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Iron in PDB 6ajr: Complex Form of Uracil Dna Glycosylase X and Uracil

Protein crystallography data

The structure of Complex Form of Uracil Dna Glycosylase X and Uracil, PDB code: 6ajr was solved by W.C.Ahn, S.Aroli, U.Varshney, E.J.Woo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.01 / 1.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.479, 51.773, 55.107, 90.00, 104.98, 90.00
R / Rfree (%) 13.8 / 16.6

Iron Binding Sites:

The binding sites of Iron atom in the Complex Form of Uracil Dna Glycosylase X and Uracil (pdb code 6ajr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Complex Form of Uracil Dna Glycosylase X and Uracil, PDB code: 6ajr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6ajr

Go back to Iron Binding Sites List in 6ajr
Iron binding site 1 out of 4 in the Complex Form of Uracil Dna Glycosylase X and Uracil


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex Form of Uracil Dna Glycosylase X and Uracil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:11.0
occ:1.00
FE1 A:SF4301 0.0 11.0 1.0
ND1 A:HIS95 2.1 11.2 1.0
S3 A:SF4301 2.3 10.3 1.0
S2 A:SF4301 2.3 11.9 1.0
S4 A:SF4301 2.3 11.2 1.0
FE3 A:SF4301 2.6 11.5 1.0
FE4 A:SF4301 2.7 11.1 1.0
FE2 A:SF4301 2.7 10.6 1.0
CE1 A:HIS95 3.0 12.3 1.0
CG A:HIS95 3.2 10.0 1.0
CB A:HIS95 3.6 10.4 1.0
S1 A:SF4301 3.8 11.4 1.0
N A:HIS95 4.1 8.6 1.0
NE2 A:HIS95 4.2 11.6 1.0
CD2 A:HIS95 4.3 11.1 1.0
N A:TYR30 4.4 11.8 1.0
CA A:HIS95 4.5 9.9 1.0
C A:LYS94 4.6 9.2 1.0
CB A:TYR30 4.6 12.5 1.0
SG A:CYS27 4.7 12.5 1.0
CB A:LYS94 4.7 12.9 1.0
CB A:LEU29 4.7 12.2 1.0
SG A:CYS24 4.7 12.5 1.0
SG A:CYS120 4.8 10.6 1.0
CA A:TYR30 4.8 12.4 1.0
CB A:CYS24 4.8 13.4 1.0
N A:LYS94 4.9 9.6 1.0
C A:LEU29 4.9 11.5 1.0
CA A:LYS94 4.9 10.3 1.0

Iron binding site 2 out of 4 in 6ajr

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Iron binding site 2 out of 4 in the Complex Form of Uracil Dna Glycosylase X and Uracil


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex Form of Uracil Dna Glycosylase X and Uracil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:10.6
occ:1.00
FE2 A:SF4301 0.0 10.6 1.0
SG A:CYS120 2.3 10.6 1.0
S4 A:SF4301 2.3 11.2 1.0
S1 A:SF4301 2.3 11.4 1.0
S3 A:SF4301 2.3 10.3 1.0
FE3 A:SF4301 2.7 11.5 1.0
FE1 A:SF4301 2.7 11.0 1.0
FE4 A:SF4301 2.7 11.1 1.0
CB A:CYS120 3.1 11.3 1.0
CA A:CYS120 3.8 10.8 1.0
S2 A:SF4301 3.9 11.9 1.0
N A:LYS94 4.1 9.6 1.0
CD1 A:TRP123 4.2 12.2 1.0
CB A:LYS94 4.3 12.9 1.0
NE1 A:TRP123 4.5 12.2 1.0
CG A:LYS94 4.5 20.8 1.0
ND1 A:HIS95 4.6 11.2 1.0
N A:CYS120 4.7 10.3 1.0
SG A:CYS24 4.7 12.5 1.0
CA A:LYS94 4.7 10.3 1.0
SG A:CYS27 4.7 12.5 1.0
N A:HIS95 4.9 8.6 1.0
C A:CYS120 4.9 11.4 1.0
CG1 A:VAL93 5.0 20.0 1.0
O A:CYS120 5.0 11.1 1.0

Iron binding site 3 out of 4 in 6ajr

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Iron binding site 3 out of 4 in the Complex Form of Uracil Dna Glycosylase X and Uracil


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex Form of Uracil Dna Glycosylase X and Uracil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:11.5
occ:1.00
FE3 A:SF4301 0.0 11.5 1.0
S4 A:SF4301 2.3 11.2 1.0
S1 A:SF4301 2.3 11.4 1.0
S2 A:SF4301 2.3 11.9 1.0
SG A:CYS24 2.4 12.5 1.0
FE1 A:SF4301 2.6 11.0 1.0
FE2 A:SF4301 2.7 10.6 1.0
FE4 A:SF4301 2.7 11.1 1.0
CB A:CYS24 3.2 13.4 1.0
N A:GLY26 3.6 13.2 1.0
S3 A:SF4301 3.9 10.3 1.0
NE1 A:TRP123 4.1 12.2 1.0
CA A:GLY26 4.1 14.1 1.0
C A:CYS24 4.2 14.1 1.0
N A:CYS27 4.3 13.5 1.0
CA A:CYS24 4.3 13.8 1.0
O A:CYS24 4.4 15.6 1.0
ND1 A:HIS95 4.4 11.2 1.0
CB A:ALA4 4.5 15.0 1.0
N A:ARG25 4.5 13.8 1.0
C A:GLY26 4.6 14.4 1.0
CD1 A:TRP123 4.6 12.2 1.0
C A:ARG25 4.6 14.4 1.0
CE1 A:HIS95 4.7 12.3 1.0
SG A:CYS120 4.7 10.6 1.0
CA A:ARG25 4.9 13.8 1.0
SG A:CYS27 5.0 12.5 1.0

Iron binding site 4 out of 4 in 6ajr

Go back to Iron Binding Sites List in 6ajr
Iron binding site 4 out of 4 in the Complex Form of Uracil Dna Glycosylase X and Uracil


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex Form of Uracil Dna Glycosylase X and Uracil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:11.1
occ:1.00
FE4 A:SF4301 0.0 11.1 1.0
S1 A:SF4301 2.3 11.4 1.0
S2 A:SF4301 2.3 11.9 1.0
S3 A:SF4301 2.3 10.3 1.0
SG A:CYS27 2.3 12.5 1.0
FE1 A:SF4301 2.7 11.0 1.0
FE2 A:SF4301 2.7 10.6 1.0
FE3 A:SF4301 2.7 11.5 1.0
CB A:CYS27 3.4 14.0 1.0
N A:CYS27 3.4 13.5 1.0
CA A:CYS27 3.8 14.8 1.0
S4 A:SF4301 3.9 11.2 1.0
C A:CYS27 4.2 14.8 1.0
C A:GLY26 4.2 14.4 1.0
O A:CYS27 4.4 16.4 1.0
CB A:LEU29 4.4 12.2 1.0
N A:LEU29 4.6 12.8 1.0
ND1 A:HIS95 4.6 11.2 1.0
N A:GLY26 4.6 13.2 1.0
CA A:GLY26 4.7 14.1 1.0
SG A:CYS120 4.7 10.6 1.0
CB A:CYS120 4.8 11.3 1.0
N A:GLY28 4.9 14.8 1.0
CG A:LEU29 4.9 12.4 1.0
SG A:CYS24 5.0 12.5 1.0
CD1 A:LEU29 5.0 13.2 1.0
N A:TYR30 5.0 11.8 1.0
CA A:LEU29 5.0 12.0 1.0

Reference:

W.C.Ahn, S.Aroli, J.H.Kim, J.H.Moon, G.S.Lee, M.H.Lee, P.B.Sang, B.H.Oh, U.Varshney, E.J.Woo. Covalent Binding of Uracil Dna Glycosylase Udgx to Abasic Dna Upon Uracil Excision. Nat.Chem.Biol. V. 15 607 2019.
ISSN: ESSN 1552-4469
PubMed: 31101917
DOI: 10.1038/S41589-019-0289-3
Page generated: Sun Dec 13 16:20:23 2020

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