Calcium in PDB 1j9h: Crystal Structure of An Rna Duplex with Uridine Bulges

The structure of Crystal Structure of An Rna Duplex with Uridine Bulges, PDB code: 1j9h was solved by Y.Xiong, J.Deng, C.Sudarsanakumar, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.40
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	47.180, 47.180, 80.040, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 23.4

The structure of Crystal Structure of An Rna Duplex with Uridine Bulges also contains other interesting chemical elements:

Bromine

(Br)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of An Rna Duplex with Uridine Bulges (pdb code 1j9h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of An Rna Duplex with Uridine Bulges, PDB code: 1j9h:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of An Rna Duplex with Uridine Bulges


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 An Rna Duplex with Uridine Bulges within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:11.5 occ:0.49 CA A:CA103 0.0 11.5 0.5 CA A:CA103 1.3 14.9 0.5 OP1 A:C5 2.0 17.0 1.0 O A:HOH234 2.0 21.8 1.0 O A:HOH179 2.5 22.9 1.0 OP2 A:U4 2.5 20.1 1.0 O D:HOH238 3.2 29.9 1.0 P A:C5 3.3 17.0 1.0 O D:HOH182 3.8 22.1 1.0 OP2 A:C5 3.8 17.4 1.0 P A:U4 4.0 16.0 1.0 O3' A:U4 4.2 16.0 1.0 C5' A:U4 4.2 16.2 1.0 O D:HOH135 4.5 17.4 1.0 O5' A:C5 4.5 16.9 1.0 O5' A:U4 4.6 15.5 1.0 O3' A:G3 4.7 15.1 1.0 C3' A:U4 4.8 15.4 1.0 O A:HOH231 4.8 22.9 1.0 C4' A:U4 4.9 15.4 1.0 OP1 A:U4 5.0 18.6 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of An Rna Duplex with Uridine Bulges


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 An Rna Duplex with Uridine Bulges within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:14.9 occ:0.45 CA A:CA103 0.0 14.9 0.5 CA A:CA103 1.3 11.5 0.5 O D:HOH238 2.1 29.9 1.0 O A:HOH234 2.4 21.8 1.0 OP1 A:C5 2.6 17.0 1.0 O D:HOH182 2.6 22.1 1.0 O A:HOH179 3.3 22.9 1.0 OP2 A:U4 3.8 20.1 1.0 OP2 D:C36 4.0 14.7 1.0 P A:C5 4.0 17.0 1.0 O D:HOH135 4.1 17.4 1.0 OP2 D:A35 4.1 18.8 1.0 OP2 A:C5 4.7 17.4 1.0 O A:HOH231 4.8 22.9 1.0 O5' A:C5 4.8 16.9 1.0 O3' A:U4 4.9 16.0 1.0 P D:A35 5.0 17.0 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of An Rna Duplex with Uridine Bulges


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 An Rna Duplex with Uridine Bulges within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca104 b:14.4 occ:0.47 CA B:CA104 0.0 14.4 0.5 CA B:CA104 1.6 18.3 0.5 O B:HOH252 2.3 42.9 1.0 OP1 B:C14 2.4 22.9 1.0 O B:HOH163 2.6 22.2 1.0 P B:C14 3.9 22.4 1.0 OP2 B:U13 4.0 20.8 1.0 O B:HOH237 4.3 26.2 1.0 O5' B:C14 4.6 20.4 1.0 OP2 B:C14 4.7 20.9 1.0 C5' B:C14 4.8 19.0 1.0 O3' B:U13 4.9 19.7 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of An Rna Duplex with Uridine Bulges


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of An Rna Duplex with Uridine Bulges within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca104 b:18.3 occ:0.52 CA B:CA104 0.0 18.3 0.5 CA B:CA104 1.6 14.4 0.5 O B:HOH163 1.9 22.2 1.0 OP1 B:C14 1.9 22.9 1.0 OP2 B:U13 2.5 20.8 1.0 P B:C14 3.3 22.4 1.0 O B:HOH237 3.4 26.2 1.0 O B:HOH252 3.6 42.9 1.0 OP2 B:C14 3.9 20.9 1.0 C5' B:U13 3.9 19.2 1.0 P B:U13 3.9 19.7 1.0 O3' B:U13 4.1 19.7 1.0 O5' B:U13 4.4 17.4 1.0 O5' B:C14 4.4 20.4 1.0 O3' B:G12 4.7 17.7 1.0 C3' B:U13 4.7 18.2 1.0 C4' B:U13 4.7 18.4 1.0 C5' B:C14 4.9 19.0 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of An Rna Duplex with Uridine Bulges


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of An Rna Duplex with Uridine Bulges within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca101 b:11.9 occ:1.00 O C:HOH110 2.3 14.3 1.0 OP2 C:U22 2.3 12.6 1.0 OP1 C:C23 2.3 12.7 1.0 O C:HOH141 2.4 14.2 1.0 P C:C23 3.6 11.8 1.0 P C:U22 3.8 12.3 1.0 OP2 C:C23 3.9 12.1 1.0 O C:HOH172 4.0 20.1 1.0 C5' C:U22 4.3 11.6 1.0 O3' C:U22 4.4 12.2 1.0 O C:HOH218 4.4 24.3 1.0 O C:HOH145 4.5 16.1 1.0 O5' C:U22 4.5 11.2 1.0 O3' C:G21 4.6 13.4 1.0 O C:HOH250 4.6 41.4 1.0 OP1 C:U22 4.7 14.0 1.0 O5' C:C23 4.8 11.1 1.0 C3' C:U22 5.0 11.1 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of An Rna Duplex with Uridine Bulges


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of An Rna Duplex with Uridine Bulges within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca102 b:12.1 occ:1.00 OP2 D:U31 2.3 12.3 1.0 OP1 D:C32 2.3 12.2 1.0 O D:HOH132 2.5 15.5 1.0 O D:HOH139 2.5 14.5 1.0 P D:C32 3.5 11.1 1.0 P D:U31 3.8 12.1 1.0 OP2 D:C32 3.9 12.3 1.0 O D:HOH166 4.0 17.1 1.0 C5' D:U31 4.3 10.3 1.0 O3' D:U31 4.4 13.1 1.0 O D:HOH201 4.6 22.4 1.0 O5' D:U31 4.6 11.5 1.0 O3' D:G30 4.6 13.4 1.0 OP1 D:U31 4.6 13.9 1.0 O D:HOH235 4.7 23.8 1.0 O5' D:C32 4.7 12.2 1.0 C3' D:U31 5.0 10.2 1.0

Y.Xiong, J.Deng, C.Sudarsanakumar, M.Sundaralingam. Crystal Structure of An Rna Duplex R(Gugucgcac)(2) with Uridine Bulges. J.Mol.Biol. V. 313 573 2001.
ISSN: ISSN 0022-2836
PubMed: 11676540
DOI: 10.1006/JMBI.2001.5045