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Iron in PDB 1ulj: Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate

Enzymatic activity of Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate

All present enzymatic activity of Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate:
1.14.12.18;

Protein crystallography data

The structure of Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate, PDB code: 1ulj was solved by Y.Furusawa, V.Nagarajan, E.Masai, M.Tanokura, M.Fukuda, T.Senda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.76 / 2.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 137.834, 137.834, 237.960, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.4

Iron Binding Sites:

The binding sites of Iron atom in the Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate (pdb code 1ulj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate, PDB code: 1ulj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 1ulj

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Iron binding site 1 out of 9 in the Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:32.7
occ:1.00
 OD2 A:ASP378 1.9 27.1 1.0
NE2 A:HIS224 2.1 31.8 1.0
NE2 A:HIS230 2.2 31.2 1.0
O A:HOH671 2.2 37.9 1.0
CG A:ASP378 2.6 28.8 1.0
OD1 A:ASP378 2.7 27.4 1.0
CE1 A:HIS230 2.9 30.8 1.0
CE1 A:HIS224 3.1 31.0 1.0
CD2 A:HIS224 3.1 30.9 1.0
NE2 A:GLN217 3.2 25.1 1.0
CD2 A:HIS230 3.3 31.4 1.0
CD A:GLN217 3.8 24.0 1.0
OE1 A:GLN217 3.9 25.0 1.0
CB A:ASP378 4.1 29.4 1.0
ND1 A:HIS230 4.1 29.4 1.0
ND1 A:HIS224 4.2 31.1 1.0
CG A:HIS224 4.2 30.7 1.0
C1 A:BNL601 4.3 50.8 1.0
CG A:HIS230 4.3 31.0 1.0
C15 A:BNL601 4.3 49.6 1.0
C14 A:BNL601 4.6 49.6 1.0
C16 A:BNL601 4.8 49.8 1.0
CE1 A:PHE368 4.9 21.0 1.0
CA A:ASP378 5.0 29.7 1.0

Iron binding site 2 out of 9 in 1ulj

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Iron binding site 2 out of 9 in the Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:34.4
occ:1.00
 FE1 A:FES500 0.0 34.4 1.0
S1 A:FES500 2.2 31.9 1.0
S2 A:FES500 2.2 35.5 1.0
SG A:CYS118 2.3 31.6 1.0
SG A:CYS98 2.3 28.1 1.0
FE2 A:FES500 2.8 33.4 1.0
CB A:CYS98 3.1 26.2 1.0
CB A:CYS118 3.2 32.8 1.0
CB A:HIS100 4.1 27.0 1.0
CB A:MET103 4.3 26.3 1.0
CB A:TYR120 4.5 33.8 1.0
N A:HIS121 4.5 34.6 1.0
CB A:TRP123 4.6 32.2 1.0
CA A:CYS98 4.6 26.0 1.0
CA A:CYS118 4.6 32.6 1.0
ND1 A:HIS121 4.7 39.6 1.0
ND1 A:HIS100 4.7 28.8 1.0
CG A:TRP123 4.7 30.7 1.0
N A:ARG101 4.8 27.9 1.0
N A:MET103 4.9 26.2 1.0
CG A:HIS100 4.9 27.8 1.0
N A:TRP123 5.0 32.4 1.0

Iron binding site 3 out of 9 in 1ulj

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Iron binding site 3 out of 9 in the Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:33.4
occ:1.00
 FE2 A:FES500 0.0 33.4 1.0
ND1 A:HIS121 2.1 39.6 1.0
S1 A:FES500 2.2 31.9 1.0
S2 A:FES500 2.2 35.5 1.0
ND1 A:HIS100 2.4 28.8 1.0
FE1 A:FES500 2.8 34.4 1.0
CG A:HIS100 3.1 27.8 1.0
CE1 A:HIS121 3.1 39.4 1.0
CG A:HIS121 3.1 37.0 1.0
CB A:HIS100 3.2 27.0 1.0
CE1 A:HIS100 3.4 28.7 1.0
CB A:HIS121 3.4 34.8 1.0
N A:HIS121 3.9 34.6 1.0
N A:ARG101 4.0 27.9 1.0
CB A:ARG101 4.2 28.5 1.0
NE2 A:HIS121 4.2 38.3 1.0
CD2 A:HIS100 4.2 28.0 1.0
CB A:TYR120 4.2 33.8 1.0
CD2 A:HIS121 4.2 37.9 1.0
CA A:HIS121 4.2 34.6 1.0
CD1 A:TYR120 4.3 32.4 1.0
SG A:CYS98 4.3 28.1 1.0
NE2 A:HIS100 4.3 28.6 1.0
CG A:TYR120 4.5 32.8 1.0
CA A:HIS100 4.5 27.2 1.0
SG A:CYS118 4.5 31.6 1.0
C A:HIS100 4.6 27.5 1.0
CA A:ARG101 4.6 28.1 1.0
C A:TYR120 4.7 34.5 1.0

