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Iron in PDB 2w3r: Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine

Enzymatic activity of Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine

All present enzymatic activity of Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine:
1.1.1.204;

Protein crystallography data

The structure of Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine, PDB code: 2w3r was solved by U.Dietzel, J.Kuper, S.Leimkuhler, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.23 / 2.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 92.770, 139.940, 158.040, 109.33, 106.15, 101.05
R / Rfree (%) 24 / 28.1

Other elements in 2w3r:

The structure of Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine 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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine (pdb code 2w3r). 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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine, PDB code: 2w3r:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 2w3r

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Iron binding site 1 out of 16 in the Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine


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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1463

b:41.7
occ:1.00
 FE1 A:FES1463 0.0 41.7 1.0
S2 A:FES1463 2.2 42.6 1.0
S1 A:FES1463 2.2 43.0 1.0
SG A:CYS134 2.3 42.6 1.0
SG A:CYS106 2.3 40.4 1.0
FE2 A:FES1463 3.1 42.9 1.0
CB A:CYS134 3.2 42.2 1.0
CB A:CYS106 3.3 40.4 1.0
CA A:CYS134 3.5 42.2 1.0
N A:ARG135 3.9 42.0 1.0
C A:CYS134 4.2 42.1 1.0
CB A:CYS136 4.2 41.8 1.0
N A:CYS106 4.2 40.5 1.0
N A:CYS136 4.2 41.8 1.0
SG A:CYS136 4.3 42.1 1.0
CA A:CYS106 4.3 40.5 1.0
N A:CYS134 4.8 42.5 1.0
CA A:CYS136 4.8 41.9 1.0
O A:LEU133 4.9 42.7 1.0
CG2 A:THR137 4.9 41.8 1.0
SG A:CYS103 4.9 42.4 1.0
CD2 B:LEU176 4.9 41.4 1.0
C A:CYS106 5.0 40.6 1.0

Iron binding site 2 out of 16 in 2w3r

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Iron binding site 2 out of 16 in the Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine


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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1463

b:42.9
occ:1.00
 FE2 A:FES1463 0.0 42.9 1.0
S2 A:FES1463 2.2 42.6 1.0
S1 A:FES1463 2.2 43.0 1.0
SG A:CYS103 2.3 42.4 1.0
SG A:CYS136 2.3 42.1 1.0
CB A:CYS103 2.8 41.0 1.0
FE1 A:FES1463 3.1 41.7 1.0
N A:CYS103 3.3 41.1 1.0
CB A:CYS136 3.4 41.8 1.0
CA A:CYS103 3.5 41.0 1.0
N A:GLY104 3.7 40.6 1.0
C A:CYS103 3.9 40.7 1.0
N A:PHE105 4.4 40.3 1.0
C A:GLN102 4.5 41.2 1.0
CA A:CYS136 4.6 41.9 1.0
N A:CYS136 4.6 41.8 1.0
SG A:CYS134 4.8 42.6 1.0
CB A:GLN102 4.8 41.2 1.0
CA A:GLY104 4.8 40.4 1.0
N A:GLN102 4.9 41.5 1.0
O A:CYS103 4.9 40.5 1.0
C A:GLY104 4.9 40.4 1.0
CA A:GLN102 4.9 41.3 1.0
N A:CYS106 5.0 40.5 1.0
SG A:CYS106 5.0 40.4 1.0

Iron binding site 3 out of 16 in 2w3r

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Iron binding site 3 out of 16 in the Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine


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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1464

b:52.5
occ:1.00
 FE1 A:FES1464 0.0 52.5 1.0
S2 A:FES1464 2.2 52.5 1.0
S1 A:FES1464 2.2 53.7 1.0
SG A:CYS44 2.3 50.5 1.0
SG A:CYS39 2.3 50.3 1.0
FE2 A:FES1464 3.1 53.8 1.0
N A:CYS44 3.2 50.6 1.0
CB A:CYS44 3.4 50.4 1.0
N A:GLY45 3.6 50.3 1.0
N A:CYS39 3.6 49.0 1.0
CA A:CYS44 3.6 50.5 1.0
CB A:CYS39 3.8 49.5 1.0
N A:ASP43 4.0 51.0 1.0
C A:CYS44 4.0 50.4 1.0
N A:ASN40 4.2 50.1 1.0
CA A:CYS39 4.2 49.6 1.0
N A:ALA46 4.3 50.3 1.0
C A:GLY38 4.3 48.6 1.0
N A:GLY38 4.4 48.0 1.0
CA A:GLY38 4.4 48.3 1.0
C A:ASP43 4.4 50.9 1.0
N A:GLY42 4.5 51.2 1.0
C A:GLY42 4.7 51.1 1.0
CA A:GLY45 4.7 50.2 1.0
CA A:ASP43 4.7 51.1 1.0
C A:CYS39 4.7 49.8 1.0
CA A:GLY42 4.8 51.1 1.0
N A:GLU41 4.8 51.0 1.0
SG A:CYS47 4.8 50.4 1.0
CB A:ALA46 4.9 50.1 1.0
SG A:CYS63 4.9 54.4 1.0
C A:GLY45 5.0 50.3 1.0

