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

Protein crystallography data

The structure of Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1, PDB code: 2gbw 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) 19.80 / 1.70
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.958, 134.958, 219.887, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 22.8

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Biphenyl 2,3-Dioxygenase From Sphingomonas Yanoikuyae B1 (pdb code 2gbw). 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, PDB code: 2gbw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 2gbw

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe456

b:37.5
occ:1.00
 OD2 A:ASP360 1.7 46.0 1.0
NE2 A:HIS212 2.0 42.8 1.0
NE2 A:HIS207 2.0 37.0 1.0
O A:HOH959 2.3 17.6 0.5
O1 A:OXY457 2.3 21.0 0.5
O2 A:OXY457 2.3 22.1 0.5
CG A:ASP360 2.7 40.7 1.0
CE1 A:HIS212 2.9 41.1 1.0
OD1 A:ASP360 3.0 45.9 1.0
CD2 A:HIS207 3.0 38.9 1.0
CE1 A:HIS207 3.0 37.8 1.0
CD2 A:HIS212 3.1 38.3 1.0
O A:HOH663 3.5 42.5 1.0
ND2 A:ASN200 4.1 43.1 1.0
ND1 A:HIS212 4.1 41.7 1.0
CB A:ASP360 4.1 41.1 1.0
ND1 A:HIS207 4.1 36.2 1.0
CG A:HIS207 4.2 34.0 1.0
CG A:HIS212 4.2 43.5 1.0
OD1 A:ASN200 4.6 42.9 1.0
CG2 A:THR211 4.8 39.9 1.0
CG A:ASN200 4.8 40.6 1.0
CE1 A:PHE350 4.9 39.3 1.0

Iron binding site 2 out of 9 in 2gbw

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe455

b:38.1
occ:1.00
 FE1 A:FES455 0.0 38.1 1.0
ND1 A:HIS82 2.1 37.8 1.0
ND1 A:HIS103 2.1 38.2 1.0
S1 A:FES455 2.2 39.0 1.0
S2 A:FES455 2.2 39.1 1.0
FE2 A:FES455 2.7 37.6 1.0
CE1 A:HIS103 3.0 37.5 1.0
CG A:HIS82 3.0 37.6 1.0
CE1 A:HIS82 3.0 37.5 1.0
CG A:HIS103 3.1 35.9 1.0
CB A:HIS82 3.3 38.0 1.0
CB A:HIS103 3.5 37.3 1.0
N A:HIS103 3.8 37.3 1.0
NE2 A:HIS103 4.1 36.6 1.0
CB A:TYR102 4.2 37.9 1.0
NE2 A:HIS82 4.2 37.2 1.0
CD2 A:HIS82 4.2 38.8 1.0
CD2 A:HIS103 4.2 36.1 1.0
CA A:HIS103 4.2 37.6 1.0
N A:ARG83 4.3 38.2 1.0
CG A:TYR102 4.4 38.0 1.0
CG A:ARG83 4.4 40.5 1.0
CD2 A:TYR102 4.4 39.4 1.0
SG A:CYS80 4.4 38.0 1.0
SG A:CYS100 4.6 40.9 1.0
C A:TYR102 4.6 38.1 1.0
CA A:HIS82 4.7 38.0 1.0
CB A:ARG83 4.7 39.8 1.0
CA A:TYR102 4.9 37.8 1.0
C A:HIS82 4.9 38.5 1.0

Iron binding site 3 out of 9 in 2gbw

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe455

b:37.6
occ:1.00
 FE2 A:FES455 0.0 37.6 1.0
S1 A:FES455 2.2 39.0 1.0
S2 A:FES455 2.2 39.1 1.0
SG A:CYS80 2.3 38.0 1.0
SG A:CYS100 2.4 40.9 1.0
FE1 A:FES455 2.7 38.1 1.0
CB A:CYS80 3.1 38.4 1.0
CB A:CYS100 3.2 40.4 1.0
CB A:HIS82 3.9 38.0 1.0
CB A:ASN85 4.3 39.5 1.0
ND1 A:HIS82 4.3 37.8 1.0
CB A:TYR102 4.5 37.9 1.0
ND1 A:HIS103 4.6 38.2 1.0
CA A:CYS80 4.6 38.8 1.0
CA A:CYS100 4.6 40.5 1.0
CG A:HIS82 4.6 37.6 1.0
N A:HIS103 4.6 37.3 1.0
N A:ARG83 4.7 38.2 1.0
CB A:TRP105 4.7 37.8 1.0
N A:HIS82 4.9 38.5 1.0
C A:CYS100 4.9 41.2 1.0
N A:ASN85 4.9 38.7 1.0
CA A:HIS82 4.9 38.0 1.0
CG A:TRP105 4.9 37.9 1.0
N A:TYR102 5.0 38.1 1.0

