Calcium in PDB 5u2r: Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+

Enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+

All present enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+:
2.7.7.7;

Protein crystallography data

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+, PDB code: 5u2r 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) 26.96 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.910, 80.160, 55.640, 90.00, 107.68, 90.00
R / Rfree (%) 19.1 / 22.9

Other elements in 5u2r:

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+ also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+ (pdb code 5u2r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+, PDB code: 5u2r:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5u2r

Go back to Calcium Binding Sites List in 5u2r
Calcium binding site 1 out of 2 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:13.7
occ:1.00
 OD1 A:ASP192 2.3 10.0 1.0
OD2 A:ASP190 2.4 15.9 1.0
O3' P:DC10 2.4 13.8 0.9
OAJ A:1S0401 2.5 10.3 1.0
OD2 A:ASP256 2.5 14.7 1.0
O A:HOH581 2.5 18.6 1.0
OD1 A:ASP190 2.7 13.3 1.0
CG A:ASP190 2.9 13.0 1.0
CG A:ASP192 3.3 10.1 1.0
OD2 A:ASP192 3.6 10.2 1.0
PAA A:1S0401 3.6 10.7 1.0
C3' P:DC10 3.6 13.9 0.9
CA A:CA403 3.6 10.9 1.0
O P:HOH106 3.7 16.0 1.0
CG A:ASP256 3.7 12.8 1.0
OAI A:1S0401 4.0 10.7 1.0
C4' P:DC10 4.2 14.2 0.9
O A:HOH690 4.2 22.1 1.0
C5' P:DC10 4.2 14.6 0.9
OAF A:1S0401 4.3 11.8 1.0
CB A:ASP190 4.4 12.2 1.0
CB A:ASP256 4.4 11.9 1.0
CB A:ASP192 4.6 10.0 1.0
O A:HOH566 4.6 18.7 1.0
OD1 A:ASP256 4.7 13.3 1.0
O A:MET191 4.8 10.4 1.0
O5' P:DC10 4.8 15.0 0.9
C2' P:DC10 4.8 14.0 0.9
OP1 P:DC10 4.8 15.9 0.9
CAX A:1S0401 4.9 12.0 1.0
OAN A:1S0401 4.9 12.7 1.0
OAG A:1S0401 5.0 10.8 1.0
OAE A:1S0401 5.0 13.3 1.0

Calcium binding site 2 out of 2 in 5u2r

Go back to Calcium Binding Sites List in 5u2r
Calcium binding site 2 out of 2 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Precatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substarte, Incoming L-Dctp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:10.9
occ:1.00
 OD2 A:ASP192 2.3 10.2 1.0
O A:HOH533 2.3 9.1 1.0
OD1 A:ASP190 2.3 13.3 1.0
OAL A:1S0401 2.3 10.4 1.0
OAN A:1S0401 2.3 12.7 1.0
OAJ A:1S0401 2.3 10.3 1.0
CG A:ASP192 3.3 10.1 1.0
O A:ASP190 3.4 12.2 1.0
PAB A:1S0401 3.4 10.7 1.0
CG A:ASP190 3.5 13.0 1.0
PAA A:1S0401 3.5 10.7 1.0
PAC A:1S0401 3.6 12.6 1.0
OD1 A:ASP192 3.6 10.0 1.0
CA A:CA402 3.6 13.7 1.0
OAG A:1S0401 3.7 10.8 1.0
C A:ASP190 3.9 11.6 1.0
OAK A:1S0401 3.9 11.5 1.0
N A:ASP190 4.1 10.7 1.0
O A:HOH690 4.1 22.1 1.0
OD2 A:ASP190 4.2 15.9 1.0
O A:HOH625 4.3 8.8 1.0
OG A:SER180 4.3 9.1 1.0
OAO A:1S0401 4.3 11.9 1.0
CAX A:1S0401 4.3 12.0 1.0
N A:SER180 4.4 9.3 1.0
CA A:ASP190 4.4 11.4 1.0
CA A:GLY179 4.4 9.2 1.0
OAF A:1S0401 4.4 11.8 1.0
CB A:ASP190 4.5 12.2 1.0
CB A:ASP192 4.6 10.0 1.0
N A:MET191 4.7 11.4 1.0
OAM A:1S0401 4.7 10.2 1.0
OAI A:1S0401 4.7 10.7 1.0
N A:ASP192 4.7 10.3 1.0
OAP A:1S0401 4.8 12.9 1.0
C A:MET191 4.9 11.1 1.0
C A:GLY179 5.0 9.2 1.0
O A:HOH581 5.0 18.6 1.0
CA A:MET191 5.0 12.1 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: Sat Dec 12 05:45:15 2020

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