Atomistry » Iron » PDB 6i95-6j55 » 6io9
Atomistry »
  Iron »
    PDB 6i95-6j55 »
      6io9 »

Iron in PDB 6io9: The Structure of Apo-Udgx

Protein crystallography data

The structure of The Structure of Apo-Udgx, PDB code: 6io9 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) 36.61 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.572, 50.958, 54.367, 90.00, 104.56, 90.00
R / Rfree (%) 19 / 22.5

Iron Binding Sites:

The binding sites of Iron atom in the The Structure of Apo-Udgx (pdb code 6io9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Structure of Apo-Udgx, PDB code: 6io9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6io9

Go back to Iron Binding Sites List in 6io9
Iron binding site 1 out of 4 in the The Structure of Apo-Udgx


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 Apo-Udgx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:22.7
occ:1.00
FE1 A:SF4301 0.0 22.7 1.0
S2 A:SF4301 2.2 27.8 1.0
S3 A:SF4301 2.2 28.6 1.0
S4 A:SF4301 2.2 27.3 1.0
SG A:CYS120 2.2 22.4 1.0
FE2 A:SF4301 2.8 25.1 1.0
FE4 A:SF4301 2.8 24.3 1.0
FE3 A:SF4301 2.8 28.4 1.0
CB A:CYS120 3.1 24.4 1.0
S1 A:SF4301 3.7 29.1 1.0
CA A:CYS120 3.8 22.9 1.0
N A:LYS94 4.1 22.8 1.0
CD1 A:TRP123 4.2 22.0 1.0
CB A:LYS94 4.5 23.0 1.0
NE1 A:TRP123 4.5 23.5 1.0
ND1 A:HIS95 4.6 23.4 1.0
N A:CYS120 4.7 23.7 1.0
SG A:CYS27 4.7 28.0 1.0
CG1 A:VAL93 4.7 37.5 1.0
SG A:CYS24 4.7 24.9 1.0
CA A:LYS94 4.8 18.9 1.0
C A:CYS120 4.9 24.7 1.0
N A:HIS95 5.0 22.4 1.0
O A:CYS120 5.0 22.8 1.0

Iron binding site 2 out of 4 in 6io9

Go back to Iron Binding Sites List in 6io9
Iron binding site 2 out of 4 in the The Structure of Apo-Udgx


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 Apo-Udgx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:25.1
occ:1.00
FE2 A:SF4301 0.0 25.1 1.0
S3 A:SF4301 2.2 28.6 1.0
S4 A:SF4301 2.2 27.3 1.0
S1 A:SF4301 2.2 29.1 1.0
SG A:CYS24 2.3 24.9 1.0
FE1 A:SF4301 2.8 22.7 1.0
FE3 A:SF4301 2.8 28.4 1.0
FE4 A:SF4301 2.8 24.3 1.0
CB A:CYS24 3.2 25.6 1.0
N A:GLY26 3.7 29.7 1.0
S2 A:SF4301 3.8 27.8 1.0
NE1 A:TRP123 4.0 23.5 1.0
CA A:GLY26 4.1 27.3 1.0
C A:CYS24 4.1 29.6 1.0
O A:CYS24 4.2 28.8 1.0
CA A:CYS24 4.3 24.1 1.0
N A:CYS27 4.3 26.1 1.0
ND1 A:HIS95 4.4 23.4 1.0
CB A:ALA4 4.4 25.4 1.0
N A:ARG25 4.5 23.9 1.0
CE1 A:HIS95 4.5 26.5 1.0
CD1 A:TRP123 4.5 22.0 1.0
C A:GLY26 4.6 27.1 1.0
C A:ARG25 4.6 28.3 1.0
SG A:CYS120 4.7 22.4 1.0
CA A:ARG25 4.9 26.9 1.0

Iron binding site 3 out of 4 in 6io9

Go back to Iron Binding Sites List in 6io9
Iron binding site 3 out of 4 in the The Structure of Apo-Udgx


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 Apo-Udgx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:28.4
occ:1.00
FE3 A:SF4301 0.0 28.4 1.0
ND1 A:HIS95 1.9 23.4 1.0
S2 A:SF4301 2.2 27.8 1.0
S4 A:SF4301 2.2 27.3 1.0
S1 A:SF4301 2.2 29.1 1.0
CE1 A:HIS95 2.7 26.5 1.0
FE2 A:SF4301 2.8 25.1 1.0
FE4 A:SF4301 2.8 24.3 1.0
FE1 A:SF4301 2.8 22.7 1.0
CG A:HIS95 3.1 22.6 1.0
CB A:HIS95 3.6 27.7 1.0
S3 A:SF4301 3.7 28.6 1.0
NE2 A:HIS95 3.9 21.3 1.0
N A:HIS95 4.0 22.4 1.0
CD2 A:HIS95 4.1 25.0 1.0
C A:LYS94 4.4 24.7 1.0
CA A:HIS95 4.4 24.4 1.0
N A:TYR30 4.6 26.6 1.0
SG A:CYS27 4.7 28.0 1.0
CB A:TYR30 4.7 27.6 1.0
SG A:CYS24 4.8 24.9 1.0
SG A:CYS120 4.8 22.4 1.0
CB A:LEU29 4.8 23.3 1.0
O A:LYS94 4.8 23.1 1.0
CA A:TYR30 4.8 27.5 1.0
N A:LYS94 4.8 22.8 1.0
O A:CYS24 4.9 28.8 1.0
CB A:LYS94 4.9 23.0 1.0
CB A:CYS24 4.9 25.6 1.0
CA A:LYS94 4.9 18.9 1.0

Iron binding site 4 out of 4 in 6io9

Go back to Iron Binding Sites List in 6io9
Iron binding site 4 out of 4 in the The Structure of Apo-Udgx


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 Apo-Udgx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:24.3
occ:1.00
FE4 A:SF4301 0.0 24.3 1.0
S3 A:SF4301 2.2 28.6 1.0
S1 A:SF4301 2.2 29.1 1.0
S2 A:SF4301 2.2 27.8 1.0
SG A:CYS27 2.2 28.0 1.0
FE1 A:SF4301 2.8 22.7 1.0
FE3 A:SF4301 2.8 28.4 1.0
FE2 A:SF4301 2.8 25.1 1.0
N A:CYS27 3.4 26.1 1.0
CB A:CYS27 3.4 29.4 1.0
CA A:CYS27 3.8 28.3 1.0
S4 A:SF4301 3.8 27.3 1.0
C A:GLY26 4.1 27.1 1.0
C A:CYS27 4.2 29.2 1.0
O A:CYS27 4.3 27.3 1.0
ND1 A:HIS95 4.4 23.4 1.0
CB A:LEU29 4.5 23.3 1.0
N A:GLY26 4.6 29.7 1.0
CA A:GLY26 4.7 27.3 1.0
N A:LEU29 4.7 27.3 1.0
SG A:CYS120 4.7 22.4 1.0
CB A:CYS120 4.8 24.4 1.0
O A:GLY26 4.9 26.1 1.0
CG A:LEU29 4.9 26.6 1.0
N A:GLY28 4.9 25.7 1.0
SG A:CYS24 5.0 24.9 1.0
CD1 A:LEU29 5.0 25.2 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 23:03:10 2024

Last articles

Cl in 3IHU
Cl in 3IGS
Cl in 3IEJ
Cl in 3IHP
Cl in 3IEQ
Cl in 3IFS
Cl in 3IE5
Cl in 3IE9
Cl in 3IEA
Cl in 3IBS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy