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Iodine in PDB 4m8o: Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp

Enzymatic activity of Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp

All present enzymatic activity of Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp, PDB code: 4m8o was solved by A.E.Sauer-Eriksson, M.Hogg, P.Osterman, E.Johansson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.05 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 148.495, 68.919, 149.852, 90.00, 109.50, 90.00
R / Rfree (%) 18 / 23.7

Other elements in 4m8o:

The structure of Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iodine atom in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp (pdb code 4m8o). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 14 binding sites of Iodine where determined in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp, PDB code: 4m8o:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 14 in 4m8o

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Iodine binding site 1 out of 14 in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:I1

b:95.0
occ:0.50
I5 P:5IU1 0.0 95.0 0.5
C5 P:5IU1 2.1 54.9 1.0
C6 P:5IU1 3.0 51.5 1.0
C4 P:5IU1 3.1 46.5 1.0
O P:HOH213 3.1 46.9 1.0
O4 P:5IU1 3.4 43.1 1.0
N1 P:5IU1 4.2 46.4 1.0
N3 P:5IU1 4.4 45.2 1.0
C2 P:5IU1 4.8 45.3 1.0

Iodine binding site 2 out of 14 in 4m8o

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Iodine binding site 2 out of 14 in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:I4

b:47.6
occ:0.50
I P:C384 0.0 47.6 0.5
C5 P:C384 2.1 39.2 1.0
O P:HOH219 2.2 7.5 0.5
C6 P:C384 3.1 40.1 1.0
C4 P:C384 3.1 34.2 1.0
N4 P:C384 3.3 29.7 1.0
O P:HOH220 3.5 13.8 0.5
C8 P:DA3 3.6 40.7 1.0
N7 P:DA3 3.8 35.9 1.0
N9 P:DA3 4.1 42.1 1.0
O P:HOH214 4.2 58.3 1.0
C2' P:DA3 4.2 52.0 1.0
N1 P:C384 4.3 40.0 1.0
N3 P:C384 4.3 33.5 1.0
C5 P:DA3 4.4 33.9 1.0
I P:C385 4.5 44.6 0.5
C4 P:DA3 4.6 36.7 1.0
N4 P:C385 4.6 25.8 1.0
C1' P:DA3 4.7 50.0 1.0
C2 P:C384 4.8 36.8 1.0

Iodine binding site 3 out of 14 in 4m8o

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Iodine binding site 3 out of 14 in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:I5

b:44.6
occ:0.50
I P:C385 0.0 44.6 0.5
O P:HOH220 2.0 13.8 0.5
C5 P:C385 2.1 35.2 1.0
O P:HOH214 2.8 58.3 1.0
C6 P:C385 3.0 37.1 1.0
O P:HOH221 3.1 69.6 1.0
C4 P:C385 3.1 29.9 1.0
N4 P:C385 3.3 25.8 1.0
C6 P:C384 3.7 40.1 1.0
C2' P:C384 3.7 49.5 1.0
C5 P:C384 3.9 39.2 1.0
N1 P:C384 4.1 40.0 1.0
N1 P:C385 4.2 38.7 1.0
N3 P:C385 4.3 31.0 1.0
O T:HOH129 4.5 24.5 1.0
C1' P:C384 4.5 50.8 1.0
I P:C384 4.5 47.6 0.5
C4 P:C384 4.6 34.2 1.0
C2 P:C384 4.7 36.8 1.0
C2 P:C385 4.8 36.1 1.0
C3' P:C384 4.9 52.7 1.0
N3 P:C384 4.9 33.5 1.0

Iodine binding site 4 out of 14 in 4m8o

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Iodine binding site 4 out of 14 in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:I7

b:35.5
occ:0.60
I P:C387 0.0 35.5 0.6
C5 P:C387 2.1 25.1 1.0
C6 P:C387 3.0 23.8 1.0
C4 P:C387 3.1 23.4 1.0
N4 P:C387 3.4 26.0 1.0
C8 P:DG6 3.8 27.1 1.0
O P:HOH202 3.8 28.2 1.0
O P:HOH218 4.0 48.1 1.0
N7 P:DG6 4.1 26.6 1.0
N1 P:C387 4.3 22.0 1.0
N9 P:DG6 4.3 28.1 1.0
C2' P:DG6 4.3 32.6 1.0
O6 P:DG8 4.3 19.4 1.0
N3 P:C387 4.4 20.7 1.0
N7 P:DG8 4.7 17.2 1.0
C5 P:DG6 4.8 23.4 1.0
C2 P:C387 4.8 20.2 1.0
C1' P:DG6 4.9 31.2 1.0
C6 P:DG8 4.9 17.3 1.0
C4 P:DG6 4.9 24.3 1.0

