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Chlorine 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
Iodine (I) 14 atoms
Zinc (Zn) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp, PDB code: 4m8o:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4m8o

Go back to Chlorine Binding Sites List in 4m8o
Chlorine binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl101

b:9.2
occ:1.00
I5 P:5IU10 1.8 13.2 0.1
O P:HOH204 2.9 40.9 1.0
O P:HOH212 3.3 34.4 1.0
O P:HOH205 3.5 5.5 0.5
C5 P:5IU10 3.9 17.4 1.0
O A:HOH1573 3.9 41.7 1.0
C6 P:5IU9 4.0 17.2 1.0
C5' P:5IU9 4.1 19.4 1.0
O P:HOH206 4.3 32.7 1.0
C3' P:5IU9 4.3 19.1 1.0
O P:HOH217 4.3 32.3 1.0
OP2 P:5IU9 4.4 21.6 1.0
OP2 P:5IU10 4.4 20.1 1.0
C5 P:5IU9 4.5 16.1 1.0
C4' P:5IU9 4.5 20.5 1.0
C6 P:5IU10 4.6 19.2 1.0
O4' P:5IU9 4.6 23.3 1.0
N1 P:5IU9 4.6 18.5 1.0
I5 P:5IU9 4.7 17.9 0.4
C1' P:5IU9 4.9 19.0 1.0
C2' P:5IU9 4.9 18.9 1.0
C4 P:5IU10 5.0 18.4 1.0

Chlorine binding site 2 out of 2 in 4m8o

Go back to Chlorine Binding Sites List in 4m8o
Chlorine binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Epsilon with An Incoming Datp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl102

b:24.0
occ:0.60
I5 P:5IU9 2.0 17.9 0.4
O P:HOH204 3.6 40.9 1.0
O P:HOH216 3.7 31.8 1.0
C5 P:5IU9 4.0 16.1 1.0
OE1 A:GLN434 4.2 39.1 1.0
C8 P:DG8 4.3 18.2 1.0
CD A:GLN434 4.4 34.5 1.0
NE2 A:GLN434 4.4 40.4 1.0
C2' P:DG8 4.5 20.8 1.0
O P:HOH217 4.6 32.3 1.0
C6 P:5IU9 4.7 17.2 1.0
N7 P:DG8 4.7 17.2 1.0
N1 A:TAU1304 4.9 66.7 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: Sat Dec 12 10:54:53 2020

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