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Calcium in PDB 8b77: The Crystal Structure of N828V Variant of Dna Pol Epsilon Containing Datp in the Polymerase Active Site

Enzymatic activity of The Crystal Structure of N828V Variant of Dna Pol Epsilon Containing Datp in the Polymerase Active Site

All present enzymatic activity of The Crystal Structure of N828V Variant of Dna Pol Epsilon Containing Datp in the Polymerase Active Site:
2.7.7.7;

Protein crystallography data

The structure of The Crystal Structure of N828V Variant of Dna Pol Epsilon Containing Datp in the Polymerase Active Site, PDB code: 8b77 was solved by V.Parkash, E.Johansson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.49 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.994, 71.03, 155.255, 90, 112.99, 90
R / Rfree (%) 23.6 / 27.3

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of N828V Variant of Dna Pol Epsilon Containing Datp in the Polymerase Active Site (pdb code 8b77). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the The Crystal Structure of N828V Variant of Dna Pol Epsilon Containing Datp in the Polymerase Active Site, PDB code: 8b77:

Calcium binding site 1 out of 1 in 8b77

Go back to Calcium Binding Sites List in 8b77
Calcium binding site 1 out of 1 in the The Crystal Structure of N828V Variant of Dna Pol Epsilon Containing Datp in the Polymerase Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of N828V Variant of Dna Pol Epsilon Containing Datp in the Polymerase Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1302

b:65.8
occ:1.00
 OD2 A:ASP877 2.0 55.4 1.0
OD1 A:ASP640 2.1 53.7 1.0
O2B A:DTP1301 2.1 57.3 1.0
O3G A:DTP1301 2.1 56.1 1.0
O2A A:DTP1301 2.1 50.9 1.0
O A:VAL641 2.2 66.7 1.0
CG A:ASP640 3.0 68.3 1.0
PB A:DTP1301 3.2 45.2 1.0
CG A:ASP877 3.2 62.1 1.0
PG A:DTP1301 3.3 47.7 1.0
OD2 A:ASP640 3.3 70.5 1.0
C A:VAL641 3.4 60.7 1.0
PA A:DTP1301 3.4 56.9 1.0
O3B A:DTP1301 3.5 36.9 1.0
O3A A:DTP1301 3.6 63.8 1.0
OD1 A:ASP877 3.9 69.0 1.0
O2G A:DTP1301 4.0 61.0 1.0
C5' A:DTP1301 4.1 47.6 1.0
CA A:ALA642 4.1 50.7 1.0
N A:VAL641 4.2 69.8 1.0
N A:SER643 4.2 49.3 1.0
N A:ALA642 4.2 61.3 1.0
O5' A:DTP1301 4.3 43.6 1.0
CB A:ASP877 4.3 53.0 1.0
CA A:VAL641 4.4 57.5 1.0
CB A:ASP640 4.4 59.1 1.0
O1G A:DTP1301 4.5 51.8 1.0
C A:ALA642 4.5 47.0 1.0
O1A A:DTP1301 4.5 51.2 1.0
O1B A:DTP1301 4.5 55.2 1.0
N A:MET644 4.5 53.1 1.0
CB A:MET644 4.6 53.1 1.0
C A:ASP640 4.7 67.6 1.0
CA A:ASP640 5.0 58.5 1.0

Reference:

V.Parkash, Y.Kulkarni, G.O.Bylund, P.Osterman, A.Barrozo, S.L.Kamerlin, E.Johansson. A Sensor Complements the Steric Gate When Dna Polymerase Epsilon Discriminates Ribonucleotides. To Be Published.
Page generated: Thu Jul 10 03:21:33 2025

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