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Iron 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:

Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron 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 Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 1lkd

Go back to Iron Binding Sites List in 1lkd
Iron binding site 1 out of 2 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 Iron with other atoms in the Fe 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:Fe500

b:12.9
occ:1.00
 OA2 A:BP6300 2.1 14.9 1.0
OE1 A:GLU260 2.1 14.1 1.0
NE2 A:HIS146 2.3 14.0 1.0
OA3 A:BP6300 2.3 13.5 1.0
NE2 A:HIS210 2.3 13.9 1.0
O A:HOH9092 2.4 19.8 1.0
CA2 A:BP6300 3.0 15.1 1.0
CE1 A:HIS146 3.0 14.1 1.0
CA3 A:BP6300 3.1 13.6 1.0
CE1 A:HIS210 3.1 14.3 1.0
CD A:GLU260 3.2 12.7 1.0
CD2 A:HIS210 3.4 10.9 1.0
CD2 A:HIS146 3.4 13.8 1.0
OE2 A:GLU260 3.8 14.9 1.0
OH A:TYR250 3.8 16.5 1.0
NE2 A:HIS195 4.1 15.8 1.0
O A:HOH9093 4.1 20.7 1.0
ND1 A:HIS146 4.2 12.9 1.0
CA1 A:BP6300 4.3 13.6 1.0
ND1 A:HIS210 4.3 12.4 1.0
CG A:GLU260 4.4 12.3 1.0
CA4 A:BP6300 4.4 12.1 1.0
CG A:HIS146 4.5 14.5 1.0
CB A:GLU260 4.5 11.8 1.0
CE2 A:TYR250 4.5 13.9 1.0
CG2 A:VAL148 4.5 18.8 1.0
CG A:HIS210 4.5 12.6 1.0
CB A:MET212 4.5 13.6 1.0
CZ A:TYR250 4.6 15.3 1.0
NE2 A:HIS241 4.7 13.4 1.0
CG A:MET212 4.7 13.5 1.0
CE1 A:HIS195 4.8 15.8 1.0
CL1 A:BP6300 4.8 12.7 1.0
CB1 A:BP6300 4.9 16.4 1.0

Iron binding site 2 out of 2 in 1lkd

Go back to Iron Binding Sites List in 1lkd
Iron binding site 2 out of 2 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 Iron with other atoms in the Fe 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:Fe501

b:33.2
occ:1.00
 O A:HOH9193 2.3 26.1 1.0
O A:HOH9191 2.3 29.3 1.0
NE2 A:HIS189 2.3 14.8 1.0
O A:HOH9190 2.4 34.7 1.0
O A:HOH9192 2.4 41.9 1.0
O A:HOH9195 2.4 37.9 1.0
CE1 A:HIS189 3.3 17.3 1.0
CD2 A:HIS189 3.3 15.2 1.0
CB A:GLN168 4.0 21.3 1.0
CG A:GLN168 4.1 27.1 1.0
O A:HOH9197 4.2 52.0 1.0
O A:HOH9194 4.3 39.6 1.0
O A:ASP269 4.4 44.6 1.0
ND1 A:HIS189 4.4 15.1 1.0
CG A:HIS189 4.5 13.4 1.0
O A:HOH8027 4.5 25.6 1.0
C A:ASP269 5.0 45.6 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: Wed Jul 16 17:25:45 2025

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