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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: Wed Jul 9 10:25:06 2025

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