Iodine binding site 5 out of 14 in 4m8o

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Iodine binding site 5 out of 14 in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:I9

b:17.9
occ:0.40
I5 P:5IU9 0.0 17.9 0.4
CL P:CL102 2.0 24.0 0.6
C5 P:5IU9 2.1 16.1 1.0
C6 P:5IU9 3.0 17.2 1.0
C4 P:5IU9 3.1 17.4 1.0
O4 P:5IU9 3.3 16.1 1.0
O P:HOH204 3.5 40.9 1.0
C8 P:DG8 3.7 18.2 1.0
O P:HOH217 3.7 32.3 1.0
N7 P:DG8 3.9 17.2 1.0
C2' P:DG8 4.3 20.8 1.0
N9 P:DG8 4.3 19.8 1.0
N1 P:5IU9 4.3 18.5 1.0
N3 P:5IU9 4.4 17.2 1.0
I5 P:5IU10 4.5 13.2 0.1
C5 P:DG8 4.6 17.4 1.0
O4 P:5IU10 4.7 19.8 1.0
CL P:CL101 4.7 9.2 1.0
O P:HOH216 4.7 31.8 1.0
C1' P:DG8 4.8 18.9 1.0
C4 P:DG8 4.8 18.4 1.0
C2 P:5IU9 4.9 17.6 1.0

Iodine binding site 6 out of 14 in 4m8o

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Iodine binding site 6 out of 14 in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:I10

b:13.2
occ:0.10
I5 P:5IU10 0.0 13.2 0.1
CL P:CL101 1.8 9.2 1.0
C5 P:5IU10 2.1 17.4 1.0
C6 P:5IU10 3.0 19.2 1.0
C4 P:5IU10 3.2 18.4 1.0
O P:HOH205 3.3 5.5 0.5
O4 P:5IU10 3.4 19.8 1.0
C6 P:5IU9 3.4 17.2 1.0
O P:HOH217 3.7 32.3 1.0
C5 P:5IU9 3.7 16.1 1.0
N1 P:5IU9 3.7 18.5 1.0
O P:HOH206 4.0 32.7 1.0
O P:HOH204 4.1 40.9 1.0
C3' P:5IU9 4.2 19.1 1.0
C2' P:5IU9 4.3 18.9 1.0
C1' P:5IU9 4.3 19.0 1.0
C4 P:5IU9 4.4 17.4 1.0
N1 P:5IU10 4.4 18.4 1.0
C2 P:5IU9 4.4 17.6 1.0
N3 P:5IU10 4.4 17.0 1.0
I5 P:5IU9 4.5 17.9 0.4
O P:HOH212 4.5 34.4 1.0
OP2 P:5IU10 4.5 20.1 1.0
O4' P:5IU9 4.6 23.3 1.0
N3 P:5IU9 4.6 17.2 1.0
N4 P:DOC11 4.8 19.7 1.0
C4' P:5IU9 4.8 20.5 1.0
O P:HOH222 4.8 8.1 0.5
C5' P:5IU9 4.9 19.4 1.0
C2 P:5IU10 4.9 18.0 1.0

Iodine binding site 7 out of 14 in 4m8o

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Iodine binding site 7 out of 14 in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
T:I2

b:0.4
occ:0.50
I5 T:5IU2 0.0 0.4 0.5
C5 T:5IU2 2.1 0.5 1.0
C6 T:5IU2 3.0 0.4 1.0
C4 T:5IU2 3.2 0.3 1.0
O4 T:5IU2 3.4 0.0 1.0
OP1 T:5IU2 4.2 0.7 1.0
I T:C383 4.2 0.4 0.5
N1 T:5IU2 4.3 0.4 1.0
N3 T:5IU2 4.5 0.9 1.0
O1P T:C383 4.7 82.9 1.0
N4 T:C383 4.9 63.7 1.0
C2 T:5IU2 4.9 0.9 1.0

Iodine binding site 8 out of 14 in 4m8o

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Iodine binding site 8 out of 14 in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
T:I3

b:0.4
occ:0.50
I T:C383 0.0 0.4 0.5
C5 T:C383 2.1 85.8 1.0
O1P T:C383 2.9 82.9 1.0
C6 T:C383 2.9 78.3 1.0
C4 T:C383 3.3 73.9 1.0
N4 T:C383 3.7 63.7 1.0
I5 T:5IU4 3.7 73.6 0.5
O5' T:C383 4.0 79.6 1.0
P T:C383 4.1 94.9 1.0
C5 T:5IU2 4.1 0.5 1.0
C6 T:5IU2 4.2 0.4 1.0
I5 T:5IU2 4.2 0.4 0.5
N1 T:C383 4.3 68.7 1.0
O4 T:5IU4 4.3 50.9 0.5
N3 T:C383 4.5 73.6 1.0
C5 T:5IU4 4.6 56.6 0.5
C2' T:5IU2 4.7 0.9 1.0
C3' T:5IU2 4.7 0.2 1.0
C4 T:5IU2 4.8 0.3 1.0
C4 T:5IU4 4.8 52.2 0.5
N1 T:5IU2 4.9 0.4 1.0
C2 T:C383 4.9 69.4 1.0
O3' T:5IU2 5.0 0.7 1.0

Iodine binding site 9 out of 14 in 4m8o

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Iodine binding site 9 out of 14 in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
T:I4

b:87.8
occ:0.50
I5 T:5IU4 0.0 87.8 0.5
C5 T:5IU4 2.1 54.0 0.5
N3 T:5IU4 3.0 48.2 0.5
C4 T:5IU4 3.1 54.3 0.5
O4 T:5IU4 3.2 50.1 0.5
C6 T:5IU4 3.2 51.5 0.5
O4 T:5IU4 3.7 50.9 0.5
C4 T:5IU4 3.8 52.2 0.5
C2 T:5IU4 3.9 48.6 0.5
O2 T:5IU4 3.9 51.3 0.5
N4 T:C383 4.0 63.7 1.0
N3 T:C383 4.1 73.6 1.0
N A:GLY838 4.2 24.2 1.0
CB A:LYS837 4.2 35.3 1.0
C4 T:C383 4.3 73.9 1.0
N3 T:5IU4 4.3 49.5 0.5
C A:LYS837 4.3 26.5 1.0
CA A:GLY838 4.4 24.4 1.0
N1 T:5IU4 4.5 44.8 0.5
O T:HOH124 4.6 39.7 1.0
O A:LYS837 4.6 24.1 1.0
C2 T:5IU4 4.9 50.2 0.5
CA A:LYS837 4.9 28.0 1.0
O T:HOH120 5.0 22.1 0.5
C2 T:C383 5.0 69.4 1.0

Iodine binding site 10 out of 14 in 4m8o

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Iodine binding site 10 out of 14 in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
T:I4

b:73.6
occ:0.50
I5 T:5IU4 0.0 73.6 0.5
C5 T:5IU4 2.1 56.6 0.5
N3 T:5IU4 3.0 49.5 0.5
C4 T:5IU4 3.1 52.2 0.5
O4 T:5IU4 3.1 50.9 0.5
C6 T:5IU4 3.2 51.8 0.5
OP1 T:5IU4 3.2 31.7 0.5
O2 T:5IU4 3.4 58.8 0.5
NH2 A:ARG836 3.5 31.8 1.0
C2 T:5IU4 3.5 50.2 0.5
I T:C383 3.7 0.4 0.5
C6 T:C383 3.8 78.3 1.0
C5 T:C383 3.8 85.8 1.0
C4 T:5IU4 3.8 54.3 0.5
OP1 T:5IU4 3.9 32.1 0.5
O4 T:5IU4 4.0 50.1 0.5
C3' T:C383 4.3 48.7 1.0
N3 T:5IU4 4.4 48.2 0.5
C2' T:C383 4.4 56.5 1.0
N1 T:5IU4 4.4 43.6 0.5
P T:5IU4 4.5 36.2 0.5
CZ A:ARG836 4.5 31.2 1.0
OG1 A:THR514 4.6 22.1 1.0
O A:HOH1726 4.6 37.0 1.0
O5' T:5IU4 4.6 35.4 0.5
N1 T:C383 4.6 68.7 1.0
O5' T:5IU4 4.7 36.1 0.5
P T:5IU4 4.7 36.3 0.5
NZ A:LYS534 4.7 35.9 1.0
C4 T:C383 4.8 73.9 1.0
N1 T:5IU4 4.8 44.8 0.5
C2 T:5IU4 4.9 48.6 0.5
NH1 A:ARG836 4.9 30.0 1.0
O3' T:C383 4.9 37.4 1.0

Reference:

M.Hogg, P.Osterman, G.O.Bylund, R.A.Ganai, E.B.Lundstrom, A.E.Sauer-Eriksson, E.Johansson. Structural Basis For Processive Dna Synthesis By Yeast Dna Polymerase Epsilon. Nat.Struct.Mol.Biol. V. 21 49 2014.
ISSN: ISSN 1545-9993
PubMed: 24292646
DOI: 10.1038/NSMB.2712
Page generated: Sun Dec 13 19:34:46 2020

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