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Iron in PDB 6iod: The Structure of Udgx in Complex with Single-Stranded Dna

Enzymatic activity of The Structure of Udgx in Complex with Single-Stranded Dna

All present enzymatic activity of The Structure of Udgx in Complex with Single-Stranded Dna:
2.7.7.7;

Protein crystallography data

The structure of The Structure of Udgx in Complex with Single-Stranded Dna, PDB code: 6iod was solved by W.Xie, J.Tu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.93 / 1.66
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 43.805, 83.862, 122.664, 90.00, 94.51, 90.00
R / Rfree (%) 18.2 / 21.7

Iron Binding Sites:

The binding sites of Iron atom in the The Structure of Udgx in Complex with Single-Stranded Dna (pdb code 6iod). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the The Structure of Udgx in Complex with Single-Stranded Dna, PDB code: 6iod:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6iod

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Iron binding site 1 out of 8 in the The Structure of Udgx in Complex with Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Structure of Udgx in Complex with Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:6.0
occ:1.00
 FE1 A:SF4301 0.0 6.0 1.0
S4 A:SF4301 2.2 5.9 1.0
S2 A:SF4301 2.2 5.4 1.0
S3 A:SF4301 2.3 4.9 1.0
SG A:CYS27 2.3 6.4 1.0
FE2 A:SF4301 2.7 6.8 1.0
FE4 A:SF4301 2.7 5.4 1.0
FE3 A:SF4301 2.7 6.9 1.0
CB A:CYS27 3.4 5.7 1.0
N A:CYS27 3.4 8.7 1.0
O A:HOH533 3.5 75.6 1.0
CA A:CYS27 3.8 5.4 1.0
S1 A:SF4301 3.9 6.1 1.0
C A:CYS27 4.2 5.7 1.0
C A:GLY26 4.2 8.6 1.0
O A:CYS27 4.3 14.7 1.0
CB A:LEU29 4.5 6.2 1.0
N A:LEU29 4.6 6.8 1.0
ND1 A:HIS95 4.6 6.5 1.0
N A:GLY26 4.6 7.8 1.0
CA A:GLY26 4.7 7.7 1.0
SG A:CYS120 4.8 4.3 1.0
CG A:LEU29 4.9 6.0 1.0
CB A:CYS120 4.9 4.9 1.0
SG A:CYS24 4.9 6.3 1.0
N A:GLY28 5.0 8.7 1.0
N A:TYR30 5.0 7.0 1.0
CD1 A:LEU29 5.0 6.1 1.0

Iron binding site 2 out of 8 in 6iod

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Iron binding site 2 out of 8 in the The Structure of Udgx in Complex with Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Structure of Udgx in Complex with Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:6.8
occ:1.00
 FE2 A:SF4301 0.0 6.8 1.0
ND1 A:HIS95 2.1 6.5 1.0
S3 A:SF4301 2.2 4.9 1.0
S1 A:SF4301 2.3 6.1 1.0
S4 A:SF4301 2.3 5.9 1.0
FE3 A:SF4301 2.6 6.9 1.0
FE4 A:SF4301 2.7 5.4 1.0
FE1 A:SF4301 2.7 6.0 1.0
CE1 A:HIS95 3.0 8.1 1.0
CG A:HIS95 3.2 5.2 1.0
CB A:HIS95 3.6 4.8 1.0
S2 A:SF4301 3.8 5.4 1.0
N A:HIS95 4.1 3.7 1.0
NE2 A:HIS95 4.1 6.7 1.0
CD2 A:HIS95 4.2 5.3 1.0
N A:TYR30 4.4 7.0 1.0
CB A:LYS94 4.5 9.6 1.0
CA A:HIS95 4.5 4.3 1.0
C A:LYS94 4.6 5.9 1.0
SG A:CYS27 4.6 6.4 1.0
CB A:TYR30 4.7 8.0 1.0
SG A:CYS24 4.7 6.3 1.0
SG A:CYS120 4.8 4.3 1.0
CB A:LEU29 4.8 6.2 1.0
CA A:TYR30 4.8 8.1 1.0
CB A:CYS24 4.8 7.1 1.0
CA A:LYS94 4.9 5.9 1.0
N A:LYS94 4.9 5.0 1.0
C A:LEU29 5.0 7.1 1.0

