Calcium in PDB 3agv: Crystal Structure of A Human Igg-Aptamer Complex

The structure of Crystal Structure of A Human Igg-Aptamer Complex, PDB code: 3agv was solved by Y.Nomura, S.Sugiyama, T.Sakamoto, S.Miyakawa, H.Adachi, K.Takano, S.Murakami, T.Inoue, Y.Mori, Y.Nakamura, H.Matsumura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.37 / 2.15
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.587, 107.238, 79.458, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 27.7

The structure of Crystal Structure of A Human Igg-Aptamer Complex also contains other interesting chemical elements:

Fluorine

(F)

18 atoms

The binding sites of Calcium atom in the Crystal Structure of A Human Igg-Aptamer Complex (pdb code 3agv). 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 A Human Igg-Aptamer Complex, PDB code: 3agv:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A Human Igg-Aptamer Complex


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 A Human Igg-Aptamer Complex within 5.0Å range: probe atom residue distance (Å) B Occ S:Ca25 b:79.5 occ:1.00 O S:HOH249 2.0 0.5 1.0 O S:HOH236 2.3 41.8 1.0 O S:HOH248 2.4 65.4 1.0 O S:HOH235 2.5 66.1 1.0 O S:HOH247 2.5 78.2 1.0 OP2 S:G7 2.7 61.9 1.0 O6 S:G17 4.0 74.3 1.0 C2' S:UFT6 4.1 63.5 1.0 O6 S:G16 4.1 87.0 1.0 N7 S:G17 4.1 74.2 1.0 P S:G7 4.1 63.0 1.0 N7 S:G16 4.3 84.9 1.0 C3' S:UFT6 4.4 63.3 1.0 F2' S:UFT6 4.6 63.4 1.0 C6 S:G16 4.7 86.2 1.0 O3' S:UFT6 4.7 62.8 1.0 C5 S:G16 4.8 85.7 1.0 C6 S:G17 4.8 75.0 1.0 N4 S:CFZ11 4.8 81.6 1.0 C5' S:G7 4.8 56.4 1.0 C5 S:G17 4.8 75.3 1.0 O5' S:G7 5.0 59.9 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A Human Igg-Aptamer Complex


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 A Human Igg-Aptamer Complex within 5.0Å range: probe atom residue distance (Å) B Occ U:Ca25 b:56.6 occ:1.00 O U:HOH234 2.3 69.1 1.0 OP2 U:G7 2.4 46.8 1.0 O U:HOH233 2.5 56.2 1.0 O U:HOH244 2.6 66.4 1.0 O U:HOH246 3.3 0.2 1.0 O U:HOH245 3.5 0.3 1.0 P U:G7 3.9 46.2 1.0 O U:HOH134 4.0 39.2 1.0 O6 U:G16 4.0 72.5 1.0 O6 U:G17 4.3 49.2 1.0 C5' U:G7 4.5 43.1 1.0 O5' U:G7 4.6 45.0 1.0 OP1 U:G7 4.6 48.7 1.0 N7 U:G16 4.7 72.6 1.0 C2' U:UFT6 4.8 50.2 1.0 O3' U:UFT6 4.9 48.1 1.0 O U:HOH82 4.9 39.6 1.0 C6 U:G16 4.9 72.7 1.0 C3' U:UFT6 4.9 49.8 1.0 F2' U:UFT6 5.0 51.2 1.0

Y.Nomura, S.Sugiyama, T.Sakamoto, S.Miyakawa, H.Adachi, K.Takano, S.Murakami, T.Inoue, Y.Mori, Y.Nakamura, H.Matsumura. Conformational Plasticity of Rna For Target Recognition As Revealed By the 2.15 A Crystal Structure of A Human Igg-Aptamer Complex Nucleic Acids Res. V. 38 7822 2010.
ISSN: ISSN 0305-1048
PubMed: 20675355
DOI: 10.1093/NAR/GKQ615