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Iron in PDB 6l6s: The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna

Enzymatic activity of The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna

All present enzymatic activity of The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna:
2.7.7.7;

Protein crystallography data

The structure of The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna, PDB code: 6l6s was solved by W.Xie, J.Tu, H.Zeng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.66 / 2.06
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 44.265, 82.348, 122.444, 90.00, 94.93, 90.00
R / Rfree (%) 20.9 / 26.1

Iron Binding Sites:

The binding sites of Iron atom in the The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna (pdb code 6l6s). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna, PDB code: 6l6s:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6l6s

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Iron binding site 1 out of 8 in the The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna


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 the Udgx Mutant H109E Crosslinked to Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:21.6
occ:1.00
 FE1 A:SF4301 0.0 21.6 1.0
S2 A:SF4301 2.2 21.3 1.0
S3 A:SF4301 2.2 18.5 1.0
S4 A:SF4301 2.2 31.4 1.0
SG A:CYS27 2.3 23.3 1.0
FE4 A:SF4301 2.9 15.8 1.0
FE3 A:SF4301 3.0 30.8 1.0
FE2 A:SF4301 3.1 27.4 1.0
CB A:CYS27 3.3 27.8 1.0
N A:CYS27 3.4 33.9 1.0
S1 A:SF4301 3.7 38.7 1.0
CA A:CYS27 3.8 34.8 1.0
C A:GLY26 4.1 30.4 1.0
C A:CYS27 4.1 37.3 1.0
O A:CYS27 4.2 41.1 1.0
CA A:GLY26 4.6 27.9 1.0
CB A:LEU29 4.6 19.5 1.0
N A:GLY26 4.6 33.1 1.0
CB A:CYS120 4.7 18.8 1.0
N A:LEU29 4.7 22.9 1.0
CD1 A:LEU29 4.8 17.1 1.0
O A:GLY26 4.9 33.5 1.0
ND1 A:HIS95 4.9 27.4 1.0
SG A:CYS120 4.9 16.8 1.0
CG A:LEU29 5.0 23.4 1.0
N A:GLY28 5.0 31.0 1.0
CB A:ALA119 5.0 18.4 1.0

Iron binding site 2 out of 8 in 6l6s

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Iron binding site 2 out of 8 in the The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna


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 the Udgx Mutant H109E Crosslinked to Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:27.4
occ:1.00
 FE2 A:SF4301 0.0 27.4 1.0
ND1 A:HIS95 1.9 27.4 1.0
S3 A:SF4301 2.2 18.5 1.0
S4 A:SF4301 2.2 31.4 1.0
S1 A:SF4301 2.2 38.7 1.0
CE1 A:HIS95 2.8 24.8 1.0
CG A:HIS95 3.0 19.5 1.0
FE4 A:SF4301 3.1 15.8 1.0
FE1 A:SF4301 3.1 21.6 1.0
FE3 A:SF4301 3.2 30.8 1.0
CB A:HIS95 3.5 14.9 1.0
NE2 A:HIS95 4.0 23.8 1.0
N A:HIS95 4.0 18.0 1.0
S2 A:SF4301 4.0 21.3 1.0
CD2 A:HIS95 4.1 23.3 1.0
N A:TYR30 4.3 25.4 1.0
CA A:HIS95 4.3 19.3 1.0
CB A:LYS94 4.4 17.1 1.0
C A:LYS94 4.5 16.1 1.0
CB A:TYR30 4.5 25.9 1.0
CA A:TYR30 4.6 25.6 1.0
CB A:LEU29 4.7 19.5 1.0
CB A:CYS24 4.8 28.7 1.0
CA A:LYS94 4.8 12.4 1.0
SG A:CYS27 4.9 23.3 1.0
N A:LYS94 4.9 12.2 1.0
C A:LEU29 5.0 26.6 1.0

Iron binding site 3 out of 8 in 6l6s

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Iron binding site 3 out of 8 in the The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna


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 the Udgx Mutant H109E Crosslinked to Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:30.8
occ:1.00
 FE3 A:SF4301 0.0 30.8 1.0
S4 A:SF4301 2.2 31.4 1.0
S2 A:SF4301 2.2 21.3 1.0
S1 A:SF4301 2.2 38.7 1.0
SG A:CYS24 2.2 28.3 1.0
FE4 A:SF4301 3.0 15.8 1.0
FE1 A:SF4301 3.0 21.6 1.0
CB A:CYS24 3.0 28.7 1.0
FE2 A:SF4301 3.2 27.4 1.0
N A:GLY26 3.6 33.1 1.0
S3 A:SF4301 3.8 18.5 1.0
NE1 A:TRP123 3.8 22.1 1.0
CA A:GLY26 4.0 27.9 1.0
CB A:ALA4 4.1 26.9 1.0
CA A:CYS24 4.2 36.3 1.0
C A:CYS24 4.2 37.7 1.0
N A:ARG25 4.4 39.0 1.0
N A:CYS27 4.4 33.9 1.0
CD1 A:TRP123 4.5 21.6 1.0
C A:GLY26 4.6 30.4 1.0
O A:CYS24 4.6 37.3 1.0
C A:ARG25 4.6 35.8 1.0
ND1 A:HIS95 4.8 27.4 1.0
CA A:ARG25 4.9 39.7 1.0
CE2 A:TRP123 5.0 25.3 1.0
SG A:CYS120 5.0 16.8 1.0

Iron binding site 4 out of 8 in 6l6s

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Iron binding site 4 out of 8 in the The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna


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 the Udgx Mutant H109E Crosslinked to Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:15.8
occ:1.00
 FE4 A:SF4301 0.0 15.8 1.0
S3 A:SF4301 2.2 18.5 1.0
S2 A:SF4301 2.2 21.3 1.0
S1 A:SF4301 2.2 38.7 1.0
SG A:CYS120 2.2 16.8 1.0
FE1 A:SF4301 2.9 21.6 1.0
CB A:CYS120 2.9 18.8 1.0
FE3 A:SF4301 3.0 30.8 1.0
FE2 A:SF4301 3.1 27.4 1.0
CA A:CYS120 3.6 11.6 1.0
S4 A:SF4301 3.7 31.4 1.0
N A:LYS94 4.0 12.2 1.0
CD1 A:TRP123 4.1 21.6 1.0
CB A:LYS94 4.1 17.1 1.0
CG A:LYS94 4.2 23.7 1.0
NE1 A:TRP123 4.4 22.1 1.0
N A:CYS120 4.5 14.0 1.0
CA A:LYS94 4.6 12.4 1.0
C A:CYS120 4.7 25.5 1.0
O A:CYS120 4.8 17.4 1.0
ND1 A:HIS95 4.9 27.4 1.0
SG A:CYS27 4.9 23.3 1.0
SG A:CYS24 4.9 28.3 1.0
N A:HIS95 5.0 18.0 1.0

Iron binding site 5 out of 8 in 6l6s

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Iron binding site 5 out of 8 in the The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:71.4
occ:0.63
 FE1 B:SF4301 0.0 71.4 0.6
S2 B:SF4301 2.2 90.2 1.0
S4 B:SF4301 2.2 99.2 1.0
S3 B:SF4301 2.2 0.3 1.0
SG B:CYS27 2.2 59.9 1.0
FE3 B:SF4301 3.1 78.9 0.6
FE2 B:SF4301 3.1 61.3 0.7
FE4 B:SF4301 3.2 52.1 0.7
CB B:CYS27 3.3 61.9 1.0
N B:CYS27 3.4 60.6 1.0
S1 B:SF4301 3.7 89.7 1.0
CA B:CYS27 3.7 60.9 1.0
C B:CYS27 4.1 61.2 1.0
CB B:LEU29 4.1 59.6 1.0
O B:CYS27 4.1 62.6 1.0
C B:GLY26 4.2 65.7 1.0
CD1 B:LEU29 4.4 53.3 1.0
N B:LEU29 4.4 61.8 1.0
CG B:LEU29 4.5 56.5 1.0
N B:TYR30 4.5 60.3 1.0
CB B:CYS120 4.7 64.4 1.0
ND1 B:HIS95 4.7 75.3 1.0
N B:GLY26 4.7 69.5 1.0
CA B:GLY26 4.7 69.5 1.0
CA B:LEU29 4.7 60.8 1.0
N B:GLY28 4.9 62.0 1.0
O B:GLY26 4.9 63.2 1.0

Iron binding site 6 out of 8 in 6l6s

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Iron binding site 6 out of 8 in the The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:61.3
occ:0.71
 FE2 B:SF4301 0.0 61.3 0.7
ND1 B:HIS95 1.8 75.3 1.0
S3 B:SF4301 2.2 0.3 1.0
S1 B:SF4301 2.2 89.7 1.0
S4 B:SF4301 2.2 99.2 1.0
CE1 B:HIS95 2.6 58.6 1.0
CG B:HIS95 2.9 52.8 1.0
FE1 B:SF4301 3.1 71.4 0.6
FE3 B:SF4301 3.2 78.9 0.6
FE4 B:SF4301 3.2 52.1 0.7
CB B:HIS95 3.4 44.4 1.0
S2 B:SF4301 3.8 90.2 1.0
NE2 B:HIS95 3.8 43.4 1.0
N B:HIS95 3.9 39.9 1.0
CD2 B:HIS95 3.9 41.0 1.0
CB B:TYR30 4.2 63.1 1.0
N B:TYR30 4.2 60.3 1.0
CA B:HIS95 4.2 40.1 1.0
CA B:TYR30 4.3 62.4 1.0
C B:LYS94 4.4 37.5 1.0
CB B:LYS94 4.5 40.7 1.0
CB B:LEU29 4.7 59.6 1.0
C B:LEU29 4.8 60.1 1.0
CB B:CYS24 4.8 71.7 1.0
CA B:LYS94 4.8 38.8 1.0
SG B:CYS120 4.9 86.5 1.0
N B:LYS94 4.9 40.6 1.0
O B:LYS94 5.0 35.8 1.0
O B:CYS24 5.0 69.0 1.0

Iron binding site 7 out of 8 in 6l6s

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Iron binding site 7 out of 8 in the The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:78.9
occ:0.64
 FE3 B:SF4301 0.0 78.9 0.6
S4 B:SF4301 2.2 99.2 1.0
S1 B:SF4301 2.2 89.7 1.0
S2 B:SF4301 2.2 90.2 1.0
SG B:CYS24 2.4 70.9 1.0
FE1 B:SF4301 3.1 71.4 0.6
FE2 B:SF4301 3.2 61.3 0.7
FE4 B:SF4301 3.2 52.1 0.7
CB B:CYS24 3.3 71.7 1.0
N B:GLY26 3.7 69.5 1.0
S3 B:SF4301 3.7 0.3 1.0
NE1 B:TRP123 3.8 57.2 1.0
CA B:GLY26 4.0 69.5 1.0
C B:CYS24 4.3 70.7 1.0
CD1 B:TRP123 4.4 52.5 1.0
N B:CYS27 4.4 60.6 1.0
CA B:CYS24 4.4 72.0 1.0
N B:ARG25 4.5 72.2 1.0
C B:GLY26 4.6 65.7 1.0
O B:CYS24 4.6 69.0 1.0
ND1 B:HIS95 4.6 75.3 1.0
SG B:CYS120 4.6 86.5 1.0
C B:ARG25 4.7 70.5 1.0
CE1 B:HIS95 4.8 58.6 1.0
CE2 B:TRP123 4.9 58.6 1.0
CB B:CYS120 5.0 64.4 1.0
CA B:ARG25 5.0 71.0 1.0

Iron binding site 8 out of 8 in 6l6s

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Iron binding site 8 out of 8 in the The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Structure of the Udgx Mutant H109E Crosslinked to Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:52.1
occ:0.71
 FE4 B:SF4301 0.0 52.1 0.7
SG B:CYS120 1.9 86.5 1.0
S3 B:SF4301 2.2 0.3 1.0
S2 B:SF4301 2.2 90.2 1.0
S1 B:SF4301 2.2 89.7 1.0
CB B:CYS120 2.4 64.4 1.0
FE1 B:SF4301 3.2 71.4 0.6
FE2 B:SF4301 3.2 61.3 0.7
FE3 B:SF4301 3.2 78.9 0.6
CA B:CYS120 3.4 54.2 1.0
S4 B:SF4301 3.8 99.2 1.0
N B:LYS94 3.9 40.6 1.0
CD1 B:TRP123 4.2 52.5 1.0
CB B:LYS94 4.2 40.7 1.0
N B:CYS120 4.4 50.7 1.0
CG B:LYS94 4.4 41.5 1.0
C B:CYS120 4.5 52.4 1.0
CA B:LYS94 4.5 38.8 1.0
O B:CYS120 4.5 53.6 1.0
NE1 B:TRP123 4.5 57.2 1.0
CG1 B:VAL93 4.7 31.7 1.0
CA B:VAL93 4.7 34.3 1.0
C B:VAL93 4.8 34.9 1.0
ND1 B:HIS95 4.8 75.3 1.0
N B:HIS95 4.8 39.9 1.0
SG B:CYS27 4.9 59.9 1.0

Reference:

W.Xie, J.Tu, H.Zeng. Structure of A Covalent Complex-Forming Udgx Mutant To Be Published.
Page generated: Wed Aug 7 00:44:29 2024

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