Iron binding site 3 out of 8 in 6iod

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Iron binding site 3 out of 8 in the The Structure of Udgx in Complex with Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Structure of Udgx in Complex with Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:6.9
occ:1.00
 FE3 A:SF4301 0.0 6.9 1.0
S4 A:SF4301 2.2 5.9 1.0
S2 A:SF4301 2.2 5.4 1.0
S1 A:SF4301 2.3 6.1 1.0
SG A:CYS24 2.4 6.3 1.0
FE2 A:SF4301 2.6 6.8 1.0
FE4 A:SF4301 2.7 5.4 1.0
FE1 A:SF4301 2.7 6.0 1.0
CB A:CYS24 3.3 7.1 1.0
N A:GLY26 3.7 7.8 1.0
S3 A:SF4301 3.8 4.9 1.0
NE1 A:TRP123 4.0 6.3 1.0
CA A:GLY26 4.1 7.7 1.0
C A:CYS24 4.2 7.0 1.0
N A:CYS27 4.3 8.7 1.0
CA A:CYS24 4.3 7.3 1.0
ND1 A:HIS95 4.4 6.5 1.0
O A:CYS24 4.4 7.3 1.0
N A:ARG25 4.5 7.0 1.0
CB A:ALA4 4.5 8.1 1.0
CD1 A:TRP123 4.6 6.4 1.0
C A:GLY26 4.6 8.6 1.0
CE1 A:HIS95 4.7 8.1 1.0
C A:ARG25 4.7 8.8 1.0
SG A:CYS120 4.7 4.3 1.0
CA A:ARG25 4.9 7.2 1.0
SG A:CYS27 4.9 6.4 1.0

Iron binding site 4 out of 8 in 6iod

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Iron binding site 4 out of 8 in the The Structure of Udgx in Complex with Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Structure of Udgx in Complex with Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:5.4
occ:1.00
 FE4 A:SF4301 0.0 5.4 1.0
S3 A:SF4301 2.2 4.9 1.0
S1 A:SF4301 2.2 6.1 1.0
S2 A:SF4301 2.3 5.4 1.0
SG A:CYS120 2.3 4.3 1.0
FE2 A:SF4301 2.7 6.8 1.0
FE3 A:SF4301 2.7 6.9 1.0
FE1 A:SF4301 2.7 6.0 1.0
CB A:CYS120 3.2 4.9 1.0
S4 A:SF4301 3.8 5.9 1.0
O A:HOH533 3.8 75.6 1.0
CA A:CYS120 3.8 4.5 1.0
N A:LYS94 4.1 5.0 1.0
CB A:LYS94 4.1 9.6 1.0
CD1 A:TRP123 4.2 6.4 1.0
NE1 A:TRP123 4.5 6.3 1.0
ND1 A:HIS95 4.5 6.5 1.0
CA A:LYS94 4.6 5.9 1.0
SG A:CYS27 4.7 6.4 1.0
N A:CYS120 4.7 4.7 1.0
SG A:CYS24 4.7 6.3 1.0
N A:HIS95 4.9 3.7 1.0
C A:CYS120 5.0 5.8 1.0

Iron binding site 5 out of 8 in 6iod

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Iron binding site 5 out of 8 in the The Structure of Udgx in Complex with Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Structure of Udgx in Complex with Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:32.8
occ:1.00
 FE1 B:SF4301 0.0 32.8 1.0
S2 B:SF4301 2.2 16.6 1.0
SG B:CYS27 2.2 29.3 1.0
S4 B:SF4301 2.2 28.4 1.0
S3 B:SF4301 2.2 30.0 1.0
FE2 B:SF4301 2.8 30.0 1.0
FE4 B:SF4301 3.0 33.4 1.0
FE3 B:SF4301 3.1 46.7 1.0
N B:CYS27 3.6 23.0 1.0
CB B:CYS27 3.6 25.3 1.0
S1 B:SF4301 3.8 35.8 1.0
CA B:CYS27 3.9 26.9 1.0
C B:CYS27 4.2 28.6 1.0
CB B:LEU29 4.2 35.6 1.0
C B:GLY26 4.2 44.5 1.0
O B:CYS27 4.2 34.0 1.0
N B:LEU29 4.4 42.9 1.0
ND1 B:HIS95 4.6 35.6 1.0
N B:GLY26 4.6 52.5 1.0
CA B:GLY26 4.7 47.1 1.0
CG B:LEU29 4.7 35.5 1.0
CD1 B:LEU29 4.8 31.6 1.0
CA B:LEU29 4.8 43.7 1.0
N B:TYR30 4.8 46.4 1.0
N B:GLY28 4.9 27.5 1.0
CB B:CYS120 4.9 38.8 1.0
O B:GLY26 4.9 51.4 1.0
CB B:HIS95 5.0 28.5 1.0

Iron binding site 6 out of 8 in 6iod

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Iron binding site 6 out of 8 in the The Structure of Udgx in Complex with Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Structure of Udgx in Complex with Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:30.0
occ:1.00
 FE2 B:SF4301 0.0 30.0 1.0
ND1 B:HIS95 1.9 35.6 1.0
S1 B:SF4301 2.2 35.8 1.0
S3 B:SF4301 2.2 30.0 1.0
S4 B:SF4301 2.2 28.4 1.0
CG B:HIS95 2.8 33.8 1.0
CE1 B:HIS95 2.8 33.5 1.0
FE1 B:SF4301 2.8 32.8 1.0
FE4 B:SF4301 3.0 33.4 1.0
FE3 B:SF4301 3.2 46.7 1.0
CB B:HIS95 3.2 28.5 1.0
S2 B:SF4301 3.8 16.6 1.0
NE2 B:HIS95 3.8 34.3 1.0
CD2 B:HIS95 3.8 34.6 1.0
N B:HIS95 4.0 19.7 1.0
CA B:HIS95 4.2 25.3 1.0
N B:TYR30 4.4 46.4 1.0
C B:LYS94 4.6 27.9 1.0
CB B:LEU29 4.7 35.6 1.0
CA B:TYR30 4.8 41.2 1.0
C B:LEU29 4.8 43.9 1.0
SG B:CYS27 4.9 29.3 1.0
CB B:TYR30 4.9 43.9 1.0
SG B:CYS24 4.9 34.7 1.0
SG B:CYS120 5.0 32.7 1.0
CB B:LYS94 5.0 32.0 1.0
CB B:CYS24 5.0 37.1 1.0

Iron binding site 7 out of 8 in 6iod

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Iron binding site 7 out of 8 in the The Structure of Udgx in Complex with Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Structure of Udgx in Complex with Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:46.7
occ:1.00
 FE3 B:SF4301 0.0 46.7 1.0
S4 B:SF4301 2.2 28.4 1.0
S1 B:SF4301 2.2 35.8 1.0
S2 B:SF4301 2.2 16.6 1.0
SG B:CYS24 2.3 34.7 1.0
FE4 B:SF4301 2.7 33.4 1.0
FE1 B:SF4301 3.1 32.8 1.0
FE2 B:SF4301 3.2 30.0 1.0
CB B:CYS24 3.4 37.1 1.0
N B:GLY26 3.6 52.5 1.0
NE1 B:TRP123 3.8 42.2 1.0
S3 B:SF4301 3.8 30.0 1.0
CA B:GLY26 4.0 47.1 1.0
CB B:ALA4 4.1 53.1 1.0
CD1 B:TRP123 4.3 39.2 1.0
N B:ARG25 4.3 48.3 1.0
C B:CYS24 4.3 39.3 1.0
SG B:CYS120 4.5 32.7 1.0
CA B:CYS24 4.5 39.9 1.0
N B:CYS27 4.5 23.0 1.0
C B:GLY26 4.6 44.5 1.0
C B:ARG25 4.6 53.1 1.0
ND1 B:HIS95 4.7 35.6 1.0
O B:CYS24 4.8 31.1 1.0
CA B:ARG25 4.8 52.5 1.0
SG B:CYS27 4.9 29.3 1.0
CE2 B:TRP123 4.9 41.8 1.0
CB B:CYS120 5.0 38.8 1.0
CA B:ALA4 5.0 54.6 1.0
CE1 B:HIS95 5.0 33.5 1.0

Iron binding site 8 out of 8 in 6iod

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Iron binding site 8 out of 8 in the The Structure of Udgx in Complex with Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Structure of Udgx in Complex with Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:33.4
occ:1.00
 FE4 B:SF4301 0.0 33.4 1.0
S1 B:SF4301 2.2 35.8 1.0
S3 B:SF4301 2.2 30.0 1.0
SG B:CYS120 2.2 32.7 1.0
S2 B:SF4301 2.2 16.6 1.0
FE3 B:SF4301 2.7 46.7 1.0
CB B:CYS120 2.9 38.8 1.0
FE2 B:SF4301 3.0 30.0 1.0
FE1 B:SF4301 3.0 32.8 1.0
S4 B:SF4301 3.6 28.4 1.0
CA B:CYS120 3.6 38.5 1.0
N B:LYS94 4.1 33.3 1.0
CD1 B:TRP123 4.2 39.2 1.0
N B:CYS120 4.5 42.3 1.0
ND1 B:HIS95 4.5 35.6 1.0
CB B:LYS94 4.5 32.0 1.0
NE1 B:TRP123 4.5 42.2 1.0
CG B:LYS94 4.5 31.2 1.0
SG B:CYS27 4.7 29.3 1.0
C B:CYS120 4.7 35.0 1.0
N B:HIS95 4.8 19.7 1.0
O B:CYS120 4.8 35.1 1.0
CA B:LYS94 4.8 31.4 1.0
SG B:CYS24 4.8 34.7 1.0
CG1 B:VAL93 5.0 22.8 1.0

Reference:

J.Tu, R.Chen, Y.Yang, W.Cao, W.Xie. Suicide Inactivation of the Uracil Dna Glycosylase Udgx By Covalent Complex Formation. Nat.Chem.Biol. V. 15 615 2019.
ISSN: ESSN 1552-4469
PubMed: 31101915
DOI: 10.1038/S41589-019-0290-X
Page generated: Tue Aug 6 23:08:10 2024

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