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Chlorine in PDB 5dbj: Crystal Structure of Halogenase Plta

Enzymatic activity of Crystal Structure of Halogenase Plta

All present enzymatic activity of Crystal Structure of Halogenase Plta:
3.8.1.1;

Protein crystallography data

The structure of Crystal Structure of Halogenase Plta, PDB code: 5dbj was solved by A.H.Pang, O.V.Tsodikov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 242.934, 94.981, 102.145, 90.00, 91.21, 90.00
R / Rfree (%) 23.9 / 29.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Halogenase Plta (pdb code 5dbj). 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 Halogenase Plta, PDB code: 5dbj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 5dbj

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Chlorine binding site 1 out of 9 in the Crystal Structure of Halogenase Plta


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Halogenase Plta within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl502

b:74.5
occ:1.00
 NH2 E:ARG277 3.6 63.6 1.0
NE E:ARG277 3.7 63.6 1.0
CB E:ASN279 3.9 65.6 1.0
N E:ASN279 3.9 66.9 1.0
CZ E:ARG277 4.2 63.1 1.0
N E:GLU278 4.2 69.0 1.0
CB E:ARG277 4.3 64.6 1.0
C E:ARG277 4.3 67.0 1.0
CA E:ARG277 4.4 66.3 1.0
CA E:ASN279 4.5 65.8 1.0
CG E:ASN279 4.6 66.7 1.0
CB E:ALA81 4.8 70.3 1.0
ND2 E:ASN279 4.8 66.6 1.0
O E:ARG277 4.8 65.9 1.0
CG E:ARG277 4.8 64.7 1.0
CD E:ARG277 4.9 63.6 1.0
C E:GLU278 5.0 68.8 1.0

Chlorine binding site 2 out of 9 in 5dbj

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Chlorine binding site 2 out of 9 in the Crystal Structure of Halogenase Plta


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 Halogenase Plta within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl503

b:75.3
occ:1.00
 N E:GLY328 2.9 52.1 1.0
N E:SER327 2.9 53.8 1.0
CA E:GLY328 3.6 51.6 1.0
CA E:PRO323 3.6 51.6 1.0
CE1 E:PHE320 3.7 52.0 1.0
C E:SER327 3.7 53.1 1.0
N1 E:FAD501 3.7 40.1 1.0
C E:SER326 3.7 53.4 1.0
C10 E:FAD501 3.8 39.5 1.0
CA E:SER327 3.8 53.9 1.0
CZ E:PHE320 3.8 51.9 1.0
CA E:SER326 3.8 52.9 1.0
N E:SER326 3.8 53.2 1.0
O E:ASP322 4.0 53.0 1.0
N10 E:FAD501 4.0 38.3 1.0
CZ2 E:TRP371 4.1 67.1 1.0
C E:PRO323 4.2 51.8 1.0
C2 E:FAD501 4.2 40.7 1.0
C1' E:FAD501 4.2 36.9 1.0
O E:PRO323 4.2 51.2 1.0
CB E:PRO323 4.3 51.4 1.0
CB E:SER327 4.3 55.0 1.0
C4X E:FAD501 4.3 39.9 1.0
N E:PRO323 4.6 52.5 1.0
C E:ASP322 4.6 52.7 1.0
O2 E:FAD501 4.7 40.6 1.0
N3 E:FAD501 4.7 41.2 1.0
C9A E:FAD501 4.7 38.4 1.0
O E:SER327 4.8 53.7 1.0
NE1 E:TRP371 4.8 67.7 1.0
C4 E:FAD501 4.8 40.8 1.0
C E:PHE325 4.8 53.5 1.0
O E:SER326 4.8 54.0 1.0
CE2 E:TRP371 4.8 67.6 1.0
CD1 E:PHE320 4.9 53.0 1.0
C E:GLY328 5.0 51.0 1.0
N5 E:FAD501 5.0 39.5 1.0

Chlorine binding site 3 out of 9 in 5dbj

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Chlorine binding site 3 out of 9 in the Crystal Structure of Halogenase Plta


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 Halogenase Plta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:70.1
occ:1.00
 N A:GLY328 2.8 56.7 1.0
N A:SER327 3.0 62.0 1.0
CA A:GLY328 3.6 55.9 1.0
CA A:PRO323 3.6 54.0 1.0
N1 A:FAD501 3.7 26.6 1.0
CE1 A:PHE320 3.7 49.8 1.0
C10 A:FAD501 3.7 26.5 1.0
C A:SER327 3.7 58.7 1.0
C A:SER326 3.7 63.1 1.0
CA A:SER326 3.8 64.1 1.0
CA A:SER327 3.8 61.2 1.0
N A:SER326 3.9 65.0 1.0
CZ A:PHE320 3.9 50.0 1.0
O A:ASP322 3.9 52.1 1.0
N10 A:FAD501 4.0 26.9 1.0
C2 A:FAD501 4.1 26.9 1.0
CZ2 A:TRP371 4.1 82.6 1.0
C4X A:FAD501 4.2 26.5 1.0
CB A:PRO323 4.2 53.1 1.0
C1' A:FAD501 4.2 27.6 1.0
N A:PRO323 4.4 53.0 1.0
C A:PRO323 4.4 56.1 1.0
C A:ASP322 4.4 52.3 1.0
CB A:SER327 4.5 62.4 1.0
N3 A:FAD501 4.6 27.0 1.0
C4 A:FAD501 4.6 26.7 1.0
O2 A:FAD501 4.6 26.9 1.0
C9A A:FAD501 4.7 26.5 1.0
O A:PRO323 4.8 55.3 1.0
O A:SER326 4.8 64.7 1.0
O A:SER327 4.8 58.2 1.0
C A:PHE325 4.8 66.4 1.0
N5 A:FAD501 4.9 26.4 1.0
CH2 A:TRP371 4.9 82.3 1.0
CD1 A:PHE320 4.9 50.2 1.0
C A:GLY328 5.0 55.3 1.0

Chlorine binding site 4 out of 9 in 5dbj

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Chlorine binding site 4 out of 9 in the Crystal Structure of Halogenase Plta


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 Halogenase Plta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:99.3
occ:1.00
 NE A:ARG277 3.3 70.3 1.0
NH2 A:ARG277 3.3 71.8 1.0
CZ A:ARG277 3.7 70.6 1.0
ND2 A:ASN279 3.7 78.2 1.0
CB A:ASN279 3.7 75.9 1.0
N A:ASN279 3.8 75.1 1.0
CB A:ARG277 3.9 69.3 1.0
C A:ARG277 4.1 71.5 1.0
CG A:ASN279 4.1 78.0 1.0
N A:GLU278 4.1 73.6 1.0
CA A:ARG277 4.2 70.6 1.0
CA A:ASN279 4.3 75.5 1.0
CD A:ARG277 4.4 68.6 1.0
CG A:ARG277 4.4 68.8 1.0
N A:LEU280 4.5 72.3 1.0
O A:ARG277 4.5 70.8 1.0
CB A:ALA81 4.6 80.2 1.0
C A:GLU278 4.8 75.0 1.0
CA A:GLU278 4.9 75.3 1.0
NH1 A:ARG277 4.9 69.5 1.0
C A:ASN279 5.0 73.8 1.0

Chlorine binding site 5 out of 9 in 5dbj

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Chlorine binding site 5 out of 9 in the Crystal Structure of Halogenase Plta


