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Iron in PDB 6ajq: E52Q Mutant Form of Uracil Dna Glycosylase X From Mycobacterium Smegmatis.

Protein crystallography data

The structure of E52Q Mutant Form of Uracil Dna Glycosylase X From Mycobacterium Smegmatis., PDB code: 6ajq 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) 18.40 / 1.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.395, 51.602, 54.436, 90.00, 105.35, 90.00
R / Rfree (%) 17.3 / 19.1

Iron Binding Sites:

The binding sites of Iron atom in the E52Q Mutant Form of Uracil Dna Glycosylase X From Mycobacterium Smegmatis. (pdb code 6ajq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the E52Q Mutant Form of Uracil Dna Glycosylase X From Mycobacterium Smegmatis., PDB code: 6ajq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6ajq

Go back to Iron Binding Sites List in 6ajq
Iron binding site 1 out of 4 in the E52Q Mutant Form of Uracil Dna Glycosylase X From Mycobacterium Smegmatis.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of E52Q Mutant Form of Uracil Dna Glycosylase X From Mycobacterium Smegmatis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:12.7
occ:1.00
FE1 A:SF4301 0.0 12.7 1.0
S3 A:SF4301 2.3 12.0 1.0
S4 A:SF4301 2.3 12.6 1.0
S2 A:SF4301 2.3 12.9 1.0
SG A:CYS24 2.3 12.9 1.0
FE4 A:SF4301 2.7 12.1 1.0
FE2 A:SF4301 2.7 11.9 1.0
FE3 A:SF4301 2.8 12.8 1.0
CB A:CYS24 3.2 14.5 1.0
N A:GLY26 3.5 14.0 1.0
S1 A:SF4301 3.9 11.5 1.0
CA A:GLY26 4.0 15.3 1.0
NE1 A:TRP123 4.1 13.8 1.0
C A:CYS24 4.2 14.2 1.0
N A:CYS27 4.3 14.0 1.0
CA A:CYS24 4.3 13.3 1.0
O A:CYS24 4.4 15.7 1.0
ND1 A:HIS95 4.4 12.7 1.0
CB A:ALA4 4.5 15.7 1.0
N A:ARG25 4.5 14.0 1.0
C A:ARG25 4.5 16.6 1.0
C A:GLY26 4.5 16.6 1.0
CD1 A:TRP123 4.6 14.0 1.0
CE1 A:HIS95 4.6 13.4 1.0
SG A:CYS120 4.7 11.6 1.0
CA A:ARG25 4.8 15.0 1.0

Iron binding site 2 out of 4 in 6ajq

Go back to Iron Binding Sites List in 6ajq
Iron binding site 2 out of 4 in the E52Q Mutant Form of Uracil Dna Glycosylase X From Mycobacterium Smegmatis.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of E52Q Mutant Form of Uracil Dna Glycosylase X From Mycobacterium Smegmatis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:11.9
occ:1.00
FE2 A:SF4301 0.0 11.9 1.0
SG A:CYS120 2.3 11.6 1.0
S3 A:SF4301 2.3 12.0 1.0
S1 A:SF4301 2.3 11.5 1.0
S4 A:SF4301 2.3 12.6 1.0
FE1 A:SF4301 2.7 12.7 1.0
FE4 A:SF4301 2.7 12.1 1.0
FE3 A:SF4301 2.7 12.8 1.0
CB A:CYS120 3.2 11.8 1.0
CA A:CYS120 3.8 13.0 1.0
S2 A:SF4301 3.9 12.9 1.0
N A:LYS94 4.0 10.6 1.0
CD1 A:TRP123 4.2 14.0 1.0
CB A:LYS94 4.5 13.2 1.0
NE1 A:TRP123 4.6 13.8 1.0
ND1 A:HIS95 4.6 12.7 1.0
SG A:CYS24 4.7 12.9 1.0
N A:CYS120 4.7 12.4 1.0
CA A:LYS94 4.7 10.8 1.0
SG A:CYS27 4.8 14.0 1.0
CA A:VAL93 4.9 11.9 1.0
CB A:VAL93 4.9 16.2 1.0
N A:HIS95 4.9 10.1 1.0
C A:VAL93 5.0 11.8 1.0
C A:CYS120 5.0 13.1 1.0

Iron binding site 3 out of 4 in 6ajq

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Iron binding site 3 out of 4 in the E52Q Mutant Form of Uracil Dna Glycosylase X From Mycobacterium Smegmatis.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of E52Q Mutant Form of Uracil Dna Glycosylase X From Mycobacterium Smegmatis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:12.8
occ:1.00
FE3 A:SF4301 0.0 12.8 1.0
S4 A:SF4301 2.3 12.6 1.0
S1 A:SF4301 2.3 11.5 1.0
S2 A:SF4301 2.3 12.9 1.0
SG A:CYS27 2.4 14.0 1.0
FE4 A:SF4301 2.7 12.1 1.0
FE2 A:SF4301 2.7 11.9 1.0
FE1 A:SF4301 2.8 12.7 1.0
CB A:CYS27 3.4 15.0 1.0
N A:CYS27 3.4 14.0 1.0
CA A:CYS27 3.8 14.6 1.0
S3 A:SF4301 3.9 12.0 1.0
C A:GLY26 4.2 16.6 1.0
C A:CYS27 4.2 13.5 1.0
O A:CYS27 4.4 16.9 1.0
CB A:LEU29 4.4 13.6 1.0
ND1 A:HIS95 4.6 12.7 1.0
N A:GLY26 4.6 14.0 1.0
N A:LEU29 4.6 15.4 1.0
CA A:GLY26 4.6 15.3 1.0
SG A:CYS120 4.7 11.6 1.0
CB A:CYS120 4.8 11.8 1.0
CG A:LEU29 4.9 13.8 1.0
SG A:CYS24 4.9 12.9 1.0
CD1 A:LEU29 5.0 13.5 1.0
N A:GLY28 5.0 17.4 1.0
O A:GLY26 5.0 18.5 1.0

Iron binding site 4 out of 4 in 6ajq

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Iron binding site 4 out of 4 in the E52Q Mutant Form of Uracil Dna Glycosylase X From Mycobacterium Smegmatis.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of E52Q Mutant Form of Uracil Dna Glycosylase X From Mycobacterium Smegmatis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:12.1
occ:1.00
FE4 A:SF4301 0.0 12.1 1.0
ND1 A:HIS95 2.1 12.7 1.0
S3 A:SF4301 2.3 12.0 1.0
S1 A:SF4301 2.3 11.5 1.0
S2 A:SF4301 2.3 12.9 1.0
FE1 A:SF4301 2.7 12.7 1.0
FE3 A:SF4301 2.7 12.8 1.0
FE2 A:SF4301 2.7 11.9 1.0
CE1 A:HIS95 2.9 13.4 1.0
CG A:HIS95 3.2 13.8 1.0
CB A:HIS95 3.6 13.0 1.0
S4 A:SF4301 3.8 12.6 1.0
N A:HIS95 4.0 10.1 1.0
NE2 A:HIS95 4.1 14.6 1.0
CD2 A:HIS95 4.2 12.4 1.0
CA A:HIS95 4.4 10.5 1.0
C A:LYS94 4.5 11.3 1.0
N A:TYR30 4.5 14.1 1.0
SG A:CYS27 4.7 14.0 1.0
CB A:LEU29 4.7 13.6 1.0
SG A:CYS24 4.7 12.9 1.0
CB A:TYR30 4.7 14.9 1.0
SG A:CYS120 4.8 11.6 1.0
N A:LYS94 4.8 10.6 1.0
CA A:TYR30 4.8 15.0 1.0
CB A:CYS24 4.8 14.5 1.0
CA A:LYS94 4.9 10.8 1.0
CB A:LYS94 4.9 13.2 1.0
C A:LEU29 5.0 14.0 1.0
O A:CYS24 5.0 15.7 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: Tue Aug 6 13:45:08 2024

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