Calcium in PDB 1dqf: Crystal Structure of Helix II of the X. Laevis Somatic 5S Rrna with A Cytosine Bulge in Two Conformations

The structure of Crystal Structure of Helix II of the X. Laevis Somatic 5S Rrna with A Cytosine Bulge in Two Conformations, PDB code: 1dqf was solved by Y.Xiong, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.20
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.150, 57.150, 43.540, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 22.1

The binding sites of Calcium atom in the Crystal Structure of Helix II of the X. Laevis Somatic 5S Rrna with A Cytosine Bulge in Two Conformations (pdb code 1dqf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Helix II of the X. Laevis Somatic 5S Rrna with A Cytosine Bulge in Two Conformations, PDB code: 1dqf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Helix II of the X. Laevis Somatic 5S Rrna with A Cytosine Bulge in Two Conformations


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Helix II of the X. Laevis Somatic 5S Rrna with A Cytosine Bulge in Two Conformations within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:31.1 occ:1.00 O B:HOH105 2.2 23.4 1.0 O B:HOH120 2.3 47.3 1.0 O B:HOH106 2.3 32.5 1.0 O3' B:C19 2.4 24.7 1.0 O B:HOH101 2.5 38.5 1.0 O2' B:C19 2.6 30.1 1.0 C3' B:C19 3.2 25.2 1.0 C2' B:C19 3.2 26.9 1.0 C4' B:C19 4.1 23.4 1.0 C1' B:C19 4.6 26.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Helix II of the X. Laevis Somatic 5S Rrna with A Cytosine Bulge in Two Conformations


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Helix II of the X. Laevis Somatic 5S Rrna with A Cytosine Bulge in Two Conformations within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:27.7 occ:0.50 OP1 B:C19 2.3 22.2 1.0 O B:HOH107 2.3 29.0 1.0 P B:C19 3.7 24.5 1.0 O B:HOH119 4.3 41.0 1.0 O5' B:C19 4.4 25.5 1.0 C5' B:C19 4.5 23.8 1.0 O3' B:G18 4.6 24.1 1.0 OP2 B:C19 4.6 25.2 1.0

Y.Xiong, M.Sundaralingam. Two Crystal Forms of Helix II of Xenopus Laevis 5S Rrna with A Cytosine Bulge. Rna V. 6 1316 2000.
ISSN: ISSN 1355-8382
PubMed: 10999608
DOI: 10.1017/S135583820000090X