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Iron in PDB 2gbx: Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl

Protein crystallography data

The structure of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl, PDB code: 2gbx was solved by D.J.Ferraro, E.N.Brown, C.Yu, R.E.Parales, D.T.Gibson, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.48 / 2.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.940, 133.940, 219.708, 90.00, 90.00, 120.00
R / Rfree (%) 23.7 / 26.8

Other elements in 2gbx:

The structure of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl also contains other interesting chemical elements:

Zinc (Zn) 9 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl (pdb code 2gbx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl, PDB code: 2gbx:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 2gbx

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Iron binding site 1 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


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 Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe456

b:31.6
occ:1.00
 O A:HOH463 2.0 45.6 1.0
NE2 A:HIS212 2.1 44.3 1.0
NE2 A:HIS207 2.3 40.6 1.0
OD2 A:ASP360 2.4 34.4 1.0
OD1 A:ASP360 3.0 34.4 1.0
CE1 A:HIS207 3.1 40.6 1.0
CE1 A:HIS212 3.1 44.3 1.0
CG A:ASP360 3.1 34.4 1.0
CD2 A:HIS212 3.1 44.3 1.0
CD2 A:HIS207 3.5 40.6 1.0
ND2 A:ASN200 4.0 35.7 1.0
ND1 A:HIS212 4.2 44.3 1.0
CG A:HIS212 4.2 44.3 1.0
ND1 A:HIS207 4.3 40.6 1.0
C6 A:BNL457 4.3 58.5 1.0
C1 A:BNL457 4.4 58.5 1.0
CE1 A:PHE350 4.4 32.1 1.0
CG A:HIS207 4.5 40.6 1.0
CB A:ASP360 4.5 34.4 1.0
OD1 A:ASN200 4.8 35.8 1.0
CZ A:PHE350 4.8 32.1 1.0
CG A:ASN200 4.9 35.7 1.0

Iron binding site 2 out of 9 in 2gbx

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Iron binding site 2 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


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 Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe455

b:16.1
occ:1.00
 FE1 A:FES455 0.0 16.1 1.0
ND1 A:HIS103 2.2 24.4 1.0
S1 A:FES455 2.2 16.0 1.0
S2 A:FES455 2.2 16.0 1.0
ND1 A:HIS82 2.2 24.1 1.0
CE1 A:HIS103 3.0 24.4 1.0
FE2 A:FES455 3.1 16.1 1.0
CG A:HIS82 3.1 24.2 1.0
CG A:HIS103 3.2 24.4 1.0
CE1 A:HIS82 3.3 24.1 1.0
CB A:HIS82 3.3 24.2 1.0
CB A:HIS103 3.6 24.4 1.0
CB A:TYR102 4.0 24.3 1.0
N A:HIS103 4.1 24.4 1.0
NE2 A:HIS103 4.1 24.4 1.0
CG A:ARG83 4.1 24.1 1.0
N A:ARG83 4.2 24.1 1.0
CD2 A:HIS103 4.2 24.4 1.0
CD2 A:HIS82 4.3 24.1 1.0
CG A:TYR102 4.3 24.3 1.0
NE2 A:HIS82 4.3 24.1 1.0
SG A:CYS80 4.4 24.3 1.0
CB A:ARG83 4.4 24.1 1.0
CA A:HIS103 4.5 24.4 1.0
CD2 A:TYR102 4.5 24.3 1.0
CA A:HIS82 4.6 24.2 1.0
SG A:CYS100 4.7 24.2 1.0
C A:HIS82 4.8 24.1 1.0
CD1 A:TRP105 4.8 24.6 1.0
C A:TYR102 4.9 24.4 1.0
NE1 A:TRP105 5.0 24.6 1.0
CA A:ARG83 5.0 24.1 1.0

Iron binding site 3 out of 9 in 2gbx

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Iron binding site 3 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


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 Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe455

b:16.1
occ:1.00
 FE2 A:FES455 0.0 16.1 1.0
S1 A:FES455 2.2 16.0 1.0
S2 A:FES455 2.2 16.0 1.0
SG A:CYS100 2.3 24.2 1.0
SG A:CYS80 2.3 24.3 1.0
CB A:CYS80 2.9 24.3 1.0
CB A:CYS100 3.0 24.2 1.0
FE1 A:FES455 3.1 16.1 1.0
CB A:HIS82 4.2 24.2 1.0
CB A:ASN85 4.3 24.1 1.0
CA A:CYS80 4.4 24.3 1.0
CB A:TYR102 4.5 24.3 1.0
CA A:CYS100 4.5 24.2 1.0
CB A:TRP105 4.6 24.6 1.0
O A:ASN85 4.8 24.1 1.0
ND1 A:HIS103 4.8 24.4 1.0
ND1 A:HIS82 4.9 24.1 1.0
N A:ARG83 4.9 24.1 1.0
CG A:TRP105 4.9 24.6 1.0
CE2 A:PHE107 4.9 24.9 1.0
N A:ASN85 4.9 24.1 1.0
N A:HIS103 5.0 24.4 1.0

Iron binding site 4 out of 9 in 2gbx

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Iron binding site 4 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe456

b:33.4
occ:1.00
 O C:HOH460 2.0 59.2 1.0
NE2 C:HIS212 2.1 47.0 1.0
NE2 C:HIS207 2.4 43.6 1.0
OD2 C:ASP360 2.4 37.7 1.0
CE1 C:HIS212 3.1 47.0 1.0
OD1 C:ASP360 3.1 37.7 1.0
CE1 C:HIS207 3.1 43.6 1.0
CG C:ASP360 3.1 37.7 1.0
CD2 C:HIS212 3.2 47.0 1.0
CD2 C:HIS207 3.6 43.6 1.0
OD1 C:ASN200 4.1 40.3 1.0
ND1 C:HIS212 4.2 47.0 1.0
CG C:HIS212 4.3 47.0 1.0
ND1 C:HIS207 4.3 43.6 1.0
C6 C:BNL458 4.3 60.2 1.0
C1 C:BNL458 4.4 60.2 1.0
CE1 C:PHE350 4.4 38.3 1.0
CB C:ASP360 4.5 37.7 1.0
CG C:HIS207 4.6 43.6 1.0
CZ C:PHE350 4.7 38.3 1.0

Iron binding site 5 out of 9 in 2gbx

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Iron binding site 5 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe455

b:30.6
occ:1.00
 FE1 C:FES455 0.0 30.6 1.0
ND1 C:HIS103 2.2 41.0 1.0
S2 C:FES455 2.2 30.6 1.0
S1 C:FES455 2.2 30.6 1.0
ND1 C:HIS82 2.3 38.6 1.0
CE1 C:HIS103 3.0 41.0 1.0
FE2 C:FES455 3.1 30.6 1.0
CG C:HIS82 3.1 38.6 1.0
CB C:HIS82 3.2 38.6 1.0
CG C:HIS103 3.3 41.0 1.0
CE1 C:HIS82 3.4 38.6 1.0
CB C:HIS103 3.7 41.0 1.0
CB C:TYR102 4.1 40.8 1.0
N C:HIS103 4.1 41.0 1.0
NE2 C:HIS103 4.1 41.0 1.0
CG C:ARG83 4.2 38.7 1.0
SG C:CYS80 4.2 38.7 1.0
N C:ARG83 4.3 38.7 1.0
CD2 C:HIS103 4.3 41.0 1.0
CD2 C:HIS82 4.3 38.6 1.0
NE2 C:HIS82 4.4 38.6 1.0
CG C:TYR102 4.5 40.8 1.0
CA C:HIS82 4.5 38.7 1.0
CA C:HIS103 4.5 41.0 1.0
CB C:ARG83 4.6 38.7 1.0
CD1 C:TRP105 4.7 41.5 1.0
C C:HIS82 4.8 38.7 1.0
CG C:TRP105 4.8 41.5 1.0
NE1 C:TRP105 4.8 41.5 1.0
CD2 C:TYR102 4.9 40.8 1.0
SG C:CYS100 4.9 40.3 1.0

Iron binding site 6 out of 9 in 2gbx

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Iron binding site 6 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe455

b:30.6
occ:1.00
 FE2 C:FES455 0.0 30.6 1.0
SG C:CYS100 2.1 40.3 1.0
S1 C:FES455 2.2 30.6 1.0
S2 C:FES455 2.2 30.6 1.0
SG C:CYS80 2.6 38.7 1.0
CB C:CYS80 3.0 38.7 1.0
CB C:CYS100 3.0 40.4 1.0
FE1 C:FES455 3.1 30.6 1.0
CB C:TYR102 4.1 40.8 1.0
CB C:ASN85 4.2 38.8 1.0
CA C:CYS100 4.4 40.4 1.0
CA C:CYS80 4.5 38.7 1.0
CB C:HIS82 4.6 38.6 1.0
CB C:TRP105 4.6 41.5 1.0
ND1 C:HIS103 4.7 41.0 1.0
N C:HIS103 4.7 41.0 1.0
N C:TYR102 4.7 40.7 1.0
O C:ASN85 4.8 38.8 1.0
C C:CYS100 4.8 40.4 1.0
N C:ASN85 4.9 38.7 1.0
CA C:TYR102 5.0 40.8 1.0
CG C:TRP105 5.0 41.5 1.0

Iron binding site 7 out of 9 in 2gbx

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Iron binding site 7 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe456

b:20.4
occ:1.00
 O E:HOH494 2.0 5.6 1.0
NE2 E:HIS212 2.1 33.8 1.0
OD2 E:ASP360 2.3 27.9 1.0
NE2 E:HIS207 2.3 30.6 1.0
CE1 E:HIS207 3.0 30.6 1.0
CE1 E:HIS212 3.0 33.8 1.0
CG E:ASP360 3.0 27.9 1.0
OD1 E:ASP360 3.1 27.9 1.0
CD2 E:HIS212 3.2 33.8 1.0
CD2 E:HIS207 3.5 30.6 1.0
OD1 E:ASN200 4.0 27.4 1.0
ND1 E:HIS212 4.2 33.8 1.0
ND1 E:HIS207 4.3 30.6 1.0
CG E:HIS212 4.3 33.8 1.0
CE1 E:PHE350 4.5 27.6 1.0
CB E:ASP360 4.5 27.9 1.0
CG E:HIS207 4.5 30.6 1.0
C1 E:BNL459 4.7 29.3 1.0
C6 E:BNL459 4.7 29.3 1.0
CG E:ASN200 4.9 27.4 1.0

Iron binding site 8 out of 9 in 2gbx

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Iron binding site 8 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe455

b:18.4
occ:1.00
 FE1 E:FES455 0.0 18.4 1.0
ND1 E:HIS103 2.1 27.8 1.0
S2 E:FES455 2.2 18.4 1.0
S1 E:FES455 2.2 18.4 1.0
ND1 E:HIS82 2.2 27.2 1.0
CE1 E:HIS103 3.0 27.8 1.0
FE2 E:FES455 3.1 18.4 1.0
CG E:HIS82 3.1 27.2 1.0
CG E:HIS103 3.1 27.8 1.0
CE1 E:HIS82 3.2 27.2 1.0
CB E:HIS82 3.3 27.2 1.0
CB E:HIS103 3.5 27.8 1.0
CB E:TYR102 4.0 27.7 1.0
N E:HIS103 4.0 27.8 1.0
NE2 E:HIS103 4.1 27.8 1.0
CG E:ARG83 4.1 27.2 1.0
CD2 E:HIS103 4.2 27.8 1.0
CD2 E:HIS82 4.3 27.2 1.0
CG E:TYR102 4.3 27.7 1.0
N E:ARG83 4.3 27.2 1.0
NE2 E:HIS82 4.3 27.2 1.0
CA E:HIS103 4.4 27.8 1.0
CD2 E:TYR102 4.4 27.7 1.0
SG E:CYS80 4.5 27.2 1.0
CB E:ARG83 4.6 27.2 1.0
CA E:HIS82 4.6 27.2 1.0
SG E:CYS100 4.8 27.6 1.0
CD1 E:TRP105 4.8 28.0 1.0
C E:HIS82 4.8 27.2 1.0
C E:TYR102 4.9 27.8 1.0
NE1 E:TRP105 4.9 28.0 1.0
CD1 E:TYR102 5.0 27.7 1.0

Iron binding site 9 out of 9 in 2gbx

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Iron binding site 9 out of 9 in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 Bound to Biphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe455

b:18.4
occ:1.00
 FE2 E:FES455 0.0 18.4 1.0
SG E:CYS100 2.1 27.6 1.0
S2 E:FES455 2.2 18.4 1.0
S1 E:FES455 2.2 18.4 1.0
SG E:CYS80 2.7 27.2 1.0
CB E:CYS80 3.0 27.2 1.0
CB E:CYS100 3.0 27.6 1.0
FE1 E:FES455 3.1 18.4 1.0
CB E:ASN85 4.0 27.2 1.0
CB E:TYR102 4.1 27.7 1.0
CB E:HIS82 4.3 27.2 1.0
CA E:CYS100 4.4 27.6 1.0
CA E:CYS80 4.5 27.2 1.0
O E:ASN85 4.5 27.2 1.0
N E:HIS103 4.8 27.8 1.0
ND1 E:HIS103 4.8 27.8 1.0
C E:CYS100 4.8 27.6 1.0
N E:TYR102 4.8 27.7 1.0
ND2 E:ASN85 4.8 27.2 1.0
CB E:TRP105 4.8 28.0 1.0
N E:ASN85 4.8 27.2 1.0
CG E:ASN85 4.8 27.2 1.0
CA E:ASN85 4.9 27.2 1.0
ND1 E:HIS82 4.9 27.2 1.0
N E:ARG83 4.9 27.2 1.0

Reference:

D.J.Ferraro, E.N.Brown, C.L.Yu, R.E.Parales, D.T.Gibson, S.Ramaswamy. Structural Investigations of the Ferredoxin and Terminal Oxygenase Components of the Biphenyl 2,3-Dioxygenase From Sphingobium Yanoikuyae B1. Bmc Struct.Biol. V. 7 10 2007.
ISSN: ESSN 1472-6807
PubMed: 17349044
DOI: 10.1186/1472-6807-7-10
Page generated: Sat Aug 3 22:30:04 2024

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