Atomistry » Calcium » PDB 5tua-5ue5 » 5u2t
Atomistry »
  Calcium »
    PDB 5tua-5ue5 »
      5u2t »

Calcium in PDB 5u2t: Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.:
2.7.7.7;

Protein crystallography data

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+., PDB code: 5u2t was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.78 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.615, 79.395, 54.795, 90.00, 107.60, 90.00
R / Rfree (%) 20 / 24.7

Other elements in 5u2t:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+. also contains other interesting chemical elements:

Fluorine (F) 1 atom
Sodium (Na) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+. (pdb code 5u2t). 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 Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+., PDB code: 5u2t:

Calcium binding site 1 out of 1 in 5u2t

Go back to Calcium Binding Sites List in 5u2t
Calcium binding site 1 out of 1 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)Ftc-Tp and CA2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:40.4
occ:1.00
 OAD A:1RY401 2.2 49.3 1.0
OD2 A:ASP192 2.3 41.9 1.0
OD1 A:ASP190 2.3 34.0 1.0
O A:HOH508 2.4 44.1 1.0
OAC A:1RY401 2.4 44.1 1.0
OAI A:1RY401 2.5 44.0 1.0
O A:HOH549 2.7 45.9 1.0
CG A:ASP192 3.1 41.0 1.0
OD1 A:ASP192 3.2 42.5 1.0
CG A:ASP190 3.4 36.7 1.0
PBA A:1RY401 3.5 46.8 1.0
PBB A:1RY401 3.5 48.0 1.0
NA P:NA101 3.5 46.6 1.0
OAR A:1RY401 3.6 46.5 1.0
PAZ A:1RY401 3.7 48.3 1.0
OD2 A:ASP190 3.7 41.1 1.0
OAQ A:1RY401 4.0 44.9 1.0
OAG A:1RY401 4.2 51.6 1.0
O A:ASP190 4.3 34.8 1.0
OAO A:1RY401 4.4 57.0 1.0
CA A:GLY179 4.5 38.8 1.0
CB A:ASP192 4.5 34.7 1.0
OAH A:1RY401 4.6 48.1 1.0
O A:HOH564 4.6 52.7 1.0
O A:HOH563 4.7 39.4 1.0
C A:ASP190 4.7 34.9 1.0
CB A:ASP190 4.7 34.1 1.0
N A:ASP190 4.8 34.9 1.0
N A:SER180 4.8 41.7 1.0
OAE A:1RY401 4.9 44.8 1.0
O3' P:DC10 4.9 41.4 1.0
OAF A:1RY401 4.9 47.6 1.0
N A:ASP192 5.0 30.4 1.0

Reference:

R.Vyas, A.J.Reed, A.T.Raper, W.J.Zahurancik, P.C.Wallenmeyer, Z.Suo. Structural Basis For the D-Stereoselectivity of Human Dna Polymerase Beta. Nucleic Acids Res. V. 45 6228 2017.
ISSN: ESSN 1362-4962
PubMed: 28402499
DOI: 10.1093/NAR/GKX252
Page generated: Mon Jul 15 11:26:40 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy