Atomistry » Iron » PDB 6i95-6j55 » 6iod
Atomistry »
  Iron »
    PDB 6i95-6j55 »
      6iod »

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

Go back to Iron Binding Sites List in 6iod
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

Go back to Iron Binding Sites List in 6iod
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

Go back to Iron Binding Sites List in 6iod
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

Go back to Iron Binding Sites List in 6iod
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

Go back to Iron Binding Sites List in 6iod
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

Go back to Iron Binding Sites List in 6iod
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

Go back to Iron Binding Sites List in 6iod
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

Go back to Iron Binding Sites List in 6iod
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy