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Iron in PDB 1uli: Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1

Enzymatic activity of Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1

All present enzymatic activity of Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1:
1.14.12.18;

Protein crystallography data

The structure of Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1, PDB code: 1uli 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) 38.07 / 2.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 137.741, 137.741, 237.744, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.1

Iron Binding Sites:

The binding sites of Iron atom in the Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1 (pdb code 1uli). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1, PDB code: 1uli:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 1uli

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Iron binding site 1 out of 10 in the Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1


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) Derived From Rhodococcus Sp. Strain RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe600

b:17.5
occ:1.00
 OD2 A:ASP378 1.8 16.1 1.0
NE2 A:HIS230 2.0 17.8 1.0
NE2 A:HIS224 2.1 17.0 1.0
O A:HOH770 2.3 22.9 1.0
CG A:ASP378 2.7 19.7 1.0
OD1 A:ASP378 2.8 21.8 1.0
CE1 A:HIS230 2.9 17.8 1.0
CD2 A:HIS224 3.0 16.4 1.0
CE1 A:HIS224 3.1 15.9 1.0
CD2 A:HIS230 3.1 18.1 1.0
NE2 A:GLN217 3.3 15.5 1.0
ND1 A:HIS230 4.0 16.7 1.0
CB A:ASP378 4.1 20.1 1.0
CD A:GLN217 4.2 15.6 1.0
CG A:HIS230 4.2 18.9 1.0
ND1 A:HIS224 4.2 15.4 1.0
CG A:HIS224 4.2 15.9 1.0
OE1 A:GLN217 4.6 14.1 1.0
CE1 A:PHE368 4.7 16.4 1.0
CA A:ASP378 4.9 20.1 1.0

Iron binding site 2 out of 10 in 1uli

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Iron binding site 2 out of 10 in the Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1


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) Derived From Rhodococcus Sp. Strain RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:14.7
occ:1.00
 FE1 A:FES500 0.0 14.7 1.0
S1 A:FES500 2.2 19.4 1.0
S2 A:FES500 2.2 16.1 1.0
SG A:CYS118 2.3 20.3 1.0
SG A:CYS98 2.3 15.3 1.0
FE2 A:FES500 2.7 20.3 1.0
CB A:CYS98 3.1 13.5 1.0
CB A:CYS118 3.2 20.1 1.0
CB A:HIS100 4.0 14.0 1.0
CB A:MET103 4.3 13.9 1.0
ND1 A:HIS100 4.3 15.3 1.0
CB A:TYR120 4.5 16.7 1.0
CB A:TRP123 4.5 17.0 1.0
N A:HIS121 4.5 17.1 1.0
CA A:CYS98 4.6 13.3 1.0
ND1 A:HIS121 4.6 19.1 1.0
CG A:HIS100 4.7 14.7 1.0
CA A:CYS118 4.7 20.0 1.0
CG A:TRP123 4.7 16.0 1.0
N A:ARG101 4.8 13.2 1.0
N A:MET103 4.9 13.6 1.0
N A:HIS100 5.0 13.6 1.0

Iron binding site 3 out of 10 in 1uli

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Iron binding site 3 out of 10 in the Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1


