Calcium in PDB 1lnt: Crystal Structure of the Highly Conserved Rna Internal Loop of Srp

The structure of Crystal Structure of the Highly Conserved Rna Internal Loop of Srp, PDB code: 1lnt was solved by J.Deng, Y.Xiong, B.Pan, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.70
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	35.610, 35.610, 133.960, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 22.5

The structure of Crystal Structure of the Highly Conserved Rna Internal Loop of Srp also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Magnesium	(Mg)	4 atoms

The binding sites of Calcium atom in the Crystal Structure of the Highly Conserved Rna Internal Loop of Srp (pdb code 1lnt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Highly Conserved Rna Internal Loop of Srp, PDB code: 1lnt:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Highly Conserved Rna Internal Loop of Srp


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 the Highly Conserved Rna Internal Loop of Srp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca112 b:40.6 occ:1.00 O A:HOH236 1.9 39.1 1.0 O A:HOH261 2.1 51.8 1.0 O A:HOH242 2.2 39.7 1.0 O A:HOH262 2.3 53.0 0.0 O A:HOH240 2.4 43.0 1.0 OP2 A:G7 2.6 38.7 1.0 O A:HOH247 2.6 41.2 1.0 P A:G7 4.0 42.4 1.0 OP1 A:A6 4.3 36.7 1.0 O6 A:G8 4.4 28.7 1.0 N7 A:G8 4.5 30.0 1.0 O5' A:G7 4.6 39.4 1.0 OP1 A:G7 4.6 48.8 1.0 O5' A:A6 4.7 36.4 1.0 P A:A6 4.8 32.6 1.0 OP2 A:A6 4.8 32.8 1.0 O4 A:U9 5.0 27.0 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Highly Conserved Rna Internal Loop of Srp


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 the Highly Conserved Rna Internal Loop of Srp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca113 b:23.4 occ:0.50 O A:HOH234 2.1 34.5 1.0 O A:HOH214 2.3 26.1 1.0 O A:HOH233 2.5 41.2 1.0 O A:HOH220 3.8 30.4 1.0 OP2 A:G12 3.9 18.8 1.0 MG A:MG104 4.0 42.0 1.0 O1P A:CBV11 4.1 24.8 1.0 O A:HOH265 4.3 43.6 1.0 O A:HOH245 4.3 38.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Highly Conserved Rna Internal Loop of Srp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Highly Conserved Rna Internal Loop of Srp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca111 b:19.5 occ:1.00 O B:HOH263 1.7 34.8 1.0 O B:HOH219 2.0 32.5 1.0 O B:HOH218 2.1 29.6 1.0 O B:HOH213 2.2 29.6 1.0 O B:HOH222 2.3 29.1 1.0 OP2 B:A20 3.7 31.1 1.0 OP2 B:C19 3.8 33.7 1.0 O4 A:U4 4.0 24.9 1.0 O B:HOH205 4.1 20.6 1.0 N7 B:A20 4.4 24.6 1.0 O A:HOH206 4.4 37.4 1.0 O6 B:G21 4.4 26.2 1.0 N7 B:G21 4.5 22.6 1.0 N3 A:C5 4.6 24.2 1.0 O6 A:G3 4.6 22.2 1.0 O B:HOH297 4.7 50.8 1.0 O2 A:C5 4.8 24.2 1.0 O A:HOH210 4.8 27.2 1.0 P B:C19 4.8 36.3 1.0 O5' B:C19 4.9 32.1 1.0 N4 B:CBV22 4.9 17.6 1.0 O A:HOH273 4.9 64.5 1.0 C8 B:A20 5.0 21.9 1.0 C2 A:C5 5.0 23.1 1.0

J.Deng, Y.Xiong, B.Pan, M.Sundaralingam. Structure of An Rna Dodecamer Containing A Fragment From Srp Domain IV of Escherichia Coli. Acta Crystallogr.,Sect.D V. 59 1004 2003.
ISSN: ISSN 0907-4449
PubMed: 12777762
DOI: 10.1107/S0907444903006747