Atomistry » Iron » PDB 2ciz-2d3q » 2ckf
Atomistry »
  Iron »
    PDB 2ciz-2d3q »
      2ckf »

Iron in PDB 2ckf: Crystal Structure of the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1

Protein crystallography data

The structure of Crystal Structure of the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1, PDB code: 2ckf was solved by J.Jakoncic, C.Meyer, Y.Jouanneau, V.Stojanoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.644, 112.730, 190.626, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.6

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1 (pdb code 2ckf). 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 the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1, PDB code: 2ckf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 2ckf

Go back to Iron Binding Sites List in 2ckf
Iron binding site 1 out of 9 in the Crystal Structure of the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1


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 the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:19.7
occ:1.00
 FE1 A:FES500 0.0 19.7 1.0
S2 A:FES500 2.1 20.0 1.0
S1 A:FES500 2.2 20.5 1.0
SG A:CYS100 2.3 21.3 1.0
SG A:CYS80 2.4 19.1 1.0
FE2 A:FES500 2.7 23.3 1.0
CB A:CYS80 3.1 17.8 1.0
CB A:CYS100 3.2 19.4 1.0
CB A:HIS82 4.0 20.5 1.0
CB A:ASN85 4.3 21.0 1.0
CB A:TYR102 4.3 20.2 1.0
ND1 A:HIS82 4.5 22.3 1.0
CA A:CYS80 4.5 17.8 1.0
N A:HIS103 4.6 21.7 1.0
CA A:CYS100 4.6 20.7 1.0
ND1 A:HIS103 4.6 21.4 1.0
N A:ARG83 4.6 18.3 1.0
CB A:TRP105 4.6 22.2 1.0
CG A:HIS82 4.7 21.9 1.0
C A:CYS100 4.9 22.3 1.0
O A:CYS100 4.9 23.0 1.0
CG A:TRP105 4.9 23.1 1.0
N A:TYR102 4.9 21.9 1.0
N A:HIS82 4.9 19.2 1.0
N A:ASN85 4.9 20.1 1.0
CA A:HIS82 5.0 19.7 1.0

Iron binding site 2 out of 9 in 2ckf

Go back to Iron Binding Sites List in 2ckf
Iron binding site 2 out of 9 in the Crystal Structure of the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1


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 the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:23.3
occ:1.00
 FE2 A:FES500 0.0 23.3 1.0
S1 A:FES500 2.1 20.5 1.0
ND1 A:HIS103 2.2 21.4 1.0
S2 A:FES500 2.2 20.0 1.0
ND1 A:HIS82 2.3 22.3 1.0
FE1 A:FES500 2.7 19.7 1.0
CE1 A:HIS103 3.1 22.9 1.0
CG A:HIS103 3.1 21.2 1.0
CG A:HIS82 3.1 21.9 1.0
CE1 A:HIS82 3.2 23.2 1.0
CB A:HIS82 3.4 20.5 1.0
CB A:HIS103 3.5 21.4 1.0
N A:HIS103 3.7 21.7 1.0
CB A:TYR102 4.0 20.2 1.0
CA A:HIS103 4.2 22.1 1.0
NE2 A:HIS103 4.2 20.7 1.0
N A:ARG83 4.2 18.3 1.0
CD2 A:HIS103 4.2 19.4 1.0
CD2 A:HIS82 4.3 24.4 1.0
NE2 A:HIS82 4.3 23.5 1.0
CG A:TYR102 4.3 20.3 1.0
CG A:ARG83 4.3 18.7 1.0
SG A:CYS80 4.4 19.1 1.0
CD2 A:TYR102 4.5 19.5 1.0
C A:TYR102 4.6 22.5 1.0
SG A:CYS100 4.6 21.3 1.0
CA A:HIS82 4.7 19.7 1.0
CB A:ARG83 4.8 18.2 1.0
CA A:TYR102 4.9 20.8 1.0
C A:HIS82 4.9 20.1 1.0
CD1 A:TRP105 5.0 24.6 1.0

Iron binding site 3 out of 9 in 2ckf

Go back to Iron Binding Sites List in 2ckf
Iron binding site 3 out of 9 in the Crystal Structure of the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1


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 the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:14.2
occ:1.00
 O A:HOH2281 1.9 25.8 1.0
OD2 A:ASP360 2.0 23.2 1.0
NE2 A:HIS212 2.0 16.0 1.0
NE2 A:HIS207 2.0 15.1 1.0
O A:HOH2204 2.6 17.4 1.0
CG A:ASP360 2.8 21.1 1.0
CE1 A:HIS212 3.0 17.4 1.0
CE1 A:HIS207 3.0 14.8 1.0
OD1 A:ASP360 3.0 28.5 1.0
CD2 A:HIS212 3.0 16.9 1.0
CD2 A:HIS207 3.1 13.1 1.0
OD1 A:ASN200 4.1 20.7 1.0
ND1 A:HIS212 4.1 14.6 1.0
ND1 A:HIS207 4.1 14.0 1.0
CG A:HIS212 4.2 20.0 1.0
CG A:HIS207 4.2 14.8 1.0
O A:HOH2274 4.2 30.6 1.0
CB A:ASP360 4.2 19.7 1.0
ND2 A:ASN200 4.5 15.4 1.0
CG A:ASN200 4.7 18.4 1.0
CE2 A:PHE350 4.7 14.8 1.0
CG2 A:THR211 4.7 16.0 1.0

Iron binding site 4 out of 9 in 2ckf

Go back to Iron Binding Sites List in 2ckf
Iron binding site 4 out of 9 in the Crystal Structure of the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1


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 the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:17.2
occ:1.00
 FE1 C:FES500 0.0 17.2 1.0
S1 C:FES500 2.2 18.7 1.0
SG C:CYS80 2.2 17.1 1.0
S2 C:FES500 2.2 17.4 1.0
SG C:CYS100 2.4 18.5 1.0
FE2 C:FES500 2.7 20.0 1.0
CB C:CYS80 3.1 17.1 1.0
CB C:CYS100 3.1 18.4 1.0
CB C:HIS82 4.0 14.5 1.0
CB C:ASN85 4.3 19.1 1.0
CB C:TYR102 4.3 14.4 1.0
ND1 C:HIS103 4.4 12.0 1.0
ND1 C:HIS82 4.5 12.8 1.0
CA C:CYS100 4.5 18.1 1.0
CA C:CYS80 4.6 17.7 1.0
N C:HIS103 4.6 14.6 1.0
N C:ARG83 4.6 14.2 1.0
CB C:TRP105 4.7 18.4 1.0
CG C:HIS82 4.7 14.8 1.0
C C:CYS100 4.8 18.4 1.0
O C:CYS100 4.8 18.7 1.0
N C:ASN85 4.8 17.5 1.0
N C:HIS82 4.9 15.3 1.0
CG C:TRP105 4.9 15.2 1.0
N C:TYR102 5.0 16.3 1.0
CA C:HIS82 5.0 15.0 1.0

Iron binding site 5 out of 9 in 2ckf

Go back to Iron Binding Sites List in 2ckf
Iron binding site 5 out of 9 in the Crystal Structure of the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1


