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Iron in PDB 8iig: Complex Form of Msmudgx H109A Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Udgx H109A

Enzymatic activity of Complex Form of Msmudgx H109A Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Udgx H109A

All present enzymatic activity of Complex Form of Msmudgx H109A Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Udgx H109A:
3.2.2.27;

Protein crystallography data

The structure of Complex Form of Msmudgx H109A Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Udgx H109A, PDB code: 8iig was solved by S.Aroli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.65 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.71, 50.72, 55.06, 90, 104.5, 90
R / Rfree (%) 18.6 / 22.2

Iron Binding Sites:

The binding sites of Iron atom in the Complex Form of Msmudgx H109A Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Udgx H109A (pdb code 8iig). 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 Msmudgx H109A Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Udgx H109A, PDB code: 8iig:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8iig

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Iron binding site 1 out of 4 in the Complex Form of Msmudgx H109A Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Udgx H109A


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 Msmudgx H109A Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Udgx H109A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:19.3
occ:1.00
 FE1 A:SF4301 0.0 19.3 1.0
S3 A:SF4301 2.3 16.1 1.0
S2 A:SF4301 2.3 14.2 1.0
S4 A:SF4301 2.3 14.9 1.0
FE4 A:SF4301 2.8 20.2 1.0
FE3 A:SF4301 2.8 17.9 1.0
FE2 A:SF4301 2.8 18.6 1.0
SG A:CYS120 3.0 14.8 1.0
CB A:CYS120 3.2 15.2 1.0
CA A:CYS120 3.9 15.8 1.0
N A:LYS94 3.9 14.7 1.0
S1 A:SF4301 4.0 16.9 1.0
CD1 A:TRP123 4.2 15.2 1.0
CB A:LYS94 4.5 16.6 1.0
CG A:LYS94 4.5 18.4 1.0
NE1 A:TRP123 4.5 18.6 1.0
N A:CYS120 4.7 17.9 1.0
CA A:VAL93 4.7 14.2 1.0
SG A:CYS24 4.7 20.2 1.0
CA A:LYS94 4.7 16.3 1.0
C A:VAL93 4.8 17.6 1.0
ND1 A:HIS95 4.9 19.2 1.0
N A:HIS95 4.9 14.6 1.0

Iron binding site 2 out of 4 in 8iig

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Iron binding site 2 out of 4 in the Complex Form of Msmudgx H109A Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Udgx H109A


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 Msmudgx H109A Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Udgx H109A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:18.6
occ:1.00
 FE2 A:SF4301 0.0 18.6 1.0
S4 A:SF4301 2.3 14.9 1.0
S1 A:SF4301 2.3 16.9 1.0
S3 A:SF4301 2.3 16.1 1.0
SG A:CYS27 2.6 15.9 1.0
FE3 A:SF4301 2.8 17.9 1.0
FE4 A:SF4301 2.8 20.2 1.0
FE1 A:SF4301 2.8 19.3 1.0
N A:CYS27 3.1 15.2 1.0
CB A:CYS27 3.2 17.0 1.0
CA A:CYS27 3.6 16.3 1.0
S2 A:SF4301 3.9 14.2 1.0
C A:GLY26 4.0 18.3 1.0
C A:CYS27 4.1 18.9 1.0
O A:CYS27 4.3 19.8 1.0
CA A:GLY26 4.4 17.6 1.0
CB A:LEU29 4.5 17.6 1.0
N A:GLY26 4.5 22.0 1.0
ND1 A:HIS95 4.8 19.2 1.0
N A:LEU29 4.8 19.5 1.0
O A:GLY26 4.8 22.8 1.0
CG A:LEU29 4.8 19.9 1.0
SG A:CYS24 4.9 20.2 1.0
CD1 A:LEU29 4.9 15.2 1.0
N A:GLY28 4.9 18.5 1.0
CB A:CYS120 5.0 15.2 1.0

Iron binding site 3 out of 4 in 8iig

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Iron binding site 3 out of 4 in the Complex Form of Msmudgx H109A Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Udgx H109A


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 Msmudgx H109A Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Udgx H109A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:17.9
occ:1.00
 FE3 A:SF4301 0.0 17.9 1.0
SG A:CYS24 2.2 20.2 1.0
S1 A:SF4301 2.3 16.9 1.0
S4 A:SF4301 2.3 14.9 1.0
S2 A:SF4301 2.3 14.2 1.0
FE2 A:SF4301 2.8 18.6 1.0
FE4 A:SF4301 2.8 20.2 1.0
FE1 A:SF4301 2.8 19.3 1.0
CB A:CYS24 3.2 19.9 1.0
N A:GLY26 3.4 22.0 1.0
CA A:GLY26 3.8 17.6 1.0
S3 A:SF4301 3.9 16.1 1.0
NE1 A:TRP123 4.1 18.6 1.0
C A:CYS24 4.1 21.6 1.0
O A:CYS24 4.1 23.3 1.0
N A:CYS27 4.1 15.2 1.0
CA A:CYS24 4.3 20.5 1.0
CB A:ALA4 4.3 16.8 1.0
C A:GLY26 4.4 18.3 1.0
N A:ARG25 4.4 21.2 1.0
C A:ARG25 4.5 20.3 1.0
CD1 A:TRP123 4.6 15.2 1.0
ND1 A:HIS95 4.6 19.2 1.0
CA A:ARG25 4.8 17.9 1.0

Iron binding site 4 out of 4 in 8iig

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Iron binding site 4 out of 4 in the Complex Form of Msmudgx H109A Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Udgx H109A


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 Msmudgx H109A Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Udgx H109A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:20.2
occ:1.00
 FE4 A:SF4301 0.0 20.2 1.0
ND1 A:HIS95 2.2 19.2 1.0
S2 A:SF4301 2.3 14.2 1.0
S3 A:SF4301 2.3 16.1 1.0
S1 A:SF4301 2.3 16.9 1.0
FE1 A:SF4301 2.8 19.3 1.0
FE3 A:SF4301 2.8 17.9 1.0
FE2 A:SF4301 2.8 18.6 1.0
CG A:HIS95 3.2 17.8 1.0
CE1 A:HIS95 3.2 18.5 1.0
CB A:HIS95 3.4 14.4 1.0
S4 A:SF4301 3.9 14.9 1.0
N A:HIS95 4.1 14.6 1.0
NE2 A:HIS95 4.3 17.9 1.0
CD2 A:HIS95 4.3 17.2 1.0
CA A:HIS95 4.4 18.3 1.0
C A:LYS94 4.5 14.7 1.0
N A:TYR30 4.6 20.7 1.0
CB A:TYR30 4.7 21.2 1.0
N A:LYS94 4.7 14.7 1.0
CB A:LEU29 4.7 17.6 1.0
SG A:CYS24 4.8 20.2 1.0
CB A:LYS94 4.8 16.6 1.0
O A:CYS24 4.9 23.3 1.0
CA A:TYR30 4.9 21.9 1.0
SG A:CYS27 4.9 15.9 1.0
CA A:LYS94 4.9 16.3 1.0
CB A:CYS24 5.0 19.9 1.0

Reference:

S.Aroli, E.J.Woo, B.Gopal, U.Varshney. Mutational and Structural Analyses of Udgx: Insights Into the Active Site Pocket Architecture and Its Evolution. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 37283083
DOI: 10.1093/NAR/GKAD486
Page generated: Sat Aug 10 05:46:35 2024

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