Calcium in PDB 476d: Calcium Form of B-Dna Undecamer Gcgaattcgcg

The structure of Calcium Form of B-Dna Undecamer Gcgaattcgcg, PDB code: 476d was solved by G.Minasov, V.Tereshko, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.30
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	38.764, 38.764, 99.084, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / 22

The binding sites of Calcium atom in the Calcium Form of B-Dna Undecamer Gcgaattcgcg (pdb code 476d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Calcium Form of B-Dna Undecamer Gcgaattcgcg, PDB code: 476d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Calcium Form of B-Dna Undecamer Gcgaattcgcg


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 B-Dna Undecamer Gcgaattcgcg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca112 b:17.2 occ:1.00 O A:HOH128 2.3 20.1 1.0 O B:HOH113 2.3 16.1 1.0 O A:HOH129 2.4 17.3 1.0 O B:HOH116 2.4 19.5 1.0 O A:HOH127 2.4 22.4 1.0 O A:HOH126 2.5 16.0 1.0 O B:HOH119 2.6 20.9 1.0 O B:HOH123 4.4 13.2 1.0 N2 A:DG4 4.4 13.3 1.0 O2 B:DC21 4.5 15.8 1.0 C5' A:DA6 4.5 19.9 1.0 O A:HOH179 4.6 26.4 0.5 O A:HOH132 4.6 21.3 1.0 O4' A:DA6 4.6 17.6 1.0 O4' B:DG22 4.6 14.4 1.0 O B:HOH188 4.6 40.0 1.0 C4' A:DA6 4.7 16.4 1.0 O A:HOH135 4.8 25.7 1.0 O4' A:DA5 4.8 14.8 1.0 O B:HOH162 4.8 25.3 1.0 C4' B:DG22 4.8 17.0 1.0 N3 A:DA5 4.8 15.9 1.0 C5' B:DG22 4.9 18.1 1.0

Calcium binding site 2 out of 6 in the Calcium Form of B-Dna Undecamer Gcgaattcgcg


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 B-Dna Undecamer Gcgaattcgcg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca120 b:15.5 occ:0.33 OP1 A:DA5 2.3 16.6 1.0 O A:HOH130 2.3 16.0 1.0 P A:DA5 3.5 15.9 1.0 OP2 A:DA5 3.9 19.4 1.0 O5' A:DA5 4.1 16.7 1.0 C5' A:DA5 4.4 15.0 1.0 O A:HOH155 4.4 28.1 1.0 O3' A:DG4 4.7 17.7 1.0 O A:HOH164 4.8 30.4 1.0

Calcium binding site 3 out of 6 in the Calcium Form of B-Dna Undecamer Gcgaattcgcg


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 B-Dna Undecamer Gcgaattcgcg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca124 b:19.9 occ:0.33 O A:HOH125 0.0 22.2 0.7 OP2 A:DG12 2.5 14.0 1.0 O A:HOH134 2.6 20.9 0.3 O A:HOH168 2.6 31.1 1.0 O A:HOH146 3.2 24.8 1.0 N7 A:DG12 3.6 12.4 1.0 P A:DG12 3.6 12.8 1.0 C8 A:DG12 3.8 12.9 1.0 O5' A:DG12 4.0 12.0 1.0 OP1 A:DG12 4.1 14.6 1.0 C5 A:DG12 4.8 12.6 1.0

Calcium binding site 4 out of 6 in the Calcium Form of B-Dna Undecamer Gcgaattcgcg


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 B-Dna Undecamer Gcgaattcgcg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:12.9 occ:1.00 OP1 B:DG24 2.2 15.1 1.0 O B:HOH102 2.3 15.9 1.0 O B:HOH103 2.4 15.3 1.0 P B:DG24 3.7 13.3 1.0 O B:HOH105 4.3 22.3 1.0 O3' B:DC23 4.4 11.7 1.0 O5' B:DG24 4.5 13.3 1.0 C5' B:DG24 4.6 13.3 1.0 OP2 B:DG24 4.6 13.6 1.0 O B:HOH157 4.7 23.6 1.0 O B:HOH129 4.8 17.8 1.0

Calcium binding site 5 out of 6 in the Calcium Form of B-Dna Undecamer Gcgaattcgcg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Calcium Form of B-Dna Undecamer Gcgaattcgcg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca104 b:19.9 occ:1.00 O B:HOH110 2.2 24.2 1.0 O B:HOH111 2.2 25.1 1.0 O B:HOH108 2.3 25.5 1.0 OP2 B:DG24 2.3 13.6 1.0 O B:HOH107 2.4 23.5 1.0 O B:HOH105 2.4 22.3 1.0 O B:HOH106 2.5 27.5 1.0 O B:HOH109 2.6 25.7 1.0 P B:DG24 3.7 13.3 1.0 O3' B:DC23 4.3 11.7 1.0 O B:HOH169 4.3 29.4 1.0 OP1 B:DG24 4.4 15.1 1.0 C3' B:DC23 4.4 11.4 1.0 N7 B:DG24 4.4 17.7 1.0 O B:HOH179 4.6 33.2 1.0 O6 B:DG24 4.6 21.6 1.0 O B:HOH164 4.7 26.9 1.0 O5' B:DG24 4.8 13.3 1.0 O B:HOH193 4.8 33.2 1.0 C5 B:DG24 4.9 14.3 1.0

Calcium binding site 6 out of 6 in the Calcium Form of B-Dna Undecamer Gcgaattcgcg


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Calcium Form of B-Dna Undecamer Gcgaattcgcg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca122 b:20.8 occ:0.33 OP2 B:DC15 2.2 20.6 1.0 O B:HOH216 2.6 36.1 0.5 P B:DC15 3.7 18.6 1.0 C3' B:DG14 4.3 16.1 1.0 O5' B:DC15 4.4 18.3 1.0 O3' B:DG14 4.5 16.3 1.0 C2' B:DG14 4.5 15.1 1.0 OP1 B:DC15 4.7 22.2 1.0

G.Minasov, V.Tereshko, M.Egli. Atomic-Resolution Crystal Structures of B-Dna Reveal Specific Influences of Divalent Metal Ions on Conformation and Packing. J.Mol.Biol. V. 291 83 1999.
ISSN: ISSN 0022-2836
PubMed: 10438608
DOI: 10.1006/JMBI.1999.2934