0
CB A:ARG279 4.1 60.6 1.0
CG A:HIS278 4.2 52.1 1.0
CG1 A:ILE276 4.3 49.9 1.0
CA A:ARG279 4.3 52.3 1.0
C A:PRO277 4.3 48.7 1.0
NE A:ARG279 4.5 89.4 1.0
CG A:PRO277 4.5 51.7 1.0
CA A:PRO277 4.6 49.8 1.0
CD A:ARG279 4.6 82.1 1.0
CA A:ILE276 4.6 49.0 1.0
N A:ILE276 4.7 45.0 1.0
CB A:ILE276 5.0 48.5 1.0
O A:ARG279 5.0 44.5 1.0

Chlorine binding site 2 out of 9 in 6p3j

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Chlorine binding site 2 out of 9 in the Crystal Structure of Ligu


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:61.6
occ:1.00
 N A:GLY101 2.8 52.4 1.0
N A:VAL286 3.4 47.1 1.0
CA A:GLY101 3.4 47.5 1.0
N A:LEU287 3.7 47.7 1.0
O A:HOH583 3.7 59.8 1.0
CB A:VAL286 3.8 50.2 1.0
C A:CYS100 3.8 53.8 1.0
CA A:VAL286 4.0 46.6 1.0
CA A:CYS100 4.0 60.4 1.0
O A:ASN99 4.1 76.7 0.5
C A:GLY101 4.2 48.3 1.0
C A:GLY285 4.2 46.4 1.0
CA A:GLY285 4.3 42.9 1.0
N A:ASN102 4.3 40.6 1.0
CG A:LEU287 4.4 61.2 1.0
C A:VAL286 4.4 45.5 1.0
ND2 A:ASN102 4.4 40.3 1.0
CG2 A:VAL286 4.4 48.0 1.0
CB A:LEU287 4.4 55.9 1.0
CD1 A:LEU287 4.6 65.9 1.0
CA A:LEU287 4.7 50.0 1.0
O A:ASN99 4.8 75.2 0.5
C A:ASN99 4.9 75.4 0.5
N A:CYS100 4.9 68.2 1.0
O A:CYS100 5.0 42.5 1.0
CG1 A:VAL286 5.0 48.7 1.0

Chlorine binding site 3 out of 9 in 6p3j

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Chlorine binding site 3 out of 9 in the Crystal Structure of Ligu


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:49.2
occ:1.00
 O A:HOH516 3.1 42.7 1.0
O A:HOH597 3.2 49.3 1.0
N A:ARG221 3.3 43.8 1.0
CA A:ASP220 3.6 40.8 1.0
OD1 A:ASP220 3.8 44.3 1.0
CB A:ASP220 3.8 42.3 1.0
CG A:ASP220 3.9 45.2 1.0
C A:ASP220 4.0 45.8 1.0
CB A:PRO322 4.0 35.0 1.0
O A:PRO322 4.0 43.2 1.0
O A:HOH513 4.1 39.0 1.0
CB A:ARG221 4.3 49.5 1.0
CA A:ARG221 4.4 46.1 1.0
CA A:PRO322 4.5 38.0 1.0
C A:PRO322 4.6 40.7 1.0
OD2 A:ASP220 4.7 46.2 1.0
N A:ASP220 4.8 41.5 1.0
O A:GLU219 4.9 41.9 1.0

Chlorine binding site 4 out of 9 in 6p3j

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Chlorine binding site 4 out of 9 in the Crystal Structure of Ligu


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:67.6
occ:1.00
 O A:HOH592 2.7 55.1 1.0
N A:VAL89 3.1 34.2 1.0
CB A:VAL89 3.8 35.3 1.0
CG A:PRO62 3.8 45.5 1.0
CG2 A:VAL89 3.8 30.9 1.0
CA A:PHE88 3.8 41.8 1.0
C A:PHE88 4.0 37.4 1.0
CA A:VAL89 4.0 37.6 1.0
CG A:PHE88 4.1 53.6 1.0
CB A:PHE88 4.2 47.1 1.0
CD2 A:PHE88 4.2 58.0 1.0
CB A:PRO62 4.3 44.4 1.0
N A:ASP90 4.5 45.6 1.0
CD A:PRO62 4.7 40.3 1.0
CD1 A:PHE88 4.8 54.7 1.0
CA A:PRO62 4.8 40.8 1.0
CE2 A:PHE88 4.8 61.5 1.0
C A:VAL89 4.8 43.0 1.0

Chlorine binding site 5 out of 9 in 6p3j

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Chlorine binding site 5 out of 9 in the Crystal Structure of Ligu


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:67.7
occ:1.00
 O A:HOH506 2.9 64.2 1.0
N A:ALA29 3.3 53.8 1.0
N A:ARG28 3.5 53.3 1.0
CB A:SER71 3.6 57.3 1.0
CB A:ALA29 3.8 59.3 1.0
CA A:SER71 3.9 54.4 1.0
O A:VAL70 3.9 56.0 1.0
CB A:ARG28 3.9 54.8 1.0
CB A:LEU27 4.0 48.4 1.0
CA A:ARG28 4.0 55.4 1.0
C A:ARG28 4.1 56.9 1.0
CA A:ALA29 4.2 57.5 1.0
C A:LEU27 4.2 55.4 1.0
CA A:LEU27 4.4 48.3 1.0
N A:LYS72 4.7 60.7 1.0
C A:VAL70 4.8 53.7 1.0
NE A:ARG28 4.8 71.8 1.0
CD2 A:LEU27 4.8 47.9 1.0
N A:SER71 4.8 50.9 1.0
CG A:LEU27 4.9 47.8 1.0
C A:SER71 4.9 59.2 1.0

Chlorine binding site 6 out of 9 in 6p3j

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Chlorine binding site 6 out of 9 in the Crystal Structure of Ligu


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:48.5
occ:1.00
 O B:HOH532 3.0 51.9 1.0
O B:HOH521 3.2 63.1 1.0
N B:ALA29 3.3 42.1 1.0
N B:ARG28 3.4 41.2 0.4
N B:ARG28 3.4 41.2 0.6
CB B:SER71 3.5 40.4 1.0
CB B:ALA29 3.9 43.4 1.0
CB B:ARG28 3.9 42.1 0.6
CA B:SER71 3.9 36.9 1.0
O B:VAL70 3.9 40.0 1.0
CB B:ARG28 4.0 42.3 0.4
CA B:ARG28 4.0 41.8 0.6
CB B:LEU27 4.0 37.9 1.0
CA B:ARG28 4.0 41.7 0.4
C B:LEU27 4.1 40.3 1.0
C B:ARG28 4.2 42.2 0.6
C B:ARG28 4.2 42.2 0.4
CA B:ALA29 4.2 43.7 1.0
CA B:LEU27 4.4 37.9 1.0
NE B:ARG28 4.6 48.5 0.6
N B:LYS72 4.8 46.2 1.0
C B:VAL70 4.8 39.3 1.0
CD2 B:LEU27 4.8 42.4 1.0
OG B:SER71 4.8 42.8 1.0
N B:SER71 4.9 39.1 1.0
CG B:LEU27 4.9 43.9 1.0
C B:SER71 5.0 43.2 1.0
NH2 B:ARG28 5.0 49.7 0.6

Chlorine binding site 7 out of 9 in 6p3j

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Chlorine binding site 7 out of 9 in the Crystal Structure of Ligu


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Ligu within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:67.0
occ:1.00
 N B:VAL89 3.1 37.8 1.0
CA B:PHE88 3.8 42.2 1.0
CB B:VAL89 3.8 35.8 1.0
CG B:PRO62 3.8 45.5 1.0
CG2 B:VAL89 4.0 34.4 1.0
C B:PHE88 4.0 38.6 1.0
CA B:VAL89 4.0 38.5 1.0
OD1 B:ASP90 4.1 59.7 0.5
CB B:PHE88 4.1 41.0 1.0
CG B:PHE88 4.1 46.0 1.0
CD2 B:PHE88 4.2 50.1 1.0
CB B:PRO62 4.4 39.8 1.0
N B:ASP90 4.5 46.4 0.5
N B:ASP90 4.5 46.4 0.5
CD B:PRO62 4.8 45.6 1.0
CD1 B:PHE88 4.8 45.7 1.0
C B:VAL89 4.8 43.2 1.0
CG B:ASP90 4.8 55.1 0.5
CE2 B:PHE88 4.9 49.5 1.0
CA B:PRO62 4.9 38.1 1.0

Chlorine binding site 8 out of 9 in 6p3j

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Chlorine binding site 8 out of 9 in the Crystal Structure of Ligu


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Ligu within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:70.2
occ:1.00
 N B:GLY101 2.8 46.9 1.0
O B:HOH573 3.4 50.1 1.0
CA B:GLY101 3.4 42.9 1.0
N B:VAL286 3.5 48.8 1.0
O B:HOH593 3.5 69.2 1.0
O B:ASN99 3.7 77.9 1.0
N B:LEU287 3.7 52.5 1.0
CB B:VAL286 3.7 49.3 1.0
C B:CYS100 3.8 54.0 1.0
CA B:CYS100 3.9 60.7 1.0
CA B:VAL286 4.0 50.1 1.0
C B:GLY101 4.2 41.9 1.0
N B:ASN102 4.4 41.9 1.0
CG B:LEU287 4.4 53.2 1.0
C B:VAL286 4.4 51.9 1.0
CG2 B:VAL286 4.4 50.1 1.0
C B:GLY285 4.4 50.5 1.0
CB B:LEU287 4.4 52.0 1.0
ND2 B:ASN102 4.5 46.2 1.0
CD1 B:LEU287 4.5 55.8 1.0
CA B:GLY285 4.5 53.5 1.0
C B:ASN99 4.6 76.1 1.0
CA B:LEU287 4.7 53.6 1.0
N B:CYS100 4.7 69.9 1.0
CG1 B:VAL286 4.7 51.1 1.0
O B:CYS100 4.9 44.0 1.0
CB B:CYS100 5.0 55.5 1.0

Chlorine binding site 9 out of 9 in 6p3j

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Chlorine binding site 9 out of 9 in the Crystal Structure of Ligu


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Ligu within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl406

b:88.6
occ:1.00
 N B:ARG279 2.9 97.1 1.0
O B:ILE276 3.2 76.6 1.0
N B:HIS278 3.3 86.9 1.0
CB B:ARG279 3.4 0.1 1.0
CD B:PRO277 3.5 82.9 1.0
C B:ILE276 3.5 77.0 1.0
N B:PRO277 3.6 80.4 1.0
C B:HIS278 3.8 94.8 1.0
CA B:ARG279 3.8 0.6 1.0
CA B:HIS278 3.8 90.9 1.0
CB B:HIS278 3.8 91.3 1.0
ND1 B:HIS278 4.1 87.8 1.0
C B:PRO277 4.4 85.0 1.0
CG B:HIS278 4.4 88.5 1.0
CG1 B:ILE276 4.5 69.6 1.0
CA B:PRO277 4.6 81.8 1.0
CA B:ILE276 4.6 71.9 1.0
CG B:PRO277 4.6 84.9 1.0
O B:ARG279 4.7 93.2 1.0
N B:ILE276 4.7 73.4 1.0
C B:ARG279 4.8 98.3 1.0
NE B:ARG279 4.8 0.7 1.0
CG B:ARG279 4.9 0.6 1.0
O B:HIS278 4.9 97.0 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 13:04:35 2024

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