Calcium in PDB 463d: Calcium Form of D(Cgcgaattcgcg)2

The structure of Calcium Form of D(Cgcgaattcgcg)2, PDB code: 463d was solved by J.Liu, J.A.Subirana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.45
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	41.117, 41.117, 99.912, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 25.7

The binding sites of Calcium atom in the Calcium Form of D(Cgcgaattcgcg)2 (pdb code 463d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Calcium Form of D(Cgcgaattcgcg)2, PDB code: 463d:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Calcium Form of D(Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calcium Form of D(Cgcgaattcgcg)2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:22.5 occ:1.00 O B:HOH114 2.3 22.7 1.0 O A:HOH117 2.3 31.0 1.0 O A:HOH113 2.4 21.8 1.0 O A:HOH115 2.4 24.4 1.0 O A:HOH116 2.4 25.4 1.0 O B:HOH111 2.5 22.9 1.0 O A:HOH112 2.6 21.6 1.0 N2 A:DG4 4.4 22.1 1.0 O B:HOH177 4.4 22.1 1.0 O2 B:DC21 4.5 25.2 1.0 O4' B:DG22 4.6 26.7 1.0 O A:HOH216 4.6 56.8 1.0 O4' A:DA6 4.6 21.9 1.0 O A:HOH176 4.7 28.6 1.0 C5' A:DA6 4.7 22.9 1.0 C4' A:DA6 4.8 20.1 1.0 C4' B:DG22 4.8 26.8 1.0 C5' B:DG22 4.9 31.3 1.0 O4' A:DA5 4.9 20.6 1.0

Calcium binding site 2 out of 4 in the Calcium Form of D(Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calcium Form of D(Cgcgaattcgcg)2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:19.0 occ:0.33 OP1 A:DA5 2.2 17.7 1.0 O A:HOH125 2.4 20.4 1.0 P A:DA5 3.5 17.2 1.0 OP2 A:DA5 4.0 19.8 1.0 O5' A:DA5 4.1 18.7 1.0 O A:HOH244 4.3 40.6 1.0 C5' A:DA5 4.4 17.5 1.0 O3' A:DG4 4.7 19.1 1.0 O A:HOH188 4.8 24.1 1.0

Calcium binding site 3 out of 4 in the Calcium Form of D(Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calcium Form of D(Cgcgaattcgcg)2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:46.5 occ:1.00 O A:HOH122 2.1 43.4 1.0 O B:HOH118 2.1 39.9 1.0 O B:HOH124 2.2 38.7 1.0 O B:HOH120 2.2 44.6 1.0 O B:HOH121 2.2 40.9 1.0 O A:HOH119 2.3 44.0 1.0 O B:HOH123 2.3 40.1 1.0 C5' B:DA18 4.1 36.5 1.0 O4' B:DA17 4.4 35.2 1.0 O A:HOH154 4.4 26.2 1.0 O B:HOH153 4.4 42.7 1.0 O4' B:DA18 4.5 32.8 1.0 N2 B:DG16 4.5 27.7 1.0 C4' B:DA18 4.5 37.0 1.0 O A:HOH225 4.6 44.5 1.0 O4' A:DG10 4.6 37.9 1.0 O2 A:DC9 4.6 32.1 1.0 O3' B:DA17 4.7 40.5 1.0 C1' B:DA17 4.8 37.0 1.0 N3 B:DA17 4.9 30.3 1.0 O5' B:DA18 4.9 44.4 1.0 C4' B:DA17 4.9 42.0 1.0 C4' A:DG10 5.0 43.1 1.0

Calcium binding site 4 out of 4 in the Calcium Form of D(Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calcium Form of D(Cgcgaattcgcg)2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca104 b:31.3 occ:1.00 OP1 B:DG24 2.2 27.4 1.0 O B:HOH126 2.2 32.4 1.0 P B:DG24 3.5 27.7 1.0 O3' B:DC23 4.1 25.6 1.0 OP2 B:DG24 4.3 26.9 1.0 O B:HOH187 4.5 57.9 0.5 O5' B:DG24 4.7 30.9 1.0 C5' B:DG24 4.9 30.6 1.0 O B:HOH155 5.0 38.9 1.0

J.Liu, J.A.Subirana. Structure of D(Cgcgaattcgcg) in the Presence of Ca(2+) Ions. J.Biol.Chem. V. 274 24749 1999.
ISSN: ISSN 0021-9258
PubMed: 10455145
DOI: 10.1074/JBC.274.35.24749