Iron binding site 4 out of 16 in 2w3r

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Iron binding site 4 out of 16 in the Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine


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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1464

b:53.8
occ:1.00
 FE2 A:FES1464 0.0 53.8 1.0
S1 A:FES1464 2.2 53.7 1.0
S2 A:FES1464 2.2 52.5 1.0
SG A:CYS47 2.3 50.4 1.0
SG A:CYS63 2.4 54.4 1.0
FE1 A:FES1464 3.1 52.5 1.0
CB A:CYS63 3.2 55.7 1.0
CB A:CYS47 3.7 50.5 1.0
N A:GLY42 4.2 51.2 1.0
N A:CYS63 4.2 55.8 1.0
CA A:CYS63 4.3 55.7 1.0
CA A:GLY42 4.3 51.1 1.0
N A:ASN40 4.5 50.1 1.0
CB A:ASN61 4.5 56.1 1.0
N A:CYS47 4.5 50.4 1.0
SG A:CYS39 4.6 50.3 1.0
CA A:ASN40 4.6 50.5 1.0
CA A:CYS47 4.7 50.5 1.0
N A:GLU41 4.7 51.0 1.0
OD1 A:ASN61 4.8 56.5 1.0
CG A:ASN61 4.9 56.2 1.0
C A:GLY42 5.0 51.1 1.0

Iron binding site 5 out of 16 in 2w3r

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Iron binding site 5 out of 16 in the Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine


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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1463

b:38.6
occ:1.00
 FE1 C:FES1463 0.0 38.6 1.0
S1 C:FES1463 2.2 41.4 1.0
S2 C:FES1463 2.2 40.7 1.0
SG C:CYS106 2.3 38.8 1.0
SG C:CYS134 2.3 40.6 1.0
FE2 C:FES1463 3.1 40.5 1.0
CB C:CYS134 3.3 41.5 1.0
CB C:CYS106 3.3 39.8 1.0
CA C:CYS134 3.5 41.5 1.0
N C:ARG135 3.9 41.4 1.0
C C:CYS134 4.1 41.4 1.0
N C:CYS136 4.3 41.4 1.0
N C:CYS106 4.4 39.7 1.0
CA C:CYS106 4.4 39.9 1.0
SG C:CYS136 4.6 41.7 1.0
CB C:CYS136 4.6 41.4 1.0
CG2 C:THR137 4.7 41.3 1.0
O C:LEU133 4.7 42.4 1.0
N C:CYS134 4.8 41.9 1.0
SG C:CYS103 4.8 41.0 1.0
N C:THR137 5.0 41.5 1.0

Iron binding site 6 out of 16 in 2w3r

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Iron binding site 6 out of 16 in the Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine


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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1463

b:40.5
occ:1.00
 FE2 C:FES1463 0.0 40.5 1.0
S2 C:FES1463 2.2 40.7 1.0
S1 C:FES1463 2.2 41.4 1.0
SG C:CYS103 2.3 41.0 1.0
SG C:CYS136 2.3 41.7 1.0
FE1 C:FES1463 3.1 38.6 1.0
CB C:CYS103 3.1 40.3 1.0
N C:CYS103 3.3 40.3 1.0
CB C:CYS136 3.4 41.4 1.0
CA C:CYS103 3.7 40.3 1.0
N C:GLY104 3.9 40.1 1.0
C C:CYS103 4.1 40.1 1.0
N C:CYS136 4.2 41.4 1.0
CA C:CYS136 4.4 41.5 1.0
C C:GLN102 4.5 40.5 1.0
N C:PHE105 4.6 39.9 1.0
CB C:GLN102 4.6 40.5 1.0
N C:GLN102 4.7 40.9 1.0
SG C:CYS134 4.8 40.6 1.0
SG C:CYS106 4.8 38.8 1.0
CA C:GLN102 4.9 40.6 1.0
CA C:GLY104 5.0 40.0 1.0
N C:ARG135 5.0 41.4 1.0

Iron binding site 7 out of 16 in 2w3r

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Iron binding site 7 out of 16 in the Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine


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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1464

b:46.4
occ:1.00
 FE1 C:FES1464 0.0 46.4 1.0
S2 C:FES1464 2.2 42.7 1.0
S1 C:FES1464 2.2 43.0 1.0
SG C:CYS44 2.3 48.9 1.0
SG C:CYS39 2.3 48.9 1.0
FE2 C:FES1464 3.1 44.2 1.0
N C:CYS39 3.3 48.8 1.0
CB C:CYS39 3.6 49.1 1.0
CB C:CYS44 3.6 49.8 1.0
N C:CYS44 3.7 50.1 1.0
N C:ASN40 3.8 49.9 1.0
CA C:CYS39 3.9 49.1 1.0
N C:GLY45 4.0 49.9 1.0
N C:GLY38 4.0 47.6 1.0
C C:GLY38 4.0 48.5 1.0
CA C:CYS44 4.1 49.8 1.0
CA C:GLY38 4.1 48.1 1.0
C C:CYS39 4.3 49.5 1.0
N C:ALA46 4.4 49.9 1.0
C C:CYS44 4.4 49.9 1.0
N C:ASP43 4.5 50.5 1.0
N C:GLY42 4.5 50.7 1.0
N C:GLU41 4.6 50.5 1.0
CB C:ALA46 4.7 49.8 1.0
CA C:ASN40 4.7 50.2 1.0
C C:ASP43 4.9 50.4 1.0
C C:GLY42 4.9 50.5 1.0
CA C:GLY42 4.9 50.5 1.0
CA C:GLY45 4.9 49.9 1.0
SG C:CYS47 5.0 49.9 1.0
O C:GLY38 5.0 48.5 1.0

Iron binding site 8 out of 16 in 2w3r

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Iron binding site 8 out of 16 in the Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine


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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1464

b:44.2
occ:1.00
 FE2 C:FES1464 0.0 44.2 1.0
S1 C:FES1464 2.2 43.0 1.0
S2 C:FES1464 2.2 42.7 1.0
SG C:CYS47 2.3 49.9 1.0
SG C:CYS63 2.6 53.8 1.0
FE1 C:FES1464 3.1 46.4 1.0
CB C:CYS63 3.5 55.2 1.0
CB C:CYS47 3.6 50.2 1.0
N C:GLY42 4.2 50.7 1.0
N C:CYS47 4.3 50.0 1.0
CA C:GLY42 4.3 50.5 1.0
CB C:ASN61 4.4 55.7 1.0
N C:CYS63 4.4 55.4 1.0
OD1 C:ASN61 4.5 55.5 1.0
CA C:CYS47 4.5 50.2 1.0
N C:ASN40 4.6 49.9 1.0
CA C:CYS63 4.6 55.3 1.0
SG C:CYS39 4.6 48.9 1.0
CA C:ASN40 4.6 50.2 1.0
N C:GLU41 4.8 50.5 1.0
CG C:ASN61 4.8 55.5 1.0
CD2 C:LEU24 5.0 53.0 1.0
C C:GLY42 5.0 50.5 1.0
N C:GLY45 5.0 49.9 1.0

Iron binding site 9 out of 16 in 2w3r

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Iron binding site 9 out of 16 in the Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine


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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1463

b:43.2
occ:1.00
 FE1 E:FES1463 0.0 43.2 1.0
S1 E:FES1463 2.2 45.1 1.0
S2 E:FES1463 2.2 45.5 1.0
SG E:CYS106 2.3 41.5 1.0
SG E:CYS134 2.3 42.4 1.0
FE2 E:FES1463 3.0 43.8 1.0
CB E:CYS106 3.3 40.7 1.0
CB E:CYS134 3.4 42.2 1.0
CA E:CYS134 3.8 42.2 1.0
N E:CYS106 4.1 40.5 1.0
CA E:CYS106 4.2 40.7 1.0
N E:ARG135 4.3 41.8 1.0
C E:CYS134 4.5 41.9 1.0
SG E:CYS136 4.6 43.5 1.0
N E:CYS136 4.6 42.1 1.0
CB E:CYS136 4.7 42.1 1.0
O E:LEU133 4.7 42.5 1.0
C E:CYS106 4.8 40.9 1.0
N E:THR107 4.8 41.1 1.0
SG E:CYS103 4.9 41.7 1.0
N E:CYS134 5.0 42.4 1.0

Iron binding site 10 out of 16 in 2w3r

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Iron binding site 10 out of 16 in the Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine


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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1463

b:43.8
occ:1.00
 FE2 E:FES1463 0.0 43.8 1.0
S2 E:FES1463 2.2 45.5 1.0
S1 E:FES1463 2.2 45.1 1.0
SG E:CYS103 2.3 41.7 1.0
SG E:CYS136 2.3 43.5 1.0
FE1 E:FES1463 3.0 43.2 1.0
CB E:CYS103 3.2 40.7 1.0
CB E:CYS136 3.4 42.1 1.0
N E:CYS103 3.6 40.6 1.0
CA E:CYS103 3.8 40.7 1.0
N E:GLY104 3.9 40.5 1.0
C E:CYS103 4.2 40.5 1.0
N E:CYS136 4.3 42.1 1.0
SG E:CYS134 4.5 42.4 1.0
N E:PHE105 4.5 40.3 1.0
CA E:CYS136 4.5 42.2 1.0
O F:GLY225 4.7 38.8 1.0
C E:GLN102 4.8 40.8 1.0
N E:ARG135 5.0 41.8 1.0

Reference:

U.Dietzel, J.Kuper, J.A.Doebbler, A.Schulte, J.J.Truglio, S.Leimkuhler, C.Kisker. Mechanism of Substrate and Inhibitor Binding of Rhodobacter Capsulatus Xanthine Dehydrogenase. J.Biol.Chem. V. 284 8768 2009.
ISSN: ISSN 0021-9258
PubMed: 19109249
DOI: 10.1074/JBC.M808114200
Page generated: Sun Aug 4 03:38:47 2024

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