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Iron in PDB 3gzx: Crystal Structure of the Biphenyl Dioxygenase in Complex with Biphenyl From Comamonas Testosteroni Sp. Strain B-356

Enzymatic activity of Crystal Structure of the Biphenyl Dioxygenase in Complex with Biphenyl From Comamonas Testosteroni Sp. Strain B-356

All present enzymatic activity of Crystal Structure of the Biphenyl Dioxygenase in Complex with Biphenyl From Comamonas Testosteroni Sp. Strain B-356:
1.14.12.18;

Protein crystallography data

The structure of Crystal Structure of the Biphenyl Dioxygenase in Complex with Biphenyl From Comamonas Testosteroni Sp. Strain B-356, PDB code: 3gzx was solved by P.Kumar, C.L.Colbert, J.T.Bolin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.18 / 1.58
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.355, 136.355, 107.155, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 21.8

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Biphenyl Dioxygenase in Complex with Biphenyl From Comamonas Testosteroni Sp. Strain B-356 (pdb code 3gzx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of the Biphenyl Dioxygenase in Complex with Biphenyl From Comamonas Testosteroni Sp. Strain B-356, PDB code: 3gzx:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 3gzx

Go back to Iron Binding Sites List in 3gzx
Iron binding site 1 out of 3 in the Crystal Structure of the Biphenyl Dioxygenase in Complex with Biphenyl From Comamonas Testosteroni Sp. Strain B-356


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 the Biphenyl Dioxygenase in Complex with Biphenyl From Comamonas Testosteroni Sp. Strain B-356 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:26.8
occ:1.00
 O A:HOH458 1.9 49.8 1.0
NE2 A:HIS233 2.1 22.8 1.0
NE2 A:HIS239 2.1 23.2 1.0
OD1 A:ASP386 2.2 27.2 1.0
OD2 A:ASP386 2.5 27.3 1.0
CG A:ASP386 2.7 26.7 1.0
CE1 A:HIS239 3.0 23.3 1.0
CD2 A:HIS233 3.0 22.9 1.0
CE1 A:HIS233 3.1 22.9 1.0
CD2 A:HIS239 3.2 23.2 1.0
OE1 A:GLN226 3.4 23.2 1.0
CD A:GLN226 3.8 22.6 1.0
NE2 A:GLN226 3.9 22.7 1.0
C17 A:BNL702 4.0 33.7 1.0
C12 A:BNL702 4.0 33.5 1.0
CB A:ASP386 4.2 26.2 1.0
ND1 A:HIS239 4.2 23.3 1.0
CG A:HIS233 4.2 22.7 1.0
ND1 A:HIS233 4.2 22.7 1.0
CG A:HIS239 4.3 23.2 1.0
O A:HOH859 4.4 31.0 1.0
C16 A:BNL702 4.6 33.7 1.0
C13 A:BNL702 4.6 33.7 1.0
CE1 A:PHE376 4.7 21.0 1.0
C1 A:BNL702 4.8 33.9 1.0
CA A:ASP386 5.0 26.1 1.0

Iron binding site 2 out of 3 in 3gzx

Go back to Iron Binding Sites List in 3gzx
Iron binding site 2 out of 3 in the Crystal Structure of the Biphenyl Dioxygenase in Complex with Biphenyl From Comamonas Testosteroni Sp. Strain B-356


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 the Biphenyl Dioxygenase in Complex with Biphenyl From Comamonas Testosteroni Sp. Strain B-356 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe700

b:17.4
occ:1.00
 FE1 A:FES700 0.0 17.4 1.0
S1 A:FES700 2.2 18.9 1.0
S2 A:FES700 2.2 18.2 1.0
SG A:CYS120 2.2 22.7 1.0
SG A:CYS100 2.3 20.0 1.0
FE2 A:FES700 2.9 17.3 1.0
CB A:CYS100 3.1 20.1 1.0
CB A:CYS120 3.1 23.0 1.0
CB A:HIS102 4.2 20.5 1.0
CB A:MET105 4.2 22.7 1.0
CB A:TYR122 4.4 21.9 1.0
CB A:TRP125 4.5 21.4 1.0
CA A:CYS100 4.6 20.1 1.0
CA A:CYS120 4.6 23.0 1.0
N A:HIS123 4.6 21.7 1.0
ND1 A:HIS102 4.6 20.2 1.0
ND1 A:HIS123 4.7 21.3 1.0
N A:ARG103 4.8 20.8 1.0
N A:MET105 4.9 22.5 1.0
CG A:TRP125 4.9 21.2 1.0
CG A:HIS102 4.9 20.4 1.0
CG A:MET105 4.9 22.4 0.5

Iron binding site 3 out of 3 in 3gzx

Go back to Iron Binding Sites List in 3gzx
Iron binding site 3 out of 3 in the Crystal Structure of the Biphenyl Dioxygenase in Complex with Biphenyl From Comamonas Testosteroni Sp. Strain B-356


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Biphenyl Dioxygenase in Complex with Biphenyl From Comamonas Testosteroni Sp. Strain B-356 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe700

b:17.3
occ:1.00
 FE2 A:FES700 0.0 17.3 1.0
ND1 A:HIS102 2.1 20.2 1.0
ND1 A:HIS123 2.1 21.3 1.0
S1 A:FES700 2.2 18.9 1.0
S2 A:FES700 2.2 18.2 1.0
FE1 A:FES700 2.9 17.4 1.0
CG A:HIS123 3.0 21.4 1.0
CG A:HIS102 3.1 20.4 1.0
CE1 A:HIS123 3.1 21.3 1.0
CE1 A:HIS102 3.1 20.2 1.0
CB A:HIS123 3.3 21.5 1.0
CB A:HIS102 3.4 20.5 1.0
N A:HIS123 3.9 21.7 1.0
CB A:TYR122 4.1 21.9 1.0
CD2 A:HIS123 4.1 21.3 1.0
NE2 A:HIS123 4.1 21.2 1.0
NE2 A:HIS102 4.2 20.3 1.0
CD2 A:HIS102 4.2 20.4 1.0
CA A:HIS123 4.2 21.6 1.0
N A:ARG103 4.3 20.8 1.0
CG A:TYR122 4.4 21.8 1.0
CB A:ARG103 4.5 21.0 1.0
SG A:CYS100 4.5 20.0 1.0
CD1 A:TYR122 4.5 21.7 1.0
CA A:HIS102 4.6 20.5 1.0
SG A:CYS120 4.6 22.7 1.0
C A:TYR122 4.7 21.9 1.0
CG A:ARG103 4.7 20.9 1.0
C A:HIS102 4.8 20.6 1.0
CA A:TYR122 5.0 22.0 1.0

Reference:

C.L.Colbert, N.Y.Agar, P.Kumar, M.N.Chakko, S.C.Sinha, J.B.Powlowski, L.D.Eltis, J.T.Bolin. Structural Characterization of Pandoraea Pnomenusa B-356 Biphenyl Dioxygenase Reveals Features of Potent Polychlorinated Biphenyl-Degrading Enzymes Plos One V. 8 52550 2013.
ISSN: ESSN 1932-6203
PubMed: 23308114
DOI: 10.1371/JOURNAL.PONE.0052550
Page generated: Tue Aug 5 01:42:10 2025

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