Atomistry » Iron » PDB 2xf2-2xuz » 2xsh
Atomistry »
  Iron »
    PDB 2xf2-2xuz »
      2xsh »

Iron in PDB 2xsh: Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl

Enzymatic activity of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl

All present enzymatic activity of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl:
1.14.12.18;

Protein crystallography data

The structure of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl, PDB code: 2xsh was solved by P.Kumar, J.T.Bolin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 138.68 / 2.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.728, 276.762, 92.317, 90.00, 117.37, 90.00
R / Rfree (%) 18.571 / 24.456

Other elements in 2xsh:

The structure of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl (pdb code 2xsh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl, PDB code: 2xsh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 18 in 2xsh

Go back to Iron Binding Sites List in 2xsh
Iron binding site 1 out of 18 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl


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 P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe900

b:38.8
occ:1.00
FE1 A:FES900 0.0 38.8 1.0
ND1 A:HIS123 2.1 34.2 1.0
ND1 A:HIS102 2.1 37.8 1.0
S2 A:FES900 2.2 40.2 1.0
S1 A:FES900 2.2 39.2 1.0
FE2 A:FES900 2.9 39.2 1.0
CG A:HIS123 3.0 35.6 1.0
CE1 A:HIS102 3.0 38.5 1.0
CE1 A:HIS123 3.0 34.0 1.0
CG A:HIS102 3.1 38.5 1.0
CB A:HIS123 3.3 37.4 1.0
CB A:HIS102 3.5 37.4 1.0
N A:HIS123 3.7 36.2 1.0
CA A:HIS123 4.1 37.3 1.0
NE2 A:HIS123 4.1 34.3 1.0
CB A:TYR122 4.1 34.1 1.0
CD2 A:HIS123 4.1 34.1 1.0
NE2 A:HIS102 4.1 39.6 1.0
N A:ARG103 4.2 36.2 1.0
CD2 A:HIS102 4.2 39.0 1.0
CB A:ARG103 4.4 35.8 1.0
CG A:TYR122 4.4 33.9 1.0
C A:TYR122 4.5 36.0 1.0
SG A:CYS120 4.5 36.9 1.0
CD1 A:TYR122 4.5 32.5 1.0
SG A:CYS100 4.7 36.5 1.0
CA A:HIS102 4.7 37.3 1.0
C A:HIS102 4.7 36.9 1.0
CA A:ARG103 4.9 35.5 1.0
CA A:TYR122 4.9 34.8 1.0
C A:HIS123 4.9 38.2 1.0

Iron binding site 2 out of 18 in 2xsh

Go back to Iron Binding Sites List in 2xsh
Iron binding site 2 out of 18 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl


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 P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe900

b:39.2
occ:1.00
FE2 A:FES900 0.0 39.2 1.0
S2 A:FES900 2.2 40.2 1.0
S1 A:FES900 2.2 39.2 1.0
SG A:CYS120 2.3 36.9 1.0
SG A:CYS100 2.4 36.5 1.0
FE1 A:FES900 2.9 38.8 1.0
CB A:CYS100 3.0 35.4 1.0
CB A:CYS120 3.1 37.6 1.0
CB A:HIS102 4.2 37.4 1.0
CB A:MET105 4.2 29.9 1.0
ND1 A:HIS102 4.5 37.8 1.0
CB A:TYR122 4.5 34.1 1.0
CA A:CYS100 4.5 35.6 1.0
N A:HIS123 4.6 36.2 1.0
CB A:TRP125 4.6 37.4 1.0
CA A:CYS120 4.6 37.3 1.0
ND1 A:HIS123 4.7 34.2 1.0
N A:ARG103 4.7 36.2 1.0
N A:MET105 4.8 31.6 1.0
CG A:TRP125 4.8 37.0 1.0
CG A:HIS102 4.8 38.5 1.0

Iron binding site 3 out of 18 in 2xsh

Go back to Iron Binding Sites List in 2xsh
Iron binding site 3 out of 18 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl


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 P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe901

b:34.6
occ:1.00
NE2 A:HIS239 2.1 33.1 1.0
OD1 A:ASP388 2.1 36.7 1.0
NE2 A:HIS233 2.2 34.1 1.0
O A:HOH2109 2.3 47.1 1.0
OD2 A:ASP388 2.5 36.5 1.0
CG A:ASP388 2.6 35.8 1.0
OE1 A:GLN226 2.9 36.3 1.0
CE1 A:HIS239 2.9 31.6 1.0
CD2 A:HIS233 3.2 32.5 1.0
CD2 A:HIS239 3.2 33.4 1.0
CE1 A:HIS233 3.2 30.5 1.0
CD A:GLN226 3.6 33.9 1.0
NE2 A:GLN226 3.9 32.2 1.0
ND1 A:HIS239 4.1 30.4 1.0
CB A:ASP388 4.1 34.8 1.0
CG A:HIS239 4.2 33.0 1.0
ND1 A:HIS233 4.3 33.4 1.0
CG A:HIS233 4.3 33.0 1.0
CL1 A:DC5902 4.4 61.5 1.0
CA5 A:DC5902 4.6 55.1 1.0
CG2 A:THR238 4.6 30.9 1.0
CG A:GLN226 4.8 32.4 1.0
CA6 A:DC5902 4.9 56.2 1.0
CA4 A:DC5902 4.9 55.2 1.0
CA A:ASP388 4.9 34.8 1.0

Iron binding site 4 out of 18 in 2xsh

Go back to Iron Binding Sites List in 2xsh
Iron binding site 4 out of 18 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl


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 P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe900

b:31.8
occ:1.00
FE1 C:FES900 0.0 31.8 1.0
ND1 C:HIS123 2.0 30.8 1.0
S2 C:FES900 2.2 33.1 1.0
S1 C:FES900 2.2 27.9 1.0
ND1 C:HIS102 2.2 29.5 1.0
FE2 C:FES900 2.8 32.6 1.0
CG C:HIS123 3.0 32.4 1.0
CE1 C:HIS123 3.0 31.8 1.0
CE1 C:HIS102 3.2 32.2 1.0
CG C:HIS102 3.3 32.1 1.0
CB C:HIS123 3.3 33.6 1.0
CB C:HIS102 3.6 32.2 1.0
N C:HIS123 3.7 32.6 1.0
NE2 C:HIS123 4.1 30.7 1.0
CA C:HIS123 4.1 33.8 1.0
CD2 C:HIS123 4.1 32.2 1.0
CB C:TYR122 4.1 31.0 1.0
N C:ARG103 4.2 31.4 1.0
NE2 C:HIS102 4.3 33.1 1.0
CD2 C:HIS102 4.4 34.0 1.0
CB C:ARG103 4.4 30.8 1.0
CG C:TYR122 4.4 31.5 1.0
C C:TYR122 4.5 32.1 1.0
SG C:CYS120 4.5 33.1 1.0
CD1 C:TYR122 4.6 33.1 1.0
SG C:CYS100 4.6 32.0 1.0
C C:HIS102 4.7 32.0 1.0
CA C:HIS102 4.7 32.1 1.0
CA C:ARG103 4.8 30.9 1.0
CA C:TYR122 4.9 31.3 1.0
C C:HIS123 4.9 34.9 1.0

Iron binding site 5 out of 18 in 2xsh

Go back to Iron Binding Sites List in 2xsh
Iron binding site 5 out of 18 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl


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 P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe900

b:32.6
occ:1.00
FE2 C:FES900 0.0 32.6 1.0
S1 C:FES900 2.2 27.9 1.0
S2 C:FES900 2.2 33.1 1.0
SG C:CYS120 2.4 33.1 1.0
SG C:CYS100 2.4 32.0 1.0
FE1 C:FES900 2.8 31.8 1.0
CB C:CYS100 3.1 30.1 1.0
CB C:CYS120 3.2 33.5 1.0
CB C:HIS102 4.2 32.2 1.0
CB C:MET105 4.3 28.0 1.0
CB C:TYR122 4.4 31.0 1.0
ND1 C:HIS102 4.5 29.5 1.0
CB C:TRP125 4.5 36.0 1.0
N C:HIS123 4.5 32.6 1.0
CA C:CYS100 4.6 30.2 1.0
ND1 C:HIS123 4.6 30.8 1.0
CA C:CYS120 4.7 33.8 1.0
N C:ARG103 4.7 31.4 1.0
CG C:TRP125 4.8 36.2 1.0
CG C:HIS102 4.8 32.1 1.0
N C:MET105 4.8 29.5 1.0

Iron binding site 6 out of 18 in 2xsh

Go back to Iron Binding Sites List in 2xsh
Iron binding site 6 out of 18 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl


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 P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe901

b:37.4
occ:1.00
O C:HOH2073 1.8 43.7 1.0
NE2 C:HIS239 2.0 39.2 1.0
OD1 C:ASP388 2.0 41.7 1.0
NE2 C:HIS233 2.2 38.4 1.0
OD2 C:ASP388 2.4 40.5 1.0
CG C:ASP388 2.5 40.1 1.0
CE1 C:HIS239 3.0 39.1 1.0
CD2 C:HIS239 3.0 37.6 1.0
OE1 C:GLN226 3.0 42.9 1.0
CD2 C:HIS233 3.1 38.7 1.0
CE1 C:HIS233 3.3 37.5 1.0
CD C:GLN226 3.5 40.5 1.0
NE2 C:GLN226 3.5 37.8 1.0
CB C:ASP388 4.0 39.1 1.0
ND1 C:HIS239 4.1 37.9 1.0
CG C:HIS239 4.1 37.8 1.0
CL1 C:DC5902 4.2 74.8 1.0
CG2 C:THR238 4.3 37.3 1.0
CG C:HIS233 4.3 39.3 1.0
ND1 C:HIS233 4.4 38.4 1.0
CA5 C:DC5902 4.7 71.7 1.0
CG C:GLN226 4.7 39.0 1.0
CA C:ASP388 4.8 39.2 1.0
CA6 C:DC5902 4.9 72.1 1.0

Iron binding site 7 out of 18 in 2xsh

Go back to Iron Binding Sites List in 2xsh
Iron binding site 7 out of 18 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl


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 P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe901

b:38.8
occ:1.00
FE1 E:FES901 0.0 38.8 1.0
ND1 E:HIS123 2.1 32.8 1.0
ND1 E:HIS102 2.1 36.8 1.0
S2 E:FES901 2.2 40.0 1.0
S1 E:FES901 2.2 38.4 1.0
FE2 E:FES901 2.9 36.6 1.0
CG E:HIS123 3.0 34.1 1.0
CE1 E:HIS102 3.1 37.9 1.0
CG E:HIS102 3.1 37.8 1.0
CE1 E:HIS123 3.1 32.3 1.0
CB E:HIS123 3.2 36.1 1.0
CB E:HIS102 3.4 36.6 1.0
N E:HIS123 3.8 35.4 1.0
N E:ARG103 4.1 35.4 1.0
CA E:HIS123 4.1 36.3 1.0
CD2 E:HIS123 4.2 32.1 1.0
NE2 E:HIS123 4.2 32.8 1.0
NE2 E:HIS102 4.2 37.9 1.0
CD2 E:HIS102 4.2 38.8 1.0
CB E:TYR122 4.3 32.8 1.0
CB E:ARG103 4.4 34.6 1.0
SG E:CYS100 4.5 38.4 1.0
CD1 E:TYR122 4.5 32.2 1.0
CG E:TYR122 4.5 33.0 1.0
SG E:CYS120 4.5 33.5 1.0
C E:TYR122 4.6 34.8 1.0
CA E:HIS102 4.7 36.4 1.0
C E:HIS102 4.8 35.7 1.0
CA E:ARG103 4.8 34.3 1.0
C E:HIS123 4.9 37.4 1.0
CA E:TYR122 5.0 34.1 1.0

Iron binding site 8 out of 18 in 2xsh

Go back to Iron Binding Sites List in 2xsh
Iron binding site 8 out of 18 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl


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 P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe901

b:36.6
occ:1.00
FE2 E:FES901 0.0 36.6 1.0
S2 E:FES901 2.2 40.0 1.0
S1 E:FES901 2.2 38.4 1.0
SG E:CYS100 2.2 38.4 1.0
SG E:CYS120 2.3 33.5 1.0
FE1 E:FES901 2.9 38.8 1.0
CB E:CYS100 3.0 36.6 1.0
CB E:CYS120 3.1 35.3 1.0
CB E:HIS102 4.2 36.6 1.0
CB E:MET105 4.3 31.0 1.0
CB E:TRP125 4.5 39.0 1.0
CA E:CYS100 4.5 36.7 1.0
CA E:CYS120 4.5 35.2 1.0
ND1 E:HIS102 4.5 36.8 1.0
N E:HIS123 4.5 35.4 1.0
CB E:TYR122 4.6 32.8 1.0
ND1 E:HIS123 4.7 32.8 1.0
N E:ARG103 4.8 35.4 1.0
CG E:TRP125 4.8 38.9 1.0
CG E:HIS102 4.9 37.8 1.0
OH E:TYR127 4.9 39.0 1.0
N E:MET105 4.9 32.0 1.0

