Calcium in PDB 1d8g: Ultrahigh Resolution Crystal Structure of B-Dna Decamer D(Ccagtactgg)

The structure of Ultrahigh Resolution Crystal Structure of B-Dna Decamer D(Ccagtactgg), PDB code: 1d8g was solved by C.L.Kielkopf, S.Ding, P.Kuhn, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.00 / 0.74
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	31.735, 25.703, 34.215, 90.00, 116.90, 90.00
R / Rfree (%)	10.5 / 13.1

The binding sites of Calcium atom in the Ultrahigh Resolution Crystal Structure of B-Dna Decamer D(Ccagtactgg) (pdb code 1d8g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Ultrahigh Resolution Crystal Structure of B-Dna Decamer D(Ccagtactgg), PDB code: 1d8g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Ultrahigh Resolution Crystal Structure of B-Dna Decamer D(Ccagtactgg)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ultrahigh Resolution Crystal Structure of B-Dna Decamer D(Ccagtactgg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:5.8 occ:0.24 O A:HOH321 1.8 14.2 0.5 O A:HOH271 1.8 26.8 1.0 O A:HOH286 2.0 5.6 0.6 O A:HOH319 2.3 8.7 0.5 O A:HOH230 2.4 12.5 0.9 O A:HOH323 2.4 8.4 0.5 O A:HOH318 2.4 7.4 0.5 OP1 A:DG10 4.5 7.5 1.0 OP2 A:DG10 4.7 7.1 1.0

Calcium binding site 2 out of 5 in the Ultrahigh Resolution Crystal Structure of B-Dna Decamer D(Ccagtactgg)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ultrahigh Resolution Crystal Structure of B-Dna Decamer D(Ccagtactgg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:7.2 occ:0.46 O A:HOH214 2.6 26.9 1.0 O A:HOH263 2.6 13.9 0.8 O A:HOH261 2.7 9.6 0.8 O A:HOH270 3.3 9.7 0.5

Calcium binding site 3 out of 5 in the Ultrahigh Resolution Crystal Structure of B-Dna Decamer D(Ccagtactgg)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ultrahigh Resolution Crystal Structure of B-Dna Decamer D(Ccagtactgg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:13.1 occ:0.86 O A:HOH265 2.1 31.6 0.9 O A:HOH264 2.2 21.8 0.8 O A:HOH266 2.3 31.0 1.0 O A:HOH267 2.4 21.9 0.8 O A:HOH240 2.4 13.2 0.7 O A:HOH268 2.5 13.8 0.8 O A:HOH219 2.5 18.6 1.0 O A:HOH240 2.5 12.2 0.3 O A:HOH241 4.3 38.5 0.6 O A:HOH254 4.5 19.9 1.0 O6 A:DG4 4.5 6.8 1.0 O A:HOH305 4.5 19.4 0.8 N7 A:DG4 4.6 7.1 1.0 O A:HOH243 4.7 9.5 0.9 O A:HOH237 4.8 17.8 1.0

Calcium binding site 4 out of 5 in the Ultrahigh Resolution Crystal Structure of B-Dna Decamer D(Ccagtactgg)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ultrahigh Resolution Crystal Structure of B-Dna Decamer D(Ccagtactgg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:9.2 occ:0.61 CA A:CA204 0.0 9.2 0.6 CA A:CA204 1.0 8.0 0.4 O A:HOH304 2.0 17.1 0.8 O A:HOH235 2.4 10.2 1.0 O A:HOH304 2.4 9.3 0.2 O A:HOH229 3.3 8.5 0.5 O A:HOH282 4.0 24.7 1.0 O A:HOH229 4.0 13.2 0.5 O A:HOH296 4.4 10.4 0.4 O2 A:DC7 4.5 7.4 1.0 O4' A:DT8 4.6 6.4 1.0 O A:HOH272 4.6 19.2 0.8 C4' A:DT8 4.9 6.5 1.0

Calcium binding site 5 out of 5 in the Ultrahigh Resolution Crystal Structure of B-Dna Decamer D(Ccagtactgg)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ultrahigh Resolution Crystal Structure of B-Dna Decamer D(Ccagtactgg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:8.0 occ:0.39 CA A:CA204 0.0 8.0 0.4 CA A:CA204 1.0 9.2 0.6 O A:HOH235 2.5 10.2 1.0 O A:HOH229 2.5 8.5 0.5 O A:HOH304 2.7 17.1 0.8 O A:HOH304 2.8 9.3 0.2 O A:HOH229 3.1 13.2 0.5 O A:HOH296 3.7 10.4 0.4 O A:HOH272 3.8 19.2 0.8 O4' A:DT8 4.4 6.4 1.0 O2 A:DT8 4.6 7.0 1.0 O A:HOH278 4.6 14.1 0.6 O2 A:DC7 4.7 7.4 1.0 C4' A:DT8 4.8 6.5 1.0 O A:HOH282 4.9 24.7 1.0

C.L.Kielkopf, S.Ding, P.Kuhn, D.C.Rees. Conformational Flexibility of B-Dna at 0.74 A Resolution: D(Ccagtactgg)(2). J.Mol.Biol. V. 296 787 2000.
ISSN: ISSN 0022-2836
PubMed: 10677281
DOI: 10.1006/JMBI.1999.3478