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 the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:20.0
occ:1.00
 FE2 C:FES500 0.0 20.0 1.0
ND1 C:HIS103 2.0 12.0 1.0
ND1 C:HIS82 2.2 12.8 1.0
S1 C:FES500 2.2 18.7 1.0
S2 C:FES500 2.2 17.4 1.0
FE1 C:FES500 2.7 17.2 1.0
CE1 C:HIS103 2.9 13.6 1.0
CG C:HIS103 3.1 13.2 1.0
CG C:HIS82 3.1 14.8 1.0
CE1 C:HIS82 3.2 14.7 1.0
CB C:HIS82 3.3 14.5 1.0
CB C:HIS103 3.5 16.2 1.0
N C:HIS103 3.8 14.6 1.0
NE2 C:HIS103 4.0 15.6 1.0
CB C:TYR102 4.1 14.4 1.0
CD2 C:HIS103 4.1 16.6 1.0
N C:ARG83 4.2 14.2 1.0
CA C:HIS103 4.2 15.5 1.0
SG C:CYS80 4.3 17.1 1.0
CD2 C:HIS82 4.3 14.7 1.0
NE2 C:HIS82 4.3 14.1 1.0
CG C:TYR102 4.4 12.5 1.0
CD2 C:TYR102 4.4 15.1 1.0
CG C:ARG83 4.4 14.2 1.0
SG C:CYS100 4.6 18.5 1.0
CA C:HIS82 4.6 15.0 1.0
C C:TYR102 4.7 13.4 1.0
CB C:ARG83 4.8 14.1 1.0
C C:HIS82 4.9 16.0 1.0
CD1 C:TRP105 4.9 17.3 1.0
CA C:TYR102 5.0 14.4 1.0

Iron binding site 6 out of 9 in 2ckf

Go back to Iron Binding Sites List in 2ckf
Iron binding site 6 out of 9 in the Crystal Structure of the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1


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 the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:29.0
occ:1.00
 NE2 C:HIS212 2.0 36.4 1.0
NE2 C:HIS207 2.1 32.5 1.0
OD2 C:ASP360 2.1 32.4 1.0
O C:HOH2106 2.6 32.8 1.0
CE1 C:HIS212 2.9 37.5 1.0
CG C:ASP360 2.9 34.4 1.0
CD2 C:HIS212 3.0 39.1 1.0
CE1 C:HIS207 3.0 32.9 1.0
CD2 C:HIS207 3.1 31.4 1.0
OD1 C:ASP360 3.1 37.6 1.0
ND1 C:HIS212 4.0 40.0 1.0
OD1 C:ASN200 4.0 38.0 1.0
CG C:HIS212 4.1 42.7 1.0
ND1 C:HIS207 4.1 32.5 1.0
CG C:HIS207 4.2 32.6 1.0
CB C:ASP360 4.4 32.0 1.0
ND2 C:ASN200 4.5 30.2 1.0
CG C:ASN200 4.7 33.5 1.0
CE2 C:PHE350 4.8 25.5 1.0
CG2 C:THR211 4.8 43.9 1.0

Iron binding site 7 out of 9 in 2ckf

Go back to Iron Binding Sites List in 2ckf
Iron binding site 7 out of 9 in the Crystal Structure of the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1


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 the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:33.2
occ:1.00
 FE1 E:FES500 0.0 33.2 1.0
S1 E:FES500 2.2 36.9 1.0
S2 E:FES500 2.2 33.2 1.0
SG E:CYS100 2.3 34.4 1.0
SG E:CYS80 2.4 32.6 1.0
FE2 E:FES500 2.8 36.5 1.0
CB E:CYS100 3.2 32.2 1.0
CB E:CYS80 3.2 31.2 1.0
CB E:HIS82 4.0 31.0 1.0
CB E:ASN85 4.3 35.2 1.0
CB E:TYR102 4.3 30.0 1.0
N E:HIS103 4.5 31.6 1.0
CA E:CYS100 4.6 33.3 1.0
CA E:CYS80 4.7 31.0 1.0
N E:ARG83 4.7 32.5 1.0
CB E:TRP105 4.7 32.5 1.0
ND1 E:HIS82 4.7 30.9 1.0
O E:CYS100 4.7 34.7 1.0
N E:HIS82 4.8 31.0 1.0
ND1 E:HIS103 4.8 28.8 1.0
C E:CYS100 4.8 33.6 1.0
CG E:HIS82 4.9 29.7 1.0
N E:TYR102 4.9 31.7 1.0
CG E:TRP105 4.9 30.5 1.0
CA E:HIS82 5.0 31.5 1.0
N E:ASN85 5.0 33.7 1.0

Iron binding site 8 out of 9 in 2ckf

Go back to Iron Binding Sites List in 2ckf
Iron binding site 8 out of 9 in the Crystal Structure of the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1


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 the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:36.5
occ:1.00
 FE2 E:FES500 0.0 36.5 1.0
S1 E:FES500 2.2 36.9 1.0
S2 E:FES500 2.2 33.2 1.0
ND1 E:HIS103 2.3 28.8 1.0
ND1 E:HIS82 2.3 30.9 1.0
FE1 E:FES500 2.8 33.2 1.0
CG E:HIS82 3.1 29.7 1.0
CG E:HIS103 3.2 30.5 1.0
CB E:HIS82 3.2 31.0 1.0
CE1 E:HIS103 3.3 32.0 1.0
CB E:HIS103 3.4 31.7 1.0
CE1 E:HIS82 3.4 30.0 1.0
N E:HIS103 3.7 31.6 1.0
CB E:TYR102 4.1 30.0 1.0
CA E:HIS103 4.2 32.0 1.0
N E:ARG83 4.2 32.5 1.0
CG E:TYR102 4.3 29.1 1.0
CD2 E:HIS82 4.3 29.5 1.0
CD2 E:HIS103 4.3 31.9 1.0
NE2 E:HIS103 4.4 32.3 1.0
CD2 E:TYR102 4.4 29.0 1.0
NE2 E:HIS82 4.4 32.1 1.0
SG E:CYS80 4.5 32.6 1.0
CG E:ARG83 4.5 32.8 1.0
CA E:HIS82 4.6 31.5 1.0
C E:TYR102 4.6 31.1 1.0
SG E:CYS100 4.6 34.4 1.0
CB E:ARG83 4.7 32.3 1.0
C E:HIS82 4.8 32.2 1.0
CA E:TYR102 4.9 30.8 1.0
CD1 E:TRP105 5.0 30.6 1.0

Iron binding site 9 out of 9 in 2ckf

Go back to Iron Binding Sites List in 2ckf
Iron binding site 9 out of 9 in the Crystal Structure of the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1


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 the Terminal Component of the Pah- Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:23.4
occ:1.00
 NE2 E:HIS212 1.6 15.8 1.0
OD2 E:ASP360 2.1 36.2 1.0
NE2 E:HIS207 2.2 25.4 1.0
CE1 E:HIS212 2.4 25.8 1.0
O E:HOH2088 2.5 26.3 1.0
O E:HOH2087 2.8 24.0 1.0
CD2 E:HIS212 2.8 27.2 1.0
CG E:ASP360 2.8 31.5 1.0
OD1 E:ASP360 2.8 36.6 1.0
CD2 E:HIS207 3.1 25.4 1.0
CE1 E:HIS207 3.2 25.1 1.0
ND1 E:HIS212 3.6 28.8 1.0
CG E:HIS212 3.8 31.1 1.0
OD1 E:ASN200 4.0 31.5 1.0
CG E:HIS207 4.3 25.0 1.0
ND1 E:HIS207 4.3 24.3 1.0
CB E:ASP360 4.3 28.2 1.0
CG2 E:THR211 4.5 34.3 1.0
ND2 E:ASN200 4.7 28.5 1.0
CE2 E:PHE350 4.7 26.2 1.0
CG E:ASN200 4.8 26.8 1.0
CZ E:PHE350 5.0 27.4 1.0

Reference:

J.Jakoncic, Y.Jouanneau, C.Meyer, V.Stojanoff. The Catalytic Pocket of the Ring-Hydroxylating Dioxygenase From Sphingomonas Chy-1. Biochem.Biophys.Res.Commun. V. 352 861 2007.
ISSN: ISSN 0006-291X
PubMed: 17157819
DOI: 10.1016/J.BBRC.2006.11.117
Page generated: Thu Jul 17 00:28:07 2025

Last articles

Na in 4C3Y
Na in 4C3X
Na in 4C3V
Na in 4C44
Na in 4C3W
Na in 4C2U
Na in 4C10
Na in 4C3U
Na in 4BZ2
Na in 4C1P
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy