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Iron in PDB 7dqx: Crystal Structure of Xanthine Dehydrogenase Family Protein

Enzymatic activity of Crystal Structure of Xanthine Dehydrogenase Family Protein

All present enzymatic activity of Crystal Structure of Xanthine Dehydrogenase Family Protein:
1.5.99.14;

Protein crystallography data

The structure of Crystal Structure of Xanthine Dehydrogenase Family Protein, PDB code: 7dqx was solved by W.Lei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 147.24 / 3.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 112.86, 126.792, 294.49, 90, 90, 90
R / Rfree (%) 28.8 / 32.6

Other elements in 7dqx:

The structure of Crystal Structure of Xanthine Dehydrogenase Family Protein also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 7dqx

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Iron binding site 1 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein


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 Family Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:66.4
occ:1.00
 FE1 C:FES201 0.0 66.4 1.0
CB C:CYS62 2.0 65.3 1.0
S1 C:FES201 2.2 64.0 1.0
S2 C:FES201 2.2 65.4 1.0
SG C:CYS50 2.3 61.9 1.0
SG C:CYS62 2.3 65.3 1.0
FE2 C:FES201 3.2 64.8 1.0
CB C:CYS50 3.2 58.5 1.0
CA C:CYS62 3.4 63.9 1.0
N C:CYS62 4.0 60.8 1.0
C C:CYS62 4.1 63.9 1.0
N C:GLY45 4.1 56.0 1.0
SG C:CYS42 4.3 64.0 1.0
O C:CYS62 4.4 64.1 1.0
CA C:CYS50 4.5 56.2 1.0
CA C:GLY45 4.6 56.3 1.0
N C:HIS44 4.6 60.9 1.0
SG C:CYS47 4.6 62.7 1.0
CB C:ARG60 4.7 54.2 1.0
C C:GLU43 4.7 64.8 1.0
CG1 C:VAL40 4.7 61.4 1.0
N C:THR63 4.8 63.0 1.0
CA C:GLU43 4.8 70.8 1.0
OE1 C:GLU43 4.8 82.1 1.0
O C:CYS42 5.0 70.9 1.0
C C:SER61 5.0 59.4 1.0

Iron binding site 2 out of 8 in 7dqx

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Iron binding site 2 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein


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 Family Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:64.8
occ:1.00
 FE2 C:FES201 0.0 64.8 1.0
S1 C:FES201 2.2 64.0 1.0
S2 C:FES201 2.2 65.4 1.0
SG C:CYS47 2.3 62.7 1.0
SG C:CYS42 2.3 64.0 1.0
SG C:CYS50 2.8 61.9 1.0
FE1 C:FES201 3.2 66.4 1.0
N C:CYS47 3.2 58.1 1.0
CB C:CYS50 3.3 58.5 1.0
N C:GLY48 3.4 56.0 1.0
N C:VAL46 3.4 55.7 1.0
CB C:CYS47 3.6 60.2 1.0
CA C:CYS47 3.8 58.4 1.0
C C:VAL46 3.9 56.6 1.0
CA C:GLY45 4.0 56.3 1.0
C C:GLY45 4.0 56.0 1.0
N C:GLY45 4.1 56.0 1.0
CB C:CYS42 4.1 64.8 1.0
C C:CYS47 4.1 58.5 1.0
CA C:VAL46 4.2 55.4 1.0
CA C:GLY48 4.4 54.5 1.0
NH1 C:ARG60 4.5 51.6 1.0
CA C:CYS50 4.5 56.2 1.0
N C:CYS50 4.6 54.4 1.0
N C:CYS42 4.6 64.2 1.0
O C:VAL46 4.7 56.7 1.0
C C:GLY48 4.7 52.5 1.0
CD C:ARG60 4.8 55.6 1.0
CA C:CYS42 4.8 65.9 1.0
SG C:CYS62 4.9 65.3 1.0
C C:CYS42 4.9 68.0 1.0
O C:GLY45 4.9 56.7 1.0

Iron binding site 3 out of 8 in 7dqx

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Iron binding site 3 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein


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 Family Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:43.3
occ:1.00
 FE1 C:FES202 0.0 43.3 1.0
S2 C:FES202 2.2 49.4 1.0
S1 C:FES202 2.2 47.7 1.0
SG C:CYS104 2.3 45.2 1.0
SG C:CYS137 2.3 45.8 1.0
FE2 C:FES202 3.2 47.2 1.0
CB C:CYS139 3.6 45.3 1.0
SG C:CYS101 3.7 49.1 1.0
CB C:CYS137 3.8 46.7 1.0
SG C:CYS139 3.9 48.1 1.0
CB C:CYS104 4.1 43.6 1.0
N C:CYS139 4.2 44.5 1.0
N C:ARG138 4.3 45.4 1.0
OG1 C:THR140 4.3 41.9 1.0
N C:GLN100 4.4 45.5 1.0
CA C:CYS139 4.4 44.2 1.0
CA C:CYS137 4.5 45.4 1.0
N C:CYS101 4.5 48.2 1.0
N C:CYS104 4.7 41.9 1.0
N C:THR140 4.7 42.7 1.0
C C:CYS137 4.8 47.6 1.0
CB C:CYS101 4.9 50.0 1.0
CA C:CYS104 4.9 43.2 1.0
C C:ARG138 5.0 45.7 1.0

Iron binding site 4 out of 8 in 7dqx

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Iron binding site 4 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein


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 Family Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:47.2
occ:1.00
 FE2 C:FES202 0.0 47.2 1.0
S2 C:FES202 2.2 49.4 1.0
S1 C:FES202 2.2 47.7 1.0
SG C:CYS139 2.3 48.1 1.0
SG C:CYS101 2.3 49.1 1.0
CB C:CYS101 2.9 50.0 1.0
FE1 C:FES202 3.2 43.3 1.0
CB C:CYS139 3.5 45.3 1.0
N C:CYS101 4.0 48.2 1.0
CA C:CYS101 4.0 48.1 1.0
N2' A:MCN801 4.4 66.7 1.0
O A:GLY266 4.4 57.6 1.0
N C:CYS139 4.5 44.5 1.0
C C:ARG138 4.5 45.7 1.0
N C:ARG138 4.6 45.4 1.0
CA C:CYS139 4.6 44.2 1.0
SG C:CYS104 4.6 45.2 1.0
C A:GLY266 4.7 57.4 1.0
CG A:MET216 4.8 54.6 1.0
N3' A:MCN801 4.8 71.1 1.0
SG C:CYS137 4.8 45.8 1.0
CZ A:PHE269 4.8 47.2 1.0
O C:ARG138 4.8 46.0 1.0
N A:GLY267 4.9 57.0 1.0
CA C:ARG138 4.9 45.8 1.0
N C:GLY102 4.9 44.4 1.0
CA A:GLY267 4.9 57.0 1.0
CB C:ARG138 4.9 46.7 1.0

Iron binding site 5 out of 8 in 7dqx

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Iron binding site 5 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein


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 Family Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:58.4
occ:1.00
 FE1 F:FES201 0.0 58.4 1.0
CB F:CYS62 2.0 56.9 1.0
S1 F:FES201 2.2 55.8 1.0
S2 F:FES201 2.2 57.6 1.0
SG F:CYS50 2.3 55.7 1.0
SG F:CYS62 2.3 57.5 1.0
CB F:CYS50 3.1 54.3 1.0
FE2 F:FES201 3.2 54.5 1.0
CA F:CYS62 3.5 54.6 1.0
N F:CYS62 4.0 53.2 1.0
C F:CYS62 4.1 52.9 1.0
N F:GLY45 4.1 51.2 1.0
CB F:ARG60 4.4 50.2 1.0
O F:CYS62 4.4 54.1 1.0
SG F:CYS42 4.5 54.1 1.0
CA F:GLY45 4.5 51.4 1.0
CA F:CYS50 4.5 53.3 1.0
N F:HIS44 4.6 53.2 1.0
N F:THR63 4.7 53.4 1.0
SG F:CYS47 4.8 53.2 1.0
C F:GLU43 4.8 54.4 1.0
CA F:GLU43 4.9 56.9 1.0
O F:CYS42 5.0 58.0 1.0
CG1 F:VAL40 5.0 56.0 1.0

Iron binding site 6 out of 8 in 7dqx

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Iron binding site 6 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein


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 Family Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:54.5
occ:1.00
 FE2 F:FES201 0.0 54.5 1.0
S1 F:FES201 2.2 55.8 1.0
S2 F:FES201 2.2 57.6 1.0
SG F:CYS47 2.3 53.2 1.0
SG F:CYS42 2.3 54.1 1.0
SG F:CYS50 2.9 55.7 1.0
N F:CYS47 3.0 51.8 1.0
FE1 F:FES201 3.2 58.4 1.0
N F:VAL46 3.3 50.6 1.0
CB F:CYS47 3.5 53.1 1.0
N F:GLY48 3.6 53.1 1.0
CB F:CYS50 3.6 54.3 1.0
CA F:CYS47 3.6 52.6 1.0
CB F:CYS42 3.7 55.0 1.0
C F:VAL46 3.8 50.7 1.0
N F:GLY45 4.0 51.2 1.0
C F:GLY45 4.1 51.0 1.0
CA F:VAL46 4.1 50.1 1.0
CA F:GLY45 4.1 51.4 1.0
C F:CYS47 4.2 53.7 1.0
N F:CYS42 4.2 55.6 1.0
C F:CYS42 4.3 56.4 1.0
CA F:CYS42 4.3 55.5 1.0
O F:CYS42 4.5 58.0 1.0
N F:GLU43 4.7 55.9 1.0
O F:VAL46 4.7 50.7 1.0
CA F:GLY48 4.7 52.7 1.0
N F:HIS44 4.7 53.2 1.0
NH1 F:ARG60 4.8 52.7 1.0
N F:CYS50 4.9 52.7 1.0
CA F:CYS50 4.9 53.3 1.0
SG F:CYS62 5.0 57.5 1.0

Iron binding site 7 out of 8 in 7dqx

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Iron binding site 7 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein


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 Family Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe202

b:48.6
occ:1.00
 FE1 F:FES202 0.0 48.6 1.0
S2 F:FES202 2.2 51.5 1.0
S1 F:FES202 2.2 46.6 1.0
SG F:CYS104 2.3 50.2 1.0
SG F:CYS137 2.3 53.9 1.0
FE2 F:FES202 3.1 50.3 1.0
CB F:CYS139 3.5 56.3 1.0
SG F:CYS101 3.7 51.0 1.0
CB F:CYS137 3.9 54.7 1.0
SG F:CYS139 3.9 56.4 1.0
CB F:CYS104 4.0 48.9 1.0
N F:CYS139 4.3 55.8 1.0
N F:ARG138 4.4 55.6 1.0
CA F:CYS139 4.4 56.0 1.0
CA F:CYS137 4.5 55.8 1.0
OG1 F:THR140 4.5 56.7 1.0
N F:CYS101 4.5 51.5 1.0
N F:GLN100 4.6 51.9 1.0
N F:CYS104 4.7 49.6 1.0
CB F:CYS101 4.8 50.9 1.0
C F:CYS137 4.8 56.4 1.0
N F:THR140 4.9 55.5 1.0
CA F:CYS104 4.9 50.6 1.0
CG F:GLN100 5.0 54.9 1.0
C F:ARG138 5.0 55.6 1.0

Iron binding site 8 out of 8 in 7dqx

Go back to Iron Binding Sites List in 7dqx
Iron binding site 8 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Family Protein


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 Family Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe202

b:50.3
occ:1.00
 FE2 F:FES202 0.0 50.3 1.0
S2 F:FES202 2.2 51.5 1.0
S1 F:FES202 2.2 46.6 1.0
SG F:CYS139 2.3 56.4 1.0
SG F:CYS101 2.3 51.0 1.0
CB F:CYS101 2.8 50.9 1.0
FE1 F:FES202 3.1 48.6 1.0
CB F:CYS139 3.5 56.3 1.0
CA F:CYS101 4.0 50.9 1.0
N F:CYS101 4.0 51.5 1.0
N2' D:MCN801 4.1 68.8 1.0
N3' D:MCN801 4.6 74.0 1.0
N F:CYS139 4.6 55.8 1.0
C F:ARG138 4.6 55.6 1.0
CA F:CYS139 4.6 56.0 1.0
CA D:GLY267 4.6 55.5 1.0
O D:GLY266 4.6 55.3 1.0
SG F:CYS104 4.7 50.2 1.0
N F:ARG138 4.8 55.6 1.0
C2' D:MCN801 4.8 74.5 1.0
N D:GLY267 4.8 54.7 1.0
C D:GLY266 4.8 55.7 1.0
SG F:CYS137 4.8 53.9 1.0
O F:ARG138 4.8 55.5 1.0
N F:GLY102 4.9 51.0 1.0
C F:CYS101 4.9 51.7 1.0
CZ D:PHE269 4.9 49.5 1.0
CG D:MET216 5.0 56.7 1.0

Reference:

W.Lei, W.Lei. N/A N/A.
Page generated: Wed Apr 5 02:48:54 2023

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