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 Halogenase Plta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:0.0
occ:1.00
 N B:ASN279 3.5 96.2 1.0
NE B:ARG277 3.7 0.5 1.0
N B:GLU278 3.7 97.3 1.0
CB B:ASN279 3.7 98.0 1.0
NH2 B:ARG277 3.7 0.9 1.0
ND2 B:ASN279 3.7 0.1 1.0
CB B:ARG277 3.9 95.2 1.0
CG B:ASN279 3.9 0.3 1.0
C B:ARG277 4.0 95.2 1.0
CZ B:ARG277 4.1 0.7 1.0
CA B:ARG277 4.1 95.5 1.0
CA B:ASN279 4.1 95.9 1.0
C B:GLU278 4.4 95.9 1.0
CA B:GLU278 4.5 97.3 1.0
N B:LEU280 4.5 90.0 1.0
CG B:ARG277 4.7 95.7 1.0
O B:ARG277 4.7 92.6 1.0
CD B:ARG277 4.7 96.9 1.0
OD1 B:ASN279 4.8 0.1 1.0
C B:ASN279 4.9 92.3 1.0
CB B:GLU278 4.9 0.2 1.0

Chlorine binding site 6 out of 9 in 5dbj

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Chlorine binding site 6 out of 9 in the Crystal Structure of Halogenase Plta


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 Halogenase Plta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:0.2
occ:1.00
 N B:GLY328 2.8 82.4 1.0
N B:SER327 3.0 87.4 1.0
CA B:GLY328 3.6 80.3 1.0
N1 B:FAD501 3.6 31.9 1.0
C10 B:FAD501 3.7 31.8 1.0
CA B:PRO323 3.7 78.5 1.0
C B:SER327 3.7 85.6 1.0
C B:SER326 3.7 88.3 1.0
O B:ASP322 3.7 78.6 1.0
CE1 B:PHE320 3.7 72.3 1.0
CA B:SER326 3.8 87.8 1.0
CZ2 B:TRP371 3.8 0.5 1.0
CA B:SER327 3.8 88.3 1.0
CZ B:PHE320 3.9 71.5 1.0
N10 B:FAD501 3.9 31.9 1.0
N B:SER326 3.9 89.1 1.0
C1' B:FAD501 4.1 32.0 1.0
C2 B:FAD501 4.1 32.4 1.0
CB B:PRO323 4.2 76.2 1.0
C4X B:FAD501 4.3 31.9 1.0
C B:ASP322 4.4 76.7 1.0
CH2 B:TRP371 4.4 0.1 1.0
CB B:SER327 4.5 90.8 1.0
N B:PRO323 4.5 76.7 1.0
C B:PRO323 4.5 81.8 1.0
C9A B:FAD501 4.6 31.9 1.0
O2 B:FAD501 4.6 32.9 1.0
N3 B:FAD501 4.6 32.3 1.0
C4 B:FAD501 4.7 32.2 1.0
O B:SER326 4.8 89.4 1.0
O B:SER327 4.9 86.5 1.0
CE2 B:TRP371 4.9 0.2 1.0
C B:GLY328 4.9 79.8 1.0
N5 B:FAD501 4.9 31.7 1.0
C B:PHE325 4.9 91.5 1.0
CD1 B:PHE320 5.0 72.1 1.0
O B:PRO323 5.0 82.7 1.0

Chlorine binding site 7 out of 9 in 5dbj

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Chlorine binding site 7 out of 9 in the Crystal Structure of Halogenase Plta


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 Halogenase Plta within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl502

b:0.7
occ:1.00
 ND2 C:ASN279 3.4 0.6 1.0
NE C:ARG277 3.5 98.0 1.0
NH2 C:ARG277 3.5 99.2 1.0
N C:ASN279 3.6 0.3 1.0
CB C:ASN279 3.7 1.0 1.0
N C:GLU278 3.8 0.1 1.0
CG C:ASN279 3.9 0.2 1.0
CZ C:ARG277 3.9 97.7 1.0
CB C:ARG277 4.0 98.1 1.0
C C:ARG277 4.1 0.8 1.0
CA C:ARG277 4.2 99.8 1.0
CA C:ASN279 4.3 0.5 1.0
CB C:ALA81 4.5 94.0 1.0
CG C:ARG277 4.5 98.0 1.0
CD C:ARG277 4.6 97.1 1.0
C C:GLU278 4.6 0.3 1.0
CA C:GLU278 4.6 0.9 1.0
N C:LEU280 4.7 0.6 1.0
OD1 C:ASN279 4.9 0.8 1.0
O C:ARG277 4.9 99.6 1.0
CB C:GLU278 5.0 0.5 1.0

Chlorine binding site 8 out of 9 in 5dbj

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Chlorine binding site 8 out of 9 in the Crystal Structure of Halogenase Plta


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 Halogenase Plta within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl503

b:82.6
occ:1.00
 N C:GLY328 2.9 64.4 1.0
N C:SER327 3.0 67.1 1.0
N1 C:FAD501 3.5 36.2 1.0
CE1 C:PHE320 3.6 62.1 1.0
CA C:GLY328 3.6 63.7 1.0
C10 C:FAD501 3.6 36.2 1.0
CA C:PRO323 3.7 65.1 1.0
C C:SER327 3.7 65.3 1.0
C C:SER326 3.7 66.5 1.0
CZ C:PHE320 3.7 62.6 1.0
CA C:SER326 3.7 66.7 1.0
CZ2 C:TRP371 3.8 71.4 1.0
CA C:SER327 3.8 66.4 1.0
N10 C:FAD501 3.9 36.0 1.0
O C:ASP322 3.9 64.2 1.0
N C:SER326 4.0 66.9 1.0
C2 C:FAD501 4.0 36.4 1.0
C1' C:FAD501 4.1 35.5 1.0
CB C:PRO323 4.2 65.0 1.0
C4X C:FAD501 4.2 36.2 1.0
C C:PRO323 4.4 66.4 1.0
CB C:SER327 4.4 67.1 1.0
CH2 C:TRP371 4.5 71.0 1.0
N C:PRO323 4.5 64.8 1.0
C C:ASP322 4.5 64.4 1.0
O2 C:FAD501 4.5 36.9 1.0
N3 C:FAD501 4.5 36.6 1.0
C9A C:FAD501 4.7 36.3 1.0
C4 C:FAD501 4.7 36.4 1.0
O C:PRO323 4.7 66.2 1.0
CE2 C:TRP371 4.7 72.2 1.0
O C:SER327 4.8 65.7 1.0
O C:SER326 4.8 65.8 1.0
CD1 C:PHE320 4.9 62.0 1.0
N5 C:FAD501 4.9 36.6 1.0
NE1 C:TRP371 5.0 72.8 1.0

Chlorine binding site 9 out of 9 in 5dbj

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Chlorine binding site 9 out of 9 in the Crystal Structure of Halogenase Plta


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 Halogenase Plta within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl502

b:0.2
occ:1.00
 NE D:ARG277 3.0 0.1 1.0
NH2 D:ARG277 3.1 0.8 1.0
ND2 D:ASN279 3.4 0.1 1.0
CZ D:ARG277 3.5 0.1 1.0
CB D:ARG277 3.7 0.9 1.0
CB D:ASN279 4.0 97.8 1.0
CD D:ARG277 4.1 0.5 1.0
CG D:ARG277 4.2 0.2 1.0
CA D:ARG277 4.2 0.1 1.0
CG D:ASN279 4.2 99.9 1.0
N D:ASN279 4.3 98.6 1.0
C D:ARG277 4.4 0.7 1.0
N D:GLU278 4.5 0.3 1.0
CA D:ASN279 4.8 97.2 1.0
NH1 D:ARG277 4.8 0.3 1.0
CB D:ALA81 4.9 0.4 1.0

Reference:

A.H.Pang, S.Garneau-Tsodikova, O.V.Tsodikov. Crystal Structure of Halogenase Plta From the Pyoluteorin Biosynthetic Pathway. J.Struct.Biol. V. 192 349 2015.
ISSN: ESSN 1095-8657
PubMed: 26416533
DOI: 10.1016/J.JSB.2015.09.013
Page generated: Sat Dec 12 11:38:16 2020

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