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) Derived From Rhodococcus Sp. Strain RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:20.3
occ:1.00
 FE2 A:FES500 0.0 20.3 1.0
ND1 A:HIS100 2.1 15.3 1.0
S1 A:FES500 2.2 19.4 1.0
ND1 A:HIS121 2.2 19.1 1.0
S2 A:FES500 2.2 16.1 1.0
FE1 A:FES500 2.7 14.7 1.0
CG A:HIS100 3.0 14.7 1.0
CE1 A:HIS100 3.1 17.4 1.0
CG A:HIS121 3.1 18.0 1.0
CE1 A:HIS121 3.2 19.7 1.0
CB A:HIS100 3.3 14.0 1.0
CB A:HIS121 3.4 17.1 1.0
N A:HIS121 3.8 17.1 1.0
CA A:HIS121 4.1 17.4 1.0
CB A:TYR120 4.2 16.7 1.0
CD2 A:HIS100 4.2 16.8 1.0
NE2 A:HIS100 4.2 16.8 1.0
N A:ARG101 4.2 13.2 1.0
CD2 A:HIS121 4.2 17.8 1.0
NE2 A:HIS121 4.2 18.9 1.0
SG A:CYS118 4.4 20.3 1.0
SG A:CYS98 4.4 15.3 1.0
CG A:TYR120 4.5 15.6 1.0
CD1 A:TYR120 4.5 14.1 1.0
CA A:HIS100 4.6 13.9 1.0
CB A:ARG101 4.6 13.5 1.0
C A:TYR120 4.6 17.2 1.0
C A:HIS100 4.7 14.0 1.0
C A:HIS121 4.9 17.6 1.0
CD1 A:TRP123 4.9 14.7 1.0
CA A:TYR120 5.0 17.2 1.0
CA A:ARG101 5.0 13.4 1.0
CG A:ARG101 5.0 14.3 1.0

Iron binding site 4 out of 10 in 1uli

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Iron binding site 4 out of 10 in the Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1


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) Derived From Rhodococcus Sp. Strain RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe700

b:17.5
occ:1.00
 NE2 F:HIS24 2.0 19.8 1.0
NE2 B:HIS24 2.0 16.7 1.0
NE2 D:HIS24 2.1 18.0 1.0
O B:HOH743 2.2 15.8 1.0
O B:HOH741 2.2 17.0 1.0
O D:HOH234 2.2 19.9 1.0
CD2 F:HIS24 3.0 17.9 1.0
CD2 B:HIS24 3.0 16.9 1.0
CD2 D:HIS24 3.0 17.7 1.0
CE1 F:HIS24 3.0 20.7 1.0
CE1 B:HIS24 3.1 18.0 1.0
CE1 D:HIS24 3.1 19.6 1.0
CG F:HIS24 4.1 17.7 1.0
ND1 F:HIS24 4.1 19.1 1.0
CG B:HIS24 4.1 16.7 1.0
CG D:HIS24 4.1 17.2 1.0
ND1 B:HIS24 4.1 17.9 1.0
ND1 D:HIS24 4.2 19.4 1.0
O F:HOH231 4.3 15.1 1.0
O D:HOH229 4.4 16.6 1.0
OE2 B:GLU27 4.4 13.9 1.0
OE2 D:GLU27 4.4 14.5 1.0
OE2 F:GLU27 4.4 14.3 1.0
O B:HOH750 4.4 16.6 1.0

Iron binding site 5 out of 10 in 1uli

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Iron binding site 5 out of 10 in the Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1


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) Derived From Rhodococcus Sp. Strain RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe600

b:22.1
occ:1.00
 OD2 C:ASP378 1.8 25.9 1.0
NE2 C:HIS230 2.0 19.9 1.0
O C:HOH755 2.1 21.2 1.0
NE2 C:HIS224 2.1 22.4 1.0
CG C:ASP378 2.6 26.8 1.0
OD1 C:ASP378 2.7 27.9 1.0
CE1 C:HIS230 2.9 21.3 1.0
CD2 C:HIS230 3.0 20.6 1.0
CD2 C:HIS224 3.1 21.3 1.0
CE1 C:HIS224 3.1 22.6 1.0
NE2 C:GLN217 3.2 16.7 1.0
ND1 C:HIS230 4.0 21.3 1.0
CB C:ASP378 4.1 26.6 1.0
CG C:HIS230 4.1 21.6 1.0
ND1 C:HIS224 4.2 21.8 1.0
CD C:GLN217 4.2 16.4 1.0
CG C:HIS224 4.2 20.6 1.0
CE1 C:PHE368 4.6 13.3 1.0
OE1 C:GLN217 4.7 16.5 1.0
CA C:ASP378 4.8 26.6 1.0
O C:HOH690 5.0 26.7 1.0