Iron binding site 9 out of 18 in 2xsh

Go back to Iron Binding Sites List in 2xsh
Iron binding site 9 out of 18 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl


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 P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe902

b:40.1
occ:1.00
O E:HOH2101 2.0 34.5 1.0
OD1 E:ASP388 2.1 42.6 1.0
NE2 E:HIS239 2.1 36.5 1.0
NE2 E:HIS233 2.2 36.1 1.0
OD2 E:ASP388 2.4 44.6 1.0
CG E:ASP388 2.6 43.0 1.0
OE1 E:GLN226 2.7 40.7 1.0
CE1 E:HIS239 3.1 36.0 1.0
CD2 E:HIS233 3.1 36.6 1.0
CD2 E:HIS239 3.1 37.2 1.0
CE1 E:HIS233 3.2 36.9 1.0
CD E:GLN226 3.5 39.5 1.0
NE2 E:GLN226 3.9 37.3 1.0
CB E:ASP388 4.1 41.0 1.0
CL1 E:DC5900 4.1 76.5 1.0
ND1 E:HIS239 4.2 36.2 1.0
CG E:HIS239 4.3 37.0 1.0
CG E:HIS233 4.3 37.9 1.0
ND1 E:HIS233 4.3 38.4 1.0
CG2 E:THR238 4.6 34.4 1.0
CG E:GLN226 4.7 39.1 1.0
CA5 E:DC5900 4.8 72.5 1.0
CA E:ASP388 4.8 40.9 1.0
CA6 E:DC5900 5.0 73.2 1.0
CA4 E:DC5900 5.0 72.8 1.0

Iron binding site 10 out of 18 in 2xsh

Go back to Iron Binding Sites List in 2xsh
Iron binding site 10 out of 18 in the Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of P4 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 in Complex with 2,6 Di Chlorobiphenyl within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe900

b:73.0
occ:1.00
FE1 G:FES900 0.0 73.0 1.0
ND1 G:HIS123 1.8 65.2 1.0
S2 G:FES900 2.2 73.3 1.0
S1 G:FES900 2.2 72.9 1.0
ND1 G:HIS102 2.4 72.1 1.0
CG G:HIS123 2.7 68.4 1.0
CE1 G:HIS123 2.8 64.7 1.0
CB G:HIS123 3.1 71.5 1.0
FE2 G:FES900 3.1 74.3 1.0
CE1 G:HIS102 3.2 72.2 1.0
CG G:HIS102 3.4 72.6 1.0
N G:HIS123 3.5 68.2 1.0
O G:HOH2019 3.7 0.7 1.0
CB G:HIS102 3.8 72.8 1.0
CB G:TYR122 3.8 62.2 1.0
CD2 G:HIS123 3.9 67.8 1.0
NE2 G:HIS123 3.9 66.0 1.0
CA G:HIS123 3.9 71.0 1.0
CG G:TYR122 4.1 61.4 1.0
C G:TYR122 4.2 66.4 1.0
O G:HOH2023 4.2 0.4 1.0
CD1 G:TYR122 4.2 59.7 1.0
N G:ARG103 4.3 68.8 1.0
NE2 G:HIS102 4.3 72.2 1.0
CB G:ARG103 4.4 67.4 1.0
CD2 G:HIS102 4.5 72.7 1.0
SG G:CYS120 4.5 66.0 1.0
CA G:TYR122 4.6 64.0 1.0
C G:HIS123 4.8 73.3 1.0
CD2 G:TYR122 4.8 61.5 1.0
O G:TYR122 4.9 66.9 1.0
CA G:ARG103 4.9 67.2 1.0
SG G:CYS100 4.9 69.3 1.0

Reference:

P.Kumar, M.Mohammadi, J.F.Viger, D.Barriault, L.Gomez-Gil, L.D.Eltis, J.T.Bolin, M.Sylvestre. Structural Insight Into the Expanded Pcb-Degrading Abilities of A Biphenyl Dioxygenase Obtained By Directed Evolution. J.Mol.Biol. V. 405 531 2011.
ISSN: ISSN 0022-2836
PubMed: 21073881
DOI: 10.1016/J.JMB.2010.11.009
Page generated: Sun Dec 13 14:56:51 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy