Calcium in PDB 477d: Calcium Form of the B-Dna Dodecamer Ggcgaattcgcg

The structure of Calcium Form of the B-Dna Dodecamer Ggcgaattcgcg, PDB code: 477d 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)	20.00 / 1.70
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	41.990, 41.990, 99.550, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 23.5

The binding sites of Calcium atom in the Calcium Form of the B-Dna Dodecamer Ggcgaattcgcg (pdb code 477d). 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 the B-Dna Dodecamer Ggcgaattcgcg, PDB code: 477d:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Calcium Form of the B-Dna Dodecamer Ggcgaattcgcg


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 the B-Dna Dodecamer Ggcgaattcgcg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca112 b:25.7 occ:1.00 O A:HOH117 2.3 24.8 1.0 O A:HOH118 2.3 28.4 1.0 O A:HOH116 2.3 24.0 1.0 O A:HOH114 2.3 22.4 1.0 O A:HOH115 2.4 30.6 1.0 O A:HOH119 2.5 26.9 1.0 O B:HOH113 2.6 26.2 1.0 N2 A:DG4 4.3 20.7 1.0 O A:HOH188 4.4 59.6 1.0 O4' A:DA6 4.6 26.9 1.0 O B:HOH123 4.6 24.8 1.0 C5' A:DA6 4.6 26.1 1.0 O2 B:DC21 4.6 25.9 1.0 O4' B:DG22 4.7 26.1 1.0 O A:HOH128 4.7 33.8 1.0 C4' A:DA6 4.7 25.6 1.0 O A:HOH218 4.8 53.4 1.0 O A:HOH135 4.8 29.1 1.0 C4' B:DG22 4.8 26.7 1.0 O4' A:DA5 4.9 24.3 1.0 N3 A:DA5 5.0 24.7 1.0

Calcium binding site 2 out of 4 in the Calcium Form of the B-Dna Dodecamer Ggcgaattcgcg


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 the B-Dna Dodecamer Ggcgaattcgcg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca120 b:23.8 occ:0.33 OP1 A:DA5 2.4 24.6 1.0 O A:HOH121 2.5 27.1 1.0 P A:DA5 3.5 20.7 1.0 OP2 A:DA5 4.0 25.1 1.0 O5' A:DA5 4.2 23.7 1.0 C5' A:DA5 4.5 23.5 1.0 O A:HOH187 4.7 31.7 1.0 O3' A:DG4 4.7 23.1 1.0

Calcium binding site 3 out of 4 in the Calcium Form of the B-Dna Dodecamer Ggcgaattcgcg


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 the B-Dna Dodecamer Ggcgaattcgcg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:28.4 occ:1.00 OP1 B:DG24 2.2 27.4 1.0 O B:HOH102 2.3 35.7 1.0 P B:DG24 3.4 26.1 1.0 O3' B:DC23 3.8 25.5 1.0 OP2 B:DG24 4.2 24.3 1.0 O5' B:DG24 4.7 27.0 1.0 O B:HOH106 5.0 43.8 1.0 C5' B:DG24 5.0 26.9 1.0

Calcium binding site 4 out of 4 in the Calcium Form of the B-Dna Dodecamer Ggcgaattcgcg


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 the B-Dna Dodecamer Ggcgaattcgcg within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca146 b:46.8 occ:1.00 O B:HOH283 2.2 40.0 1.0 O B:HOH186 2.2 43.8 1.0 O B:HOH282 2.4 44.4 1.0 C5' B:DA18 4.1 41.0 1.0 N2 B:DG16 4.3 32.9 1.0 O4' B:DA17 4.3 37.6 1.0 O4' B:DA18 4.4 37.9 1.0 C4' B:DA18 4.4 38.6 1.0 O A:HOH147 4.6 30.5 1.0 C1' B:DA17 4.6 37.3 1.0 O2 A:DC9 4.7 36.4 1.0 O4' A:DG10 4.7 37.5 1.0 O3' B:DA17 4.7 42.9 1.0 N3 B:DA17 4.8 33.8 1.0 C4' B:DA17 4.8 37.9 1.0 C4' A:DG10 4.9 37.4 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