Iron binding site 6 out of 10 in 1uli

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Iron binding site 6 out of 10 in the Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1


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) Derived From Rhodococcus Sp. Strain RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:13.7
occ:1.00
 FE1 C:FES500 0.0 13.7 1.0
S1 C:FES500 2.2 18.7 1.0
S2 C:FES500 2.2 13.3 1.0
SG C:CYS118 2.3 19.4 1.0
SG C:CYS98 2.3 12.1 1.0
FE2 C:FES500 2.7 18.3 1.0
CB C:CYS98 3.0 12.8 1.0
CB C:CYS118 3.2 18.4 1.0
CB C:HIS100 4.0 15.1 1.0
CB C:MET103 4.2 13.7 1.0
ND1 C:HIS100 4.4 16.4 1.0
CB C:TYR120 4.5 18.1 1.0
CA C:CYS98 4.5 12.5 1.0
N C:HIS121 4.6 17.4 1.0
CB C:TRP123 4.6 16.6 1.0
ND1 C:HIS121 4.6 16.5 1.0
CA C:CYS118 4.7 18.4 1.0
CG C:HIS100 4.7 15.9 1.0
CG C:TRP123 4.8 15.9 1.0
N C:ARG101 4.8 14.8 1.0
N C:MET103 4.9 13.7 1.0
N C:HIS100 4.9 14.2 1.0
C C:CYS98 5.0 13.5 1.0

Iron binding site 7 out of 10 in 1uli

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Iron binding site 7 out of 10 in the Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1


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) Derived From Rhodococcus Sp. Strain RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:18.3
occ:1.00
 FE2 C:FES500 0.0 18.3 1.0
S1 C:FES500 2.2 18.7 1.0
S2 C:FES500 2.2 13.3 1.0
ND1 C:HIS100 2.2 16.4 1.0
ND1 C:HIS121 2.3 16.5 1.0
FE1 C:FES500 2.7 13.7 1.0
CG C:HIS121 3.1 18.4 1.0
CG C:HIS100 3.1 15.9 1.0
CE1 C:HIS121 3.2 17.0 1.0
CE1 C:HIS100 3.2 18.0 1.0
CB C:HIS121 3.3 17.8 1.0
CB C:HIS100 3.4 15.1 1.0
N C:HIS121 3.7 17.4 1.0
CA C:HIS121 4.1 17.8 1.0
CB C:TYR120 4.1 18.1 1.0
CD2 C:HIS121 4.1 18.2 1.0
NE2 C:HIS121 4.2 15.2 1.0
CD2 C:HIS100 4.2 18.2 1.0
NE2 C:HIS100 4.3 17.2 1.0
N C:ARG101 4.3 14.8 1.0
SG C:CYS98 4.4 12.1 1.0
SG C:CYS118 4.4 19.4 1.0
CG C:TYR120 4.4 18.0 1.0
CD1 C:TYR120 4.5 17.2 1.0
C C:TYR120 4.6 17.8 1.0
CB C:ARG101 4.6 15.1 1.0
CA C:HIS100 4.6 14.8 1.0
C C:HIS100 4.8 14.8 1.0
C C:HIS121 4.8 17.8 1.0
CA C:TYR120 4.9 18.2 1.0

Iron binding site 8 out of 10 in 1uli

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Iron binding site 8 out of 10 in the Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1


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) Derived From Rhodococcus Sp. Strain RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe600

b:19.4
occ:1.00
 OD2 E:ASP378 2.0 23.1 1.0
NE2 E:HIS230 2.0 19.8 1.0
NE2 E:HIS224 2.1 23.9 1.0
O E:HOH771 2.3 25.4 1.0
CG E:ASP378 2.7 22.9 1.0
OD1 E:ASP378 2.8 23.3 1.0
CE1 E:HIS230 2.9 20.5 1.0
CD2 E:HIS224 3.1 22.3 1.0
CE1 E:HIS224 3.1 24.0 1.0
CD2 E:HIS230 3.1 20.4 1.0
NE2 E:GLN217 3.2 14.9 1.0
ND1 E:HIS230 4.1 20.2 1.0
CD E:GLN217 4.1 15.6 1.0
ND1 E:HIS224 4.2 22.9 1.0
CB E:ASP378 4.2 22.0 1.0
CG E:HIS224 4.2 21.6 1.0
CG E:HIS230 4.2 21.2 1.0
OE1 E:GLN217 4.5 16.7 1.0
O E:HOH755 4.6 23.4 1.0
CE1 E:PHE368 4.7 13.1 1.0
CA E:ASP378 5.0 22.3 1.0