Iron binding site 4 out of 9 in 2gbw

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe456

b:26.3
occ:1.00
 OD2 C:ASP360 1.8 35.5 1.0
NE2 C:HIS212 2.0 27.4 1.0
NE2 C:HIS207 2.1 26.3 1.0
O2 E:OXY457 2.3 25.0 0.5
O E:HOH811 2.3 21.0 0.5
O1 E:OXY457 2.3 26.8 0.5
CG C:ASP360 2.8 33.2 1.0
CE1 C:HIS212 3.0 28.4 1.0
CE1 C:HIS207 3.0 26.8 1.0
OD1 C:ASP360 3.0 39.6 1.0
CD2 C:HIS207 3.1 27.3 1.0
CD2 C:HIS212 3.1 27.8 1.0
OD1 C:ASN200 4.0 32.4 1.0
ND1 C:HIS212 4.1 27.1 1.0
ND1 C:HIS207 4.1 27.4 1.0
CG C:HIS212 4.2 30.4 1.0
CB C:ASP360 4.2 31.5 1.0
CG C:HIS207 4.2 27.5 1.0
O C:HOH675 4.2 48.4 1.0
ND2 C:ASN200 4.6 26.6 1.0
CG C:ASN200 4.7 29.6 1.0
CG2 C:THR211 4.8 29.7 1.0
CE1 C:PHE350 4.8 27.9 1.0

Iron binding site 5 out of 9 in 2gbw

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe455

b:24.4
occ:1.00
 FE1 C:FES455 0.0 24.4 1.0
ND1 C:HIS82 2.1 22.4 1.0
ND1 C:HIS103 2.1 22.8 1.0
S1 C:FES455 2.2 25.0 1.0
S2 C:FES455 2.2 25.2 1.0
FE2 C:FES455 2.7 23.9 1.0
CE1 C:HIS103 3.0 21.9 1.0
CG C:HIS82 3.1 22.8 1.0
CE1 C:HIS82 3.1 23.7 1.0
CG C:HIS103 3.1 23.7 1.0
CB C:HIS82 3.4 23.1 1.0
CB C:HIS103 3.5 23.3 1.0
N C:HIS103 3.8 23.2 1.0
NE2 C:HIS103 4.2 24.3 1.0
CB C:TYR102 4.2 23.7 1.0
NE2 C:HIS82 4.2 24.2 1.0
CD2 C:HIS82 4.2 21.9 1.0
CD2 C:HIS103 4.2 24.1 1.0
CA C:HIS103 4.2 24.1 1.0
N C:ARG83 4.2 23.3 1.0
CG C:ARG83 4.4 25.9 1.0
SG C:CYS80 4.4 22.8 1.0
CD2 C:TYR102 4.4 26.6 1.0
CG C:TYR102 4.4 22.7 1.0
SG C:CYS100 4.5 24.5 1.0
C C:TYR102 4.7 23.5 1.0
CA C:HIS82 4.7 22.2 1.0
CB C:ARG83 4.8 24.8 1.0
C C:HIS82 4.9 23.2 1.0
CA C:TYR102 5.0 24.0 1.0
CD1 C:TRP105 5.0 23.4 1.0

Iron binding site 6 out of 9 in 2gbw

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe455

b:23.9
occ:1.00
 FE2 C:FES455 0.0 23.9 1.0
S2 C:FES455 2.2 25.2 1.0
S1 C:FES455 2.2 25.0 1.0
SG C:CYS100 2.3 24.5 1.0
SG C:CYS80 2.3 22.8 1.0
FE1 C:FES455 2.7 24.4 1.0
CB C:CYS80 3.1 24.6 1.0
CB C:CYS100 3.1 23.9 1.0
CB C:HIS82 4.0 23.1 1.0
ND1 C:HIS82 4.4 22.4 1.0
CB C:TYR102 4.5 23.7 1.0
CA C:CYS100 4.5 25.4 1.0
CB C:ASN85 4.5 26.1 1.0
CA C:CYS80 4.6 23.9 1.0
ND1 C:HIS103 4.6 22.8 1.0
N C:ARG83 4.7 23.3 1.0
CG C:HIS82 4.7 22.8 1.0
N C:HIS103 4.7 23.2 1.0
CB C:TRP105 4.7 23.5 1.0
N C:HIS82 4.9 22.5 1.0
C C:CYS100 4.9 25.9 1.0
N C:ASN85 4.9 24.4 1.0
CA C:HIS82 5.0 22.2 1.0
N C:TYR102 5.0 24.6 1.0
CG C:TRP105 5.0 22.1 1.0

Iron binding site 7 out of 9 in 2gbw

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe456

b:30.6
occ:1.00
 OD2 E:ASP360 1.9 39.4 1.0
NE2 E:HIS212 1.9 33.5 1.0
NE2 E:HIS207 2.0 27.2 1.0
O2 C:OXY457 2.2 30.0 0.5
O C:HOH898 2.3 21.9 0.5
O1 C:OXY457 2.4 29.2 0.5
CG E:ASP360 2.8 33.7 1.0
CE1 E:HIS212 2.9 35.7 1.0
CD2 E:HIS212 3.0 36.4 1.0
CD2 E:HIS207 3.0 31.7 1.0
OD1 E:ASP360 3.0 35.1 1.0
CE1 E:HIS207 3.0 28.3 1.0
ND1 E:HIS212 4.0 35.1 1.0
OD1 E:ASN200 4.0 37.2 1.0
CG E:HIS212 4.1 36.8 1.0
ND1 E:HIS207 4.1 26.7 1.0
CG E:HIS207 4.1 29.3 1.0
CB E:ASP360 4.2 31.8 1.0
ND2 E:ASN200 4.6 33.5 1.0
CG E:ASN200 4.8 32.7 1.0
CG2 E:THR211 4.8 37.4 1.0

Iron binding site 8 out of 9 in 2gbw

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe455

b:29.3
occ:1.00
 FE1 E:FES455 0.0 29.3 1.0
ND1 E:HIS103 2.1 28.8 1.0
ND1 E:HIS82 2.2 27.2 1.0
S1 E:FES455 2.2 30.4 1.0
S2 E:FES455 2.3 29.1 1.0
FE2 E:FES455 2.7 28.4 1.0
CE1 E:HIS103 3.0 27.8 1.0
CG E:HIS103 3.1 26.4 1.0
CG E:HIS82 3.1 30.0 1.0
CE1 E:HIS82 3.2 28.6 1.0
CB E:HIS82 3.4 28.2 1.0
CB E:HIS103 3.4 28.6 1.0
N E:HIS103 4.0 29.3 1.0
NE2 E:HIS103 4.1 30.6 1.0
CB E:TYR102 4.1 29.4 1.0
CD2 E:HIS103 4.2 28.3 1.0
CA E:HIS103 4.3 29.3 1.0
CD2 E:HIS82 4.3 30.4 1.0
N E:ARG83 4.3 28.6 1.0
NE2 E:HIS82 4.3 29.5 1.0
SG E:CYS80 4.4 29.9 1.0
CG E:TYR102 4.4 29.5 1.0
CG E:ARG83 4.4 30.0 1.0
CD2 E:TYR102 4.5 28.3 1.0
SG E:CYS100 4.5 30.9 1.0
CA E:HIS82 4.7 29.3 1.0
C E:TYR102 4.7 29.2 1.0
CB E:ARG83 4.8 29.6 1.0
C E:HIS82 4.9 28.4 1.0
CD1 E:TRP105 4.9 27.9 1.0
CA E:TYR102 5.0 30.3 1.0

Iron binding site 9 out of 9 in 2gbw

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe455

b:28.4
occ:1.00
 FE2 E:FES455 0.0 28.4 1.0
S1 E:FES455 2.2 30.4 1.0
S2 E:FES455 2.2 29.1 1.0
SG E:CYS100 2.2 30.9 1.0
SG E:CYS80 2.3 29.9 1.0
FE1 E:FES455 2.7 29.3 1.0
CB E:CYS100 3.1 32.3 1.0
CB E:CYS80 3.1 29.8 1.0
CB E:HIS82 4.0 28.2 1.0
CB E:ASN85 4.3 32.0 1.0
ND1 E:HIS82 4.4 27.2 1.0
CB E:TYR102 4.5 29.4 1.0
ND1 E:HIS103 4.5 28.8 1.0
CA E:CYS100 4.5 32.2 1.0
CA E:CYS80 4.6 29.6 1.0
CB E:TRP105 4.7 29.4 1.0
N E:ARG83 4.7 28.6 1.0
CG E:HIS82 4.7 30.0 1.0
N E:HIS103 4.7 29.3 1.0
C E:CYS100 4.9 32.8 1.0
N E:HIS82 4.9 28.5 1.0
CG E:TRP105 4.9 27.0 1.0
CA E:HIS82 4.9 29.3 1.0
N E:ASN85 5.0 32.2 1.0
N E:TYR102 5.0 29.4 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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