Calcium in PDB 3zq4: Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1

The structure of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1, PDB code: 3zq4 was solved by J.A.Newman, L.Hewitt, C.Rodrigues, A.Solovyova, C.R.Harwood, R.J.Lewis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.76 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	177.823, 209.430, 74.106, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25.8

The structure of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Calcium atom in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 (pdb code 3zq4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1, PDB code: 3zq4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1558 b:58.9 occ:1.00 OD1 A:ASP443 2.5 65.6 1.0 O A:GLY49 3.0 57.8 1.0 OD2 A:ASP443 3.0 48.3 1.0 CG A:ASP443 3.1 57.4 1.0 O C:GLU463 3.8 45.5 1.0 OD1 A:ASP51 3.8 61.8 1.0 OE2 C:GLU464 3.9 40.6 1.0 C A:GLY49 4.0 48.8 1.0 OE1 C:GLU464 4.2 43.9 1.0 CD C:GLU464 4.4 49.4 1.0 OE1 C:GLU463 4.4 92.8 1.0 CA A:GLY49 4.5 53.4 1.0 CG A:ASP51 4.5 64.2 1.0 OD2 A:ASP51 4.5 69.8 1.0 CB A:ASP443 4.6 44.9 1.0 CG C:ARG544 4.7 72.1 1.0 C C:GLU463 4.8 52.7 1.0

Calcium binding site 2 out of 4 in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1558 b:63.6 occ:1.00 OD1 C:ASP443 2.5 46.2 1.0 O C:GLY49 2.9 64.7 1.0 CG C:ASP443 3.3 