Calcium in PDB 5jrc: Crystal Structure of NEC3PO in Complex with Ssrna.

The structure of Crystal Structure of NEC3PO in Complex with Ssrna., PDB code: 5jrc was solved by J.Zhang, J.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.07 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	165.416, 77.648, 87.754, 90.00, 118.81, 90.00
R / Rfree (%)	20.6 / 23

The binding sites of Calcium atom in the Crystal Structure of NEC3PO in Complex with Ssrna. (pdb code 5jrc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of NEC3PO in Complex with Ssrna., PDB code: 5jrc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of NEC3PO in Complex with Ssrna.


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 NEC3PO in Complex with Ssrna. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:52.1 occ:1.00 O A:HOH364 2.3 43.7 1.0 OE2 A:GLU85 2.4 23.1 1.0 OE1 A:GLU121 2.9 24.3 1.0 CD A:GLU85 3.1 20.6 1.0 OE1 A:GLU85 3.1 21.0 1.0 O A:HOH368 3.4 33.5 1.0 CD A:GLU121 4.0 22.9 1.0 CG A:GLU121 4.5 19.6 1.0 CG A:GLU85 4.6 19.1 1.0 O A:ASP117 4.8 17.4 1.0 CB A:ASP117 4.9 18.2 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of NEC3PO in Complex with Ssrna.


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 NEC3PO in Complex with Ssrna. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:57.9 occ:1.00 O B:HOH360 2.2 38.2 1.0 OE2 B:GLU85 2.5 19.7 1.0 OE1 B:GLU85 2.9 13.6 1.0 CD B:GLU85 3.1 14.7 1.0 O B:HOH307 3.2 34.3 1.0 OE2 B:GLU121 3.5 35.9 1.0 CD B:GLU121 4.6 24.6 1.0 CG B:GLU85 4.6 12.2 1.0 O B:HOH317 4.6 28.0 1.0 CB B:ASP117 4.8 14.9 1.0 CG B:GLU121 4.9 23.9 1.0 O B:ASP117 4.9 16.5 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of NEC3PO in Complex with Ssrna.


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 NEC3PO in Complex with Ssrna. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:16.3 occ:1.00 OE1 C:GLU85 2.0 20.7 1.0 OD2 C:ASP117 2.2 44.1 1.0 OP1 E:A5 2.4 16.4 1.0 OE1 C:GLU82 2.4 22.3 1.0 OE2 C:GLU82 2.5 35.5 1.0 O C:HOH322 2.6 21.6 1.0 CD C:GLU82 2.8 29.2 1.0 CG C:ASP117 3.0 36.5 1.0 O3' E:A4 3.0 15.3 1.0 CD C:GLU85 3.2 20.8 1.0 CB C:ASP117 3.2 33.5 1.0 P E:A5 3.3 15.8 1.0 OE2 C:GLU85 3.8 26.2 1.0 CA C:CA202 3.9 17.1 1.0 OD1 C:ASP117 4.1 44.5 1.0 CG C:GLU82 4.3 24.3 1.0 O5' E:A5 4.3 17.6 1.0 O C:HOH319 4.3 26.6 1.0 C5' E:A5 4.3 17.0 1.0 CG C:GLU85 4.3 20.9 1.0 CB C:GLU85 4.4 18.3 1.0 C3' E:A4 4.4 16.7 1.0 O C:HOH302 4.4 32.3 1.0 OP2 E:A5 4.4 14.7 1.0 CA C:GLU82 4.5 20.8 1.0 O2' E:A4 4.5 14.4 1.0 O C:HOH301 4.6 40.2 1.0 CA C:ASP117 4.8 28.5 1.0 C4' E:A4 4.8 17.0 1.0 CB C:GLU82 4.8 22.3 1.0 NE2 C:GLN81 4.8 24.5 1.0 N C:GLU82 4.9 15.9 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of NEC3PO in Complex with Ssrna.


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 NEC3PO in Complex with Ssrna. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:17.1 occ:1.00 O C:HOH319 2.3 26.6 1.0 OP1 E:A5 2.3 16.4 1.0 O E:HOH103 2.3 9.0 1.0 OE2 C:GLU85 2.3 26.2 1.0 OE1 C:GLU121 2.5 16.4 1.0 O E:HOH104 2.7 19.3 1.0 CD C:GLU85 3.0 20.8 1.0 OE1 C:GLU85 3.1 20.7 1.0 P E:A5 3.4 15.8 1.0 CD C:GLU121 3.6 14.9 1.0 CA C:CA201 3.9 16.3 1.0 OP2 E:A5 4.0 14.7 1.0 O5' E:A5 4.0 17.6 1.0 CG C:GLU121 4.0 14.9 1.0 CB C:ASP117 4.2 33.5 1.0 C5' E:A5 4.2 17.0 1.0 O C:ASP117 4.3 20.9 1.0 CG C:GLU85 4.4 20.9 1.0 OE1 C:GLU82 4.5 22.3 1.0 OP2 E:A6 4.6 24.9 1.0 CG C:ASP117 4.7 36.5 1.0 O C:HOH302 4.7 32.3 1.0 OE2 C:GLU121 4.7 17.6 1.0 O3' E:A4 4.8 15.3 1.0 OP1 E:A6 4.8 20.3 1.0 OD2 C:ASP117 4.8 44.1 1.0 NH1 C:ARG124 4.8 14.2 1.0 C C:ASP117 4.9 22.4 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of NEC3PO in Complex with Ssrna.


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 NEC3PO in Complex with Ssrna. within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:39.9 occ:1.00 O D:HOH345 2.2 35.6 1.0 O D:HOH341 2.3 27.2 1.0 O D:HOH311 2.3 26.1 1.0 OE2 D:GLU85 2.4 19.3 1.0 O D:HOH327 2.6 27.4 1.0 OE2 D:GLU121 2.8 30.1 1.0 CD D:GLU85 3.3 17.9 1.0 OE1 D:GLU85 3.4 20.3 1.0 CD D:GLU121 3.9 32.3 1.0 CG D:GLU121 4.3 29.6 1.0 O D:HOH331 4.4 29.8 1.0 CG D:GLU85 4.7 16.4 1.0 O D:ASP117 4.7 20.0 1.0 CB D:ASP117 4.9 20.4 1.0 OE1 D:GLU121 5.0 35.5 1.0

J.Zhang, H.Liu, Q.Yao, X.Yu, Y.Chen, R.Cui, B.Wu, L.Zheng, J.Zuo, Z.Huang, J.Ma, J.Gan. Structural Basis For Single-Stranded Rna Recognition and Cleavage By C3PO Nucleic Acids Res. V. 44 9494 2016.
ISSN: ESSN 1362-4962
PubMed: 27596600
DOI: 10.1093/NAR/GKW776