Atomistry » Iron » PDB 2g6o-2grx » 2gbx
Atomistry »
  Iron »
    PDB 2g6o-2grx »
      2gbx »

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

Go back to Iron Binding Sites List in 2gbx
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

Go back to Iron Binding Sites List in 2gbx
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

Go back to Iron Binding Sites List in 2gbx
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

Go back to Iron Binding Sites List in 2gbx
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

Go back to Iron Binding Sites List in 2gbx
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

Go back to Iron Binding Sites List in 2gbx
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

Go back to Iron Binding Sites List in 2gbx
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

Go back to Iron Binding Sites List in 2gbx
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

Go back to Iron Binding Sites List in 2gbx
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy