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Iron in PDB 1jro: Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus

Enzymatic activity of Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus

All present enzymatic activity of Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus:
1.1.1.204;

Protein crystallography data

The structure of Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus, PDB code: 1jro was solved by J.J.Truglio, K.Theis, S.Leimkuhler, R.Rappa, K.V.Rajagopalan, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 92.875, 141.053, 158.113, 109.53, 105.83, 101.33
R / Rfree (%) 21.3 / 25.2

Other elements in 1jro:

The structure of Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus also contains other interesting chemical elements:

Molybdenum (Mo) 4 atoms
Calcium (Ca) 4 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus (pdb code 1jro). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus, PDB code: 1jro:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 1jro

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Iron binding site 1 out of 16 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus


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 Xanthine Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:13.5
occ:1.00
 FE1 A:FES3001 0.0 13.5 1.0
SG A:CYS103 2.1 10.9 1.0
SG A:CYS136 2.1 18.9 1.0
S2 A:FES3001 2.2 7.2 1.0
S1 A:FES3001 2.2 12.1 1.0
FE2 A:FES3001 2.8 15.4 1.0
CB A:CYS103 3.3 15.2 1.0
CB A:CYS136 3.4 21.2 1.0
N A:CYS103 3.6 16.0 1.0
CA A:CYS103 3.9 15.1 1.0
N A:GLY104 4.1 15.3 1.0
N A:CYS136 4.2 21.4 1.0
SG A:CYS134 4.3 19.8 1.0
C A:CYS103 4.4 14.8 1.0
CA A:CYS136 4.4 20.4 1.0
SG A:CYS106 4.5 20.0 1.0
N A:PHE105 4.5 16.7 1.0
C A:GLN102 4.8 17.5 1.0
N A:ARG135 4.9 22.8 1.0
N A:CYS106 4.9 15.3 1.0

Iron binding site 2 out of 16 in 1jro

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Iron binding site 2 out of 16 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus


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 Xanthine Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:15.4
occ:1.00
 FE2 A:FES3001 0.0 15.4 1.0
S1 A:FES3001 2.1 12.1 1.0
S2 A:FES3001 2.1 7.2 1.0
SG A:CYS106 2.2 20.0 1.0
SG A:CYS134 2.2 19.8 1.0
FE1 A:FES3001 2.8 13.5 1.0
CB A:CYS134 3.2 20.8 1.0
CB A:CYS106 3.5 16.2 1.0
CA A:CYS134 3.7 21.2 1.0
N A:CYS106 4.3 15.3 1.0
SG A:CYS136 4.3 18.9 1.0
N A:ARG135 4.3 22.8 1.0
C A:CYS134 4.4 22.4 1.0
N A:CYS136 4.4 21.4 1.0
CA A:CYS106 4.4 16.3 1.0
CB A:CYS136 4.5 21.2 1.0
SG A:CYS103 4.6 10.9 1.0
CG2 A:THR137 4.7 19.9 1.0
C A:CYS106 4.9 17.0 1.0
O A:LEU133 5.0 20.9 1.0
N A:CYS134 5.0 21.4 1.0

Iron binding site 3 out of 16 in 1jro

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Iron binding site 3 out of 16 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus


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 Xanthine Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:24.4
occ:1.00
 FE1 A:FES3002 0.0 24.4 1.0
S1 A:FES3002 2.2 19.0 1.0
S2 A:FES3002 2.2 15.4 1.0
SG A:CYS63 2.3 27.4 1.0
SG A:CYS47 2.3 22.3 1.0
FE2 A:FES3002 2.9 22.7 1.0
CB A:CYS63 3.2 30.4 1.0
CB A:CYS47 3.5 21.2 1.0
N A:CYS47 4.3 19.7 1.0
N A:CYS63 4.3 29.0 1.0
SG A:CYS39 4.3 23.5 1.0
CA A:CYS63 4.4 29.7 1.0
N A:ASN40 4.4 26.9 1.0
N A:GLY42 4.4 32.0 1.0
CB A:ASN61 4.4 26.4 1.0
CA A:ASN40 4.5 28.1 1.0
CA A:CYS47 4.5 20.9 1.0
SG A:CYS44 4.5 26.5 1.0
CA A:GLY42 4.7 30.7 1.0
N A:GLU41 4.7 30.8 1.0
OD1 A:ASN61 4.8 35.4 1.0
N A:GLY45 4.9 23.6 1.0
N A:ALA46 5.0 19.4 1.0
C A:ASN40 5.0 29.3 1.0

Iron binding site 4 out of 16 in 1jro

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Iron binding site 4 out of 16 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus


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 Xanthine Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:22.7
occ:1.00
 FE2 A:FES3002 0.0 22.7 1.0
SG A:CYS44 2.0 26.5 1.0
S2 A:FES3002 2.2 15.4 1.0
S1 A:FES3002 2.2 19.0 1.0
SG A:CYS39 2.3 23.5 1.0
FE1 A:FES3002 2.9 24.4 1.0
N A:CYS44 3.2 29.4 1.0
N A:CYS39 3.2 23.3 1.0
CB A:CYS44 3.2 26.9 1.0
CA A:CYS44 3.6 27.8 1.0
CB A:CYS39 3.6 24.7 1.0
N A:ASN40 3.8 26.9 1.0
CA A:CYS39 3.9 24.3 1.0
C A:GLY38 3.9 24.3 1.0
N A:GLY45 3.9 23.6 1.0
C A:CYS44 4.1 26.0 1.0
N A:GLY38 4.1 25.2 1.0
CA A:GLY38 4.2 23.8 1.0
N A:ALA46 4.3 19.4 1.0
C A:CYS39 4.3 25.5 1.0
C A:ASP43 4.4 31.2 1.0
SG A:CYS63 4.6 27.4 1.0
N A:ASP43 4.6 31.0 1.0
N A:GLY42 4.6 32.0 1.0
N A:GLU41 4.7 30.8 1.0
SG A:CYS47 4.7 22.3 1.0
CA A:ASN40 4.8 28.1 1.0
O A:GLY38 4.8 25.3 1.0
C A:GLY42 4.9 30.6 1.0
CB A:ALA46 5.0 17.5 1.0

Iron binding site 5 out of 16 in 1jro

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Iron binding site 5 out of 16 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus


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 Xanthine Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3001

b:9.7
occ:1.00
 FE1 C:FES3001 0.0 9.7 1.0
SG C:CYS136 2.1 14.2 1.0
S1 C:FES3001 2.1 8.2 1.0
SG C:CYS103 2.1 12.7 1.0
S2 C:FES3001 2.2 10.0 1.0
FE2 C:FES3001 2.8 10.1 1.0
CB C:CYS103 3.1 10.8 1.0
N C:CYS103 3.4 11.7 1.0
CB C:CYS136 3.4 12.0 1.0
O D:HOH3027 3.5 3.7 1.0
CA C:CYS103 3.7 11.1 1.0
N C:GLY104 4.0 14.2 1.0
N C:CYS136 4.2 14.4 1.0
C C:CYS103 4.2 11.4 1.0
CA C:CYS136 4.4 13.3 1.0
SG C:CYS106 4.4 11.7 1.0
SG C:CYS134 4.5 10.2 1.0
N C:PHE105 4.5 12.5 1.0
C C:GLN102 4.6 12.8 1.0
N C:ARG135 5.0 13.8 1.0
N C:GLN102 5.0 13.5 1.0
N C:CYS106 5.0 12.2 1.0

Iron binding site 6 out of 16 in 1jro

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Iron binding site 6 out of 16 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus


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 Xanthine Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3001

b:10.1
occ:1.00
 FE2 C:FES3001 0.0 10.1 1.0
S2 C:FES3001 2.1 10.0 1.0
S1 C:FES3001 2.2 8.2 1.0
SG C:CYS134 2.2 10.2 1.0
SG C:CYS106 2.2 11.7 1.0
FE1 C:FES3001 2.8 9.7 1.0
CB C:CYS134 3.2 14.1 1.0
CB C:CYS106 3.5 9.3 1.0
CA C:CYS134 3.6 13.3 1.0
N C:ARG135 4.1 13.8 1.0
N C:CYS136 4.1 14.4 1.0
SG C:CYS136 4.1 14.2 1.0
C C:CYS134 4.2 13.6 1.0
CB C:CYS136 4.4 12.0 1.0
N C:CYS106 4.4 12.2 1.0
CA C:CYS106 4.6 11.1 1.0
SG C:CYS103 4.6 12.7 1.0
CA C:CYS136 4.8 13.3 1.0
O C:HOH3012 4.8 12.5 1.0
CG2 C:THR137 4.8 2.6 1.0
N C:THR137 4.9 10.6 1.0
O C:LEU133 4.9 15.8 1.0
N C:CYS134 5.0 14.4 1.0

Iron binding site 7 out of 16 in 1jro

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Iron binding site 7 out of 16 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus


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 Xanthine Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3002

b:14.8
occ:1.00
 FE1 C:FES3002 0.0 14.8 1.0
S2 C:FES3002 2.2 16.9 1.0
S1 C:FES3002 2.3 15.6 1.0
SG C:CYS47 2.3 12.5 1.0
SG C:CYS63 2.5 15.2 1.0
FE2 C:FES3002 2.8 15.2 1.0
CB C:CYS63 3.5 19.5 1.0
CB C:CYS47 3.6 14.9 1.0
SG C:CYS39 4.2 16.5 1.0
N C:CYS47 4.3 15.5 1.0
N C:GLY42 4.3 26.0 1.0
N C:ASN40 4.3 21.4 1.0
CB C:ASN61 4.5 16.9 1.0
N C:CYS63 4.5 18.6 1.0
CA C:CYS47 4.5 14.4 1.0
SG C:CYS44 4.6 13.8 1.0
CA C:ASN40 4.6 23.5 1.0
CA C:GLY42 4.6 24.6 1.0
CA C:CYS63 4.6 20.2 1.0
OD1 C:ASN61 4.6 25.9 1.0
N C:GLU41 4.6 25.2 1.0
N C:GLY45 4.8 16.7 1.0
CG C:ASN61 4.8 19.9 1.0
N C:ALA46 4.8 15.6 1.0
C C:ASN40 5.0 24.6 1.0

Iron binding site 8 out of 16 in 1jro

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Iron binding site 8 out of 16 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus


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 Xanthine Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3002

b:15.2
occ:1.00
 FE2 C:FES3002 0.0 15.2 1.0
S2 C:FES3002 2.1 16.9 1.0
SG C:CYS39 2.2 16.5 1.0
SG C:CYS44 2.2 13.8 1.0
S1 C:FES3002 2.2 15.6 1.0
FE1 C:FES3002 2.8 14.8 1.0
N C:CYS39 3.2 19.7 1.0
N C:CYS44 3.3 21.5 1.0
CB C:CYS39 3.3 17.9 1.0
CB C:CYS44 3.3 18.6 1.0
CA C:CYS44 3.7 19.7 1.0
N C:ASN40 3.7 21.4 1.0
CA C:CYS39 3.7 18.5 1.0
C C:GLY38 3.8 22.0 1.0
N C:GLY45 4.0 16.7 1.0
N C:GLY38 4.1 22.0 1.0
CA C:GLY38 4.1 21.6 1.0
C C:CYS44 4.2 18.9 1.0
C C:CYS39 4.2 19.2 1.0
N C:ALA46 4.3 15.6 1.0
C C:ASP43 4.5 24.8 1.0
N C:GLU41 4.6 25.2 1.0
N C:GLY42 4.6 26.0 1.0
N C:ASP43 4.7 25.4 1.0
O C:GLY38 4.7 23.2 1.0
CA C:ASN40 4.8 23.5 1.0
SG C:CYS47 4.8 12.5 1.0
CB C:ALA46 4.8 13.6 1.0
SG C:CYS63 4.8 15.2 1.0
C C:GLY42 4.9 25.7 1.0

Iron binding site 9 out of 16 in 1jro

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Iron binding site 9 out of 16 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus


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 Xanthine Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe3001

b:18.4
occ:1.00
 FE1 E:FES3001 0.0 18.4 1.0
SG E:CYS103 2.1 17.3 1.0
S2 E:FES3001 2.2 19.4 1.0
SG E:CYS136 2.2 22.4 1.0
S1 E:FES3001 2.2 22.1 1.0
FE2 E:FES3001 2.6 16.8 1.0
CB E:CYS136 3.1 22.0 1.0
CB E:CYS103 3.1 21.8 1.0
N E:CYS103 3.4 22.1 1.0
CA E:CYS103 3.7 21.9 1.0
N E:CYS136 4.0 21.6 1.0
SG E:CYS134 4.1 20.7 1.0
N E:GLY104 4.1 23.0 1.0
CA E:CYS136 4.2 21.4 1.0
C E:CYS103 4.3 22.4 1.0
SG E:CYS106 4.4 19.2 1.0
C E:GLN102 4.6 22.8 1.0
N E:PHE105 4.7 24.4 1.0
N E:ARG135 4.7 19.2 1.0
N E:CYS106 4.9 22.2 1.0
CB E:GLN102 5.0 21.8 1.0

Iron binding site 10 out of 16 in 1jro

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Iron binding site 10 out of 16 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus


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 Xanthine Dehydrogenase From Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe3001

b:16.8
occ:1.00
 FE2 E:FES3001 0.0 16.8 1.0
SG E:CYS106 2.1 19.2 1.0
S2 E:FES3001 2.1 19.4 1.0
SG E:CYS134 2.1 20.7 1.0
S1 E:FES3001 2.2 22.1 1.0
FE1 E:FES3001 2.6 18.4 1.0
CB E:CYS134 3.3 20.6 1.0
CB E:CYS106 3.5 22.7 1.0
CA E:CYS134 4.0 20.9 1.0
N E:CYS106 4.1 22.2 1.0
CB E:CYS136 4.1 22.0 1.0
SG E:CYS136 4.3 22.4 1.0
SG E:CYS103 4.3 17.3 1.0
CA E:CYS106 4.4 22.1 1.0
N E:ARG135 4.5 19.2 1.0
N E:CYS136 4.5 21.6 1.0
C E:CYS134 4.6 20.2 1.0
CG2 E:THR137 4.8 13.3 1.0
N E:GLY104 4.9 23.0 1.0
CA E:CYS136 4.9 21.4 1.0
N E:THR107 4.9 25.2 1.0
N E:CYS103 4.9 22.1 1.0

Reference:

J.J.Truglio, K.Theis, S.Leimkuhler, R.Rappa, K.V.Rajagopalan, C.Kisker. Crystal Structures of the Active and Alloxanthine-Inhibited Forms of Xanthine Dehydrogenase From Rhodobacter Capsulatus Structure V. 10 115 2002.
ISSN: ISSN 0969-2126
PubMed: 11796116
DOI: 10.1016/S0969-2126(01)00697-9
Page generated: Sat Aug 3 08:38:29 2024

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