Iron binding site 4 out of 9 in 1ulj

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Iron binding site 4 out of 9 in the Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe600

b:50.1
occ:1.00
 OD2 C:ASP378 2.0 32.5 1.0
NE2 C:HIS230 2.1 39.6 1.0
NE2 C:HIS224 2.3 39.4 1.0
OD1 C:ASP378 2.5 34.5 1.0
CG C:ASP378 2.7 33.9 1.0
CE1 C:HIS230 2.9 40.3 1.0
CD2 C:HIS230 3.2 40.8 1.0
CD2 C:HIS224 3.2 40.1 1.0
NE2 C:GLN217 3.2 30.6 1.0
CE1 C:HIS224 3.3 39.5 1.0
C3 C:BNL1001 3.8 63.7 1.0
CD C:GLN217 4.0 31.4 1.0
C17 C:BNL1001 4.0 65.7 1.0
ND1 C:HIS230 4.1 40.2 1.0
CB C:ASP378 4.2 33.8 1.0
C4 C:BNL1001 4.2 63.2 1.0
OE1 C:GLN217 4.2 31.6 1.0
CG C:HIS230 4.2 41.2 1.0
ND1 C:HIS224 4.3 39.9 1.0
CG C:HIS224 4.3 40.3 1.0
C2 C:BNL1001 4.5 64.1 1.0
CE1 C:PHE368 4.8 27.1 1.0
C16 C:BNL1001 4.8 65.3 1.0
C12 C:BNL1001 4.9 65.9 1.0

Iron binding site 5 out of 9 in 1ulj

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Iron binding site 5 out of 9 in the Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:31.1
occ:1.00
 FE1 C:FES500 0.0 31.1 1.0
S2 C:FES500 2.2 28.7 1.0
S1 C:FES500 2.2 31.5 1.0
SG C:CYS98 2.3 26.0 1.0
SG C:CYS118 2.4 32.2 1.0
FE2 C:FES500 2.7 32.8 1.0
CB C:CYS98 3.1 23.7 1.0
CB C:CYS118 3.4 30.9 1.0
CB C:HIS100 4.1 26.9 1.0
CB C:MET103 4.3 26.4 1.0
CB C:TYR120 4.4 32.8 1.0
ND1 C:HIS121 4.5 33.0 1.0
N C:HIS121 4.5 33.3 1.0
CA C:CYS98 4.6 23.6 1.0
CB C:TRP123 4.6 30.6 1.0
ND1 C:HIS100 4.7 28.7 1.0
CA C:CYS118 4.8 31.0 1.0
N C:ARG101 4.8 27.0 1.0
CG C:TRP123 4.8 29.7 1.0
N C:MET103 4.9 25.9 1.0
CG C:HIS100 4.9 27.1 1.0
C C:CYS98 5.0 24.3 1.0

Iron binding site 6 out of 9 in 1ulj

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Iron binding site 6 out of 9 in the Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:32.8
occ:1.00
 FE2 C:FES500 0.0 32.8 1.0
ND1 C:HIS121 2.0 33.0 1.0
S1 C:FES500 2.2 31.5 1.0
S2 C:FES500 2.2 28.7 1.0
ND1 C:HIS100 2.3 28.7 1.0
FE1 C:FES500 2.7 31.1 1.0
CE1 C:HIS121 2.9 33.0 1.0
CG C:HIS121 3.1 33.4 1.0
CG C:HIS100 3.1 27.1 1.0
CB C:HIS100 3.2 26.9 1.0
CE1 C:HIS100 3.4 29.0 1.0
CB C:HIS121 3.5 33.3 1.0
N C:HIS121 3.8 33.3 1.0
NE2 C:HIS121 4.1 32.7 1.0
CB C:TYR120 4.1 32.8 1.0
CD2 C:HIS121 4.2 33.2 1.0
N C:ARG101 4.2 27.0 1.0
CA C:HIS121 4.2 33.2 1.0
CD2 C:HIS100 4.3 27.9 1.0
NE2 C:HIS100 4.4 28.4 1.0
SG C:CYS98 4.4 26.0 1.0
CG C:TYR120 4.4 32.4 1.0
CB C:ARG101 4.5 27.0 1.0
CA C:HIS100 4.5 26.5 1.0
CD1 C:TYR120 4.5 32.1 1.0
C C:TYR120 4.7 33.2 1.0
C C:HIS100 4.7 26.5 1.0
SG C:CYS118 4.7 32.2 1.0
CA C:ARG101 4.9 26.9 1.0
C C:HIS121 4.9 33.4 1.0
CA C:TYR120 5.0 32.8 1.0

Iron binding site 7 out of 9 in 1ulj

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Iron binding site 7 out of 9 in the Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe600

b:33.8
occ:1.00
 NE2 E:HIS224 2.0 39.1 1.0
OD2 E:ASP378 2.1 31.6 1.0
NE2 E:HIS230 2.2 43.3 1.0
OD1 E:ASP378 2.5 35.0 1.0
CG E:ASP378 2.6 31.8 1.0
CE1 E:HIS224 2.9 38.4 1.0
CE1 E:HIS230 2.9 42.7 1.0
CD2 E:HIS224 3.1 38.9 1.0
NE2 E:GLN217 3.3 28.2 1.0
CD2 E:HIS230 3.3 43.9 1.0
OE1 E:GLN217 3.6 31.5 1.0
CD E:GLN217 3.7 29.7 1.0
ND1 E:HIS224 4.0 38.4 1.0
CB E:ASP378 4.1 31.5 1.0
ND1 E:HIS230 4.1 42.6 1.0
C17 E:BNL2001 4.2 43.9 1.0
CG E:HIS224 4.2 38.9 1.0
CG E:HIS230 4.3 42.4 1.0
C3 E:BNL2001 4.4 47.7 1.0
C12 E:BNL2001 4.5 41.8 1.0
C16 E:BNL2001 4.8 44.7 1.0
CG E:GLN217 4.9 28.7 1.0
CA E:ASP378 5.0 31.7 1.0
CE1 E:PHE368 5.0 26.1 1.0

Iron binding site 8 out of 9 in 1ulj

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Iron binding site 8 out of 9 in the Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:26.7
occ:1.00
 FE1 E:FES500 0.0 26.7 1.0
S1 E:FES500 2.2 23.6 1.0
S2 E:FES500 2.2 22.0 1.0
SG E:CYS118 2.3 22.5 1.0
SG E:CYS98 2.4 21.9 1.0
FE2 E:FES500 2.8 24.5 1.0
CB E:CYS98 3.1 21.4 1.0
CB E:CYS118 3.3 25.6 1.0
CB E:HIS100 4.0 22.6 1.0
CB E:MET103 4.3 23.4 1.0
ND1 E:HIS121 4.5 24.1 1.0
CB E:TYR120 4.5 25.5 1.0
CB E:TRP123 4.5 26.1 1.0
CA E:CYS98 4.5 21.3 1.0
ND1 E:HIS100 4.5 23.7 1.0
N E:HIS121 4.6 25.9 1.0
CA E:CYS118 4.7 25.7 1.0
N E:ARG101 4.7 22.4 1.0
CG E:TRP123 4.8 26.0 1.0
CG E:HIS100 4.8 23.4 1.0
N E:MET103 4.9 23.3 1.0
N E:HIS100 4.9 22.4 1.0
C E:CYS98 5.0 21.6 1.0

Iron binding site 9 out of 9 in 1ulj

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Iron binding site 9 out of 9 in the Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Biphenyl Dioxygenase (BPHA1A2) in Complex with the Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:24.5
occ:1.00
 FE2 E:FES500 0.0 24.5 1.0
ND1 E:HIS100 2.2 23.7 1.0
ND1 E:HIS121 2.2 24.1 1.0
S1 E:FES500 2.2 23.6 1.0
S2 E:FES500 2.2 22.0 1.0
FE1 E:FES500 2.8 26.7 1.0
CG E:HIS121 3.0 25.7 1.0
CG E:HIS100 3.0 23.4 1.0
CE1 E:HIS121 3.1 25.3 1.0
CE1 E:HIS100 3.2 24.3 1.0
CB E:HIS100 3.2 22.6 1.0
CB E:HIS121 3.4 25.9 1.0
N E:HIS121 3.8 25.9 1.0
CD2 E:HIS121 4.0 25.2 1.0
NE2 E:HIS121 4.0 24.3 1.0
N E:ARG101 4.1 22.4 1.0
CA E:HIS121 4.1 26.1 1.0
CB E:TYR120 4.2 25.5 1.0
CD2 E:HIS100 4.2 24.0 1.0
NE2 E:HIS100 4.3 22.8 1.0
CB E:ARG101 4.3 22.9 1.0
CG E:TYR120 4.5 26.2 1.0
CD1 E:TYR120 4.5 25.9 1.0
CA E:HIS100 4.5 22.4 1.0
SG E:CYS118 4.5 22.5 1.0
SG E:CYS98 4.6 21.9 1.0
C E:TYR120 4.6 25.6 1.0
C E:HIS100 4.6 22.4 1.0
CA E:ARG101 4.8 22.6 1.0
C E:HIS121 4.9 26.3 1.0
CA E:TYR120 5.0 25.5 1.0

Reference:

Y.Furusawa, V.Nagarajan, M.Tanokura, E.Masai, M.Fukuda, T.Senda. Crystal Structure of the Terminal Oxygenase Component of Biphenyl Dioxygenase Derived From Rhodococcus Sp. Strain RHA1 J.Mol.Biol. V. 342 1041 2004.
ISSN: ISSN 0022-2836
PubMed: 15342255
DOI: 10.1016/J.JMB.2004.07.062
Page generated: Sat Aug 3 15:53:28 2024

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