Iron binding site 9 out of 10 in 1uli

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Iron binding site 9 out of 10 in the Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1


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) Derived From Rhodococcus Sp. Strain RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:10.1
occ:1.00
 FE1 E:FES500 0.0 10.1 1.0
S1 E:FES500 2.2 15.1 1.0
S2 E:FES500 2.2 11.8 1.0
SG E:CYS118 2.3 15.1 1.0
SG E:CYS98 2.3 10.9 1.0
FE2 E:FES500 2.7 14.7 1.0
CB E:CYS98 3.1 10.3 1.0
CB E:CYS118 3.2 15.9 1.0
CB E:HIS100 4.0 10.9 1.0
CB E:MET103 4.2 10.6 1.0
ND1 E:HIS100 4.5 12.7 1.0
CB E:TRP123 4.5 12.1 1.0
CB E:TYR120 4.5 13.9 1.0
CA E:CYS98 4.5 10.4 1.0
ND1 E:HIS121 4.5 12.9 1.0
N E:HIS121 4.6 14.2 1.0
CA E:CYS118 4.6 15.8 1.0
N E:ARG101 4.7 10.7 1.0
CG E:TRP123 4.7 12.0 1.0
CG E:HIS100 4.7 12.7 1.0
N E:MET103 4.8 10.3 1.0
OH E:TYR125 4.9 9.4 1.0
N E:HIS100 5.0 10.6 1.0

Iron binding site 10 out of 10 in 1uli

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Iron binding site 10 out of 10 in the Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Biphenyl Dioxygenase (BPHA1A2) Derived From Rhodococcus Sp. Strain RHA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:14.7
occ:1.00
 FE2 E:FES500 0.0 14.7 1.0
ND1 E:HIS121 2.2 12.9 1.0
S1 E:FES500 2.2 15.1 1.0
ND1 E:HIS100 2.2 12.7 1.0
S2 E:FES500 2.2 11.8 1.0
FE1 E:FES500 2.7 10.1 1.0
CG E:HIS121 3.1 13.3 1.0
CE1 E:HIS121 3.1 12.0 1.0
CG E:HIS100 3.1 12.7 1.0
CE1 E:HIS100 3.2 14.1 1.0
CB E:HIS100 3.3 10.9 1.0
CB E:HIS121 3.4 13.7 1.0
N E:HIS121 3.8 14.2 1.0
CB E:TYR120 4.1 13.9 1.0
CA E:HIS121 4.1 13.6 1.0
CD2 E:HIS121 4.2 13.9 1.0
NE2 E:HIS121 4.2 11.9 1.0
N E:ARG101 4.2 10.7 1.0
CD2 E:HIS100 4.3 12.5 1.0
NE2 E:HIS100 4.3 11.7 1.0
SG E:CYS98 4.4 10.9 1.0
SG E:CYS118 4.4 15.1 1.0
CG E:TYR120 4.5 13.3 1.0
CD1 E:TYR120 4.5 11.8 1.0
CA E:HIS100 4.6 10.8 1.0
C E:TYR120 4.6 14.3 1.0
CB E:ARG101 4.6 10.6 1.0
C E:HIS100 4.7 10.9 1.0
C E:HIS121 4.9 13.3 1.0
CD1 E:TRP123 4.9 11.6 1.0
CA E:TYR120 4.9 14.2 1.0
CA E:ARG101 5.0 10.5 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 15:53:12 2024

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