Calcium in PDB 5ktv: Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5

The structure of Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5, PDB code: 5ktv was solved by A.F.Ahmad Sobri, R.L.Brady, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.05 / 2.35
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	40.924, 40.924, 102.147, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 23.8

The binding sites of Calcium atom in the Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5 (pdb code 5ktv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5, PDB code: 5ktv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:95.1 occ:1.00 OP2 A:DG12 2.6 68.0 1.0 N7 A:DG12 3.2 51.6 1.0 C8 A:DG12 3.9 56.3 1.0 P A:DG12 4.1 60.2 1.0 C5 A:DG12 4.2 53.6 1.0 O6 A:DG12 4.5 66.2 1.0 C6 A:DG12 4.7 69.4 1.0 O5' A:DG12 4.8 68.2 1.0 OP1 A:DG12 4.9 67.0 1.0 O3' A:DC11 5.0 47.1 1.0

Calcium binding site 2 out of 9 in the Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:0.1 occ:1.00 OP2 A:DG10 2.4 62.6 1.0 O5' A:DG10 3.2 66.2 1.0 P A:DG10 3.2 78.2 1.0 C3' A:1W59 3.3 73.3 1.0 C2' A:1W59 3.3 74.4 1.0 O3' A:1W59 3.7 65.9 1.0 C8 A:DG10 4.3 67.1 1.0 C2' A:DG10 4.3 65.5 1.0 C5' A:DG10 4.6 66.1 1.0 O5' A:1W59 4.6 99.0 1.0 OP1 A:DG10 4.6 61.6 1.0 C4' A:1W59 4.7 76.0 1.0 C1' A:1W59 4.8 72.3 1.0 C3' A:DG10 4.9 57.2 1.0 O4' A:DG10 4.9 68.5 1.0 C1' A:DG10 5.0 58.1 1.0 N9 A:DG10 5.0 61.3 1.0

Calcium binding site 3 out of 9 in the Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:0.9 occ:0.30 OP1 A:DC3 3.5 96.4 1.0 OP2 A:DC3 3.7 84.8 1.0 P A:DC3 4.0 1.0 1.0 O5' A:DC3 4.6 77.5 1.0

Calcium binding site 4 out of 9 in the Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca104 b:64.6 occ:1.00 OP1 A:DG12 2.4 67.0 1.0 P A:DG12 3.5 60.2 1.0 O3' A:DC11 3.8 47.1 1.0 OP2 A:DG12 4.3 68.0 1.0 O5' A:DG12 4.8 68.2 1.0

Calcium binding site 5 out of 9 in the Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca105 b:0.7 occ:1.00 O B:HOH209 2.9 68.7 1.0 O4' A:DA6 4.3 85.5 1.0 C5' A:DA6 4.4 91.0 1.0 O2 B:1W521 4.4 72.6 1.0 N2 A:DG4 4.4 65.6 1.0 C4' A:DA6 4.5 89.3 1.0 N3 A:DA5 4.6 66.9 1.0 O4' A:DA5 4.8 92.2 1.0

Calcium binding site 6 out of 9 in the Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5 within 5.0Å range:

Calcium binding site 7 out of 9 in the Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:72.5 occ:0.33 OP1 B:DA17 2.4 67.0 1.0 P B:DA17 3.5 69.5 1.0 OP2 B:DA17 3.9 72.1 1.0 O5' B:DA17 4.2 73.1 1.0 C5' B:DA17 4.8 67.7 1.0 O3' B:DG16 4.8 66.2 1.0

Calcium binding site 8 out of 9 in the Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:0.5 occ:0.33 O B:HOH210 3.2 72.6 1.0

Calcium binding site 9 out of 9 in the Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Mis-Pairing of Unnatural Base Z-G Dna Duplex at pH 8.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca104 b:66.1 occ:1.00 O A:HOH201 2.3 51.3 1.0 O B:HOH212 2.4 55.5 1.0 O B:HOH203 2.5 71.6 1.0 O B:HOH211 2.5 65.4 1.0 N2 B:DG16 4.2 62.9 1.0 O A:HOH202 4.4 55.7 1.0 O2 A:1W59 4.4 65.3 1.0 O4' B:DA18 4.6 68.9 1.0 O4' A:DG10 4.7 68.5 1.0 N3 B:DA17 4.7 48.5 1.0 C5' B:DA18 4.8 63.3 1.0 C4' B:DA18 4.8 58.9 1.0 O4' B:DA17 4.8 66.8 1.0 C4' A:DG10 4.9 67.8 1.0

L.F.Reichenbach, A.F.Ahmad Sobri, N.R.Zaccai, C.Agnew, N.Burton, L.P.Eperon, S.De Ornellas, I.C.Eperon, R.L.Brady, G.A.Burley. Structural Basis of the Mispairing of An Artificially Expanded Genetic Information System Chemistry 2017.
ISSN: ISSN 0947-6539
DOI: 10.1016/J.CHEMPR.2016.11.009