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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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