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Chlorine in PDB 1lkd: Crystal Structure of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb)

Enzymatic activity of Crystal Structure of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb)

All present enzymatic activity of Crystal Structure of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb):
1.13.11.39;

Protein crystallography data

The structure of Crystal Structure of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb), PDB code: 1lkd was solved by S.Dai, J.T.Bolin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 1.70
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 122.640, 122.640, 107.232, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 22

Other elements in 1lkd:

The structure of Crystal Structure of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb) also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb) (pdb code 1lkd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb), PDB code: 1lkd:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 1lkd

Go back to Chlorine Binding Sites List in 1lkd
Chlorine binding site 1 out of 4 in the Crystal Structure of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb)


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 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl300

b:12.7
occ:1.00
 CL1 A:BP6300 0.0 12.7 1.0
CB2 A:BP6300 1.7 18.5 1.0
CB3 A:BP6300 2.7 19.6 1.0
CB1 A:BP6300 2.8 16.4 1.0
CA1 A:BP6300 3.2 13.6 1.0
O A:HOH9092 3.4 19.8 1.0
CG2 A:VAL148 3.4 18.8 1.0
CA2 A:BP6300 3.5 15.1 1.0
OA2 A:BP6300 3.5 14.9 1.0
CG1 A:VAL148 3.8 17.1 1.0
CE2 A:PHE187 3.8 13.6 1.0
CZ A:PHE187 3.9 13.0 1.0
CE1 A:HIS210 4.0 14.3 1.0
CB4 A:BP6300 4.0 21.1 1.0
CA6 A:BP6300 4.0 13.6 1.0
CB6 A:BP6300 4.1 17.6 1.0
CE A:MET175 4.2 33.6 1.0
CB A:VAL148 4.2 15.5 1.0
CB A:ALA198 4.3 11.0 1.0
CA3 A:BP6300 4.5 13.6 1.0
CB5 A:BP6300 4.6 19.6 1.0
CE2 A:PHE202 4.7 22.3 1.0
FE A:FE2500 4.8 12.9 1.0
NE2 A:HIS210 4.8 13.9 1.0
ND1 A:HIS210 4.9 12.4 1.0
CA5 A:BP6300 4.9 13.6 1.0
CZ A:PHE202 5.0 23.7 1.0
CD2 A:PHE187 5.0 12.5 1.0

Chlorine binding site 2 out of 4 in 1lkd

Go back to Chlorine Binding Sites List in 1lkd
Chlorine binding site 2 out of 4 in the Crystal Structure of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb)


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 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl300

b:7.7
occ:1.00
 CL2 A:BP6300 0.0 7.7 1.0
CB6 A:BP6300 1.7 17.6 1.0
CB5 A:BP6300 2.7 19.6 1.0
CB1 A:BP6300 2.8 16.4 1.0
O A:HOH9189 2.9 63.5 1.0
CA1 A:BP6300 3.2 13.6 1.0
CE1 A:HIS241 3.3 14.6 1.0
OH A:TYR250 3.5 16.5 1.0
CA6 A:BP6300 3.6 13.6 1.0
CB A:PRO280 3.7 15.9 1.0
CG A:PRO280 3.9 16.0 1.0
ND1 A:HIS241 4.0 13.3 1.0
CB4 A:BP6300 4.0 21.1 1.0
CB2 A:BP6300 4.1 18.5 1.0
CA2 A:BP6300 4.1 15.1 1.0
CZ A:TYR250 4.2 15.3 1.0
C5 A:P6G600 4.2 45.2 1.0
C3 A:P6G600 4.2 43.0 1.0
OG A:SER281 4.4 20.1 1.0
CE1 A:TYR250 4.4 14.3 1.0
NE2 A:HIS241 4.5 13.4 1.0
O7 A:P6G600 4.5 47.4 1.0
OA2 A:BP6300 4.5 14.9 1.0
CB3 A:BP6300 4.6 19.6 1.0
O4 A:P6G600 4.6 43.9 1.0
CA5 A:BP6300 4.7 13.6 1.0
O A:PRO280 4.8 14.0 1.0
ND1 A:HIS285 4.9 13.4 1.0
CA A:PRO280 4.9 13.8 1.0
C A:PRO280 4.9 14.4 1.0
CE A:MET175 4.9 33.6 1.0

Chlorine binding site 3 out of 4 in 1lkd

Go back to Chlorine Binding Sites List in 1lkd
Chlorine binding site 3 out of 4 in the Crystal Structure of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb)


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 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:37.9
occ:1.00
 CL1 A:BP6301 0.0 37.9 1.0
CB2 A:BP6301 1.7 37.7 1.0
CB3 A:BP6301 2.7 37.5 1.0
CB1 A:BP6301 2.8 37.4 1.0
CA1 A:BP6301 3.2 36.9 1.0
CD2 A:LEU204 3.4 25.0 1.0
CA2 A:BP6301 3.5 37.3 1.0
OA2 A:BP6301 3.5 38.0 1.0
CD A:PRO205 3.9 24.2 1.0
CB4 A:BP6301 4.0 38.3 1.0
CA6 A:BP6301 4.0 36.1 1.0
CB6 A:BP6301 4.1 37.1 1.0
CA3 A:BP6301 4.5 37.7 1.0
CB5 A:BP6301 4.6 37.4 1.0
CG A:PRO205 4.7 24.9 1.0
CG A:LEU204 4.7 26.3 1.0
CA A:LEU204 4.7 22.2 1.0
O A:PRO203 4.8 22.5 1.0
CB A:LEU204 4.8 22.4 1.0
CA5 A:BP6301 4.9 36.5 1.0

Chlorine binding site 4 out of 4 in 1lkd

Go back to Chlorine Binding Sites List in 1lkd
Chlorine binding site 4 out of 4 in the Crystal Structure of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb)


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 2,3-Dihydroxybiphenyl 1,2-Dioxygenase (Dhbd) Complexed with 2',6'-Dicl Dihydroxybiphenyl (Dhb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:36.0
occ:1.00
 CL2 A:BP6301 0.0 36.0 1.0
CB6 A:BP6301 1.7 37.1 1.0
CB5 A:BP6301 2.7 37.4 1.0
CB1 A:BP6301 2.8 37.4 1.0
O A:SER255 3.0 22.7 1.0
CA1 A:BP6301 3.3 36.9 1.0
CE A:LYS206 3.3 25.4 1.0
CA A:GLY256 3.3 19.2 1.0
C A:GLY256 3.6 19.7 1.0
CA6 A:BP6301 3.6 36.1 1.0
N A:VAL257 3.8 17.3 1.0
CG A:LYS206 3.9 22.7 1.0
C A:SER255 3.9 20.8 1.0
CB4 A:BP6301 4.0 38.3 1.0
CB2 A:BP6301 4.1 37.7 1.0
N A:GLY256 4.1 18.8 1.0
CA2 A:BP6301 4.1 37.3 1.0
CD A:LYS206 4.1 23.8 1.0
O A:GLY256 4.2 20.6 1.0
NZ A:LYS206 4.3 26.0 1.0
CB3 A:BP6301 4.6 37.5 1.0
OA2 A:BP6301 4.6 38.0 1.0
CA5 A:BP6301 4.7 36.5 1.0
CA A:VAL257 4.8 18.2 1.0

Reference:

S.Dai, F.H.Vaillancourt, H.Maaroufi, N.M.Drouin, D.B.Neau, V.Snieckus, J.T.Bolin, L.D.Eltis. Identification and Analysis of A Bottleneck in Pcb Biodegradation Nat.Struct.Biol. V. 9 934 2002.
ISSN: ISSN 1072-8368
PubMed: 12415290
DOI: 10.1038/NSB866
Page generated: Fri Jul 19 23:53:16 2024

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