Iron in PDB 8iii: Complex Form of Msmudgx H109C Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Msmudgx H109A

Enzymatic activity of Complex Form of Msmudgx H109C Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Msmudgx H109A

All present enzymatic activity of Complex Form of Msmudgx H109C Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Msmudgx H109A:
3.2.2.27;

Protein crystallography data

The structure of Complex Form of Msmudgx H109C Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Msmudgx H109A, PDB code: 8iii was solved by S.Aroli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.47 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.48, 51.37, 54.99, 90, 104.72, 90
R / Rfree (%) 20.1 / 23.3

Iron Binding Sites:

The binding sites of Iron atom in the Complex Form of Msmudgx H109C Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Msmudgx H109A (pdb code 8iii). 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 H109C Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Msmudgx H109A, PDB code: 8iii:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8iii

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Iron binding site 1 out of 4 in the Complex Form of Msmudgx H109C Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Msmudgx 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 H109C Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Msmudgx H109A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:11.8
occ:1.00
 FE1 A:SF4301 0.0 11.8 1.0
S2 A:SF4301 2.3 9.5 1.0
SG A:CYS120 2.3 9.6 1.0
S3 A:SF4301 2.3 10.4 1.0
S4 A:SF4301 2.3 11.4 1.0
FE4 A:SF4301 2.7 12.4 1.0
FE3 A:SF4301 2.7 11.2 1.0
FE2 A:SF4301 2.8 12.2 1.0
CB A:CYS120 3.3 10.9 1.0
S1 A:SF4301 3.9 11.5 1.0
CA A:CYS120 3.9 10.4 1.0
N A:LYS94 4.0 9.8 1.0
CD1 A:TRP123 4.2 10.6 1.0
CB A:LYS94 4.3 12.1 1.0
NE1 A:TRP123 4.5 10.6 1.0
CG A:LYS94 4.6 15.1 1.0
SG A:CYS24 4.6 11.1 1.0
CA A:LYS94 4.7 10.2 1.0
SG A:CYS27 4.7 11.3 1.0
N A:CYS120 4.8 11.0 1.0
ND1 A:HIS95 4.8 12.6 1.0
N A:HIS95 4.8 10.2 1.0
CA A:VAL93 4.9 11.4 1.0
C A:VAL93 5.0 11.1 1.0
CB A:VAL93 5.0 14.1 1.0

Iron binding site 2 out of 4 in 8iii

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Iron binding site 2 out of 4 in the Complex Form of Msmudgx H109C Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Msmudgx 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 H109C Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Msmudgx H109A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:12.2
occ:1.00
 FE2 A:SF4301 0.0 12.2 1.0
S1 A:SF4301 2.3 11.5 1.0
S4 A:SF4301 2.3 11.4 1.0
SG A:CYS27 2.3 11.3 1.0
S3 A:SF4301 2.3 10.4 1.0
FE4 A:SF4301 2.7 12.4 1.0
FE3 A:SF4301 2.7 11.2 1.0
FE1 A:SF4301 2.8 11.8 1.0
CB A:CYS27 3.4 11.7 1.0
N A:CYS27 3.4 13.5 1.0
CA A:CYS27 3.8 13.7 1.0
S2 A:SF4301 3.9 9.5 1.0
C A:CYS27 4.1 13.8 1.0
C A:GLY26 4.2 15.1 1.0
O A:CYS27 4.3 15.1 1.0
CB A:LEU29 4.5 12.1 1.0
N A:LEU29 4.5 13.0 1.0
N A:GLY26 4.6 13.0 1.0
CA A:GLY26 4.7 13.4 1.0
ND1 A:HIS95 4.8 12.6 1.0
SG A:CYS120 4.8 9.6 1.0
N A:GLY28 4.9 14.4 1.0
SG A:CYS24 4.9 11.1 1.0
CG A:LEU29 4.9 12.9 1.0
N A:TYR30 4.9 13.6 1.0
O A:GLY26 5.0 14.7 1.0
CB A:CYS120 5.0 10.9 1.0

Iron binding site 3 out of 4 in 8iii

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Iron binding site 3 out of 4 in the Complex Form of Msmudgx H109C Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Msmudgx 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 H109C Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Msmudgx H109A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:11.2
occ:1.00
 FE3 A:SF4301 0.0 11.2 1.0
S4 A:SF4301 2.2 11.4 1.0
S1 A:SF4301 2.3 11.5 1.0
SG A:CYS24 2.3 11.1 1.0
S2 A:SF4301 2.3 9.5 1.0
FE1 A:SF4301 2.7 11.8 1.0
FE4 A:SF4301 2.7 12.4 1.0
FE2 A:SF4301 2.7 12.2 1.0
CB A:CYS24 3.2 13.1 1.0
N A:GLY26 3.6 13.0 1.0
S3 A:SF4301 3.9 10.4 1.0
CA A:GLY26 4.1 13.4 1.0
NE1 A:TRP123 4.1 10.6 1.0
C A:CYS24 4.2 13.6 1.0
N A:CYS27 4.3 13.5 1.0
CA A:CYS24 4.3 13.4 1.0
O A:CYS24 4.3 14.3 1.0
N A:ARG25 4.4 13.5 1.0
C A:GLY26 4.5 15.1 1.0
CB A:ALA4 4.6 12.3 1.0
ND1 A:HIS95 4.6 12.6 1.0
CD1 A:TRP123 4.6 10.6 1.0
C A:ARG25 4.6 13.5 1.0
SG A:CYS120 4.7 9.6 1.0
CA A:ARG25 4.9 13.0 1.0
CE1 A:HIS95 4.9 12.0 1.0
SG A:CYS27 5.0 11.3 1.0

Iron binding site 4 out of 4 in 8iii

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Iron binding site 4 out of 4 in the Complex Form of Msmudgx H109C Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Msmudgx 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 H109C Mutant and Uracil- Obtained From Uracil Dna (Ttutt) Post Its Cleavage By Msmudgx H109A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:12.4
occ:1.00
 FE4 A:SF4301 0.0 12.4 1.0
S2 A:SF4301 2.3 9.5 1.0
ND1 A:HIS95 2.3 12.6 1.0
S3 A:SF4301 2.3 10.4 1.0
S1 A:SF4301 2.3 11.5 1.0
FE2 A:SF4301 2.7 12.2 1.0
FE1 A:SF4301 2.7 11.8 1.0
FE3 A:SF4301 2.7 11.2 1.0
CE1 A:HIS95 3.2 12.0 1.0
CG A:HIS95 3.3 11.7 1.0
CB A:HIS95 3.5 12.5 1.0
S4 A:SF4301 3.8 11.4 1.0
N A:HIS95 4.0 10.2 1.0
NE2 A:HIS95 4.3 12.6 1.0
CD2 A:HIS95 4.4 12.1 1.0
CA A:HIS95 4.4 11.6 1.0
N A:TYR30 4.4 13.6 1.0
CB A:LYS94 4.6 12.1 1.0
C A:LYS94 4.6 11.0 1.0
CB A:TYR30 4.6 14.1 1.0
SG A:CYS27 4.6 11.3 1.0
CB A:LEU29 4.7 12.1 1.0
SG A:CYS24 4.7 11.1 1.0
CA A:TYR30 4.7 13.7 1.0
SG A:CYS120 4.8 9.6 1.0
N A:LYS94 4.8 9.8 1.0
CB A:CYS24 4.8 13.1 1.0
CA A:LYS94 4.9 10.2 1.0
C A:LEU29 4.9 13.8 1.0
O A:CYS24 5.0 14.3 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: Thu Jul 27 17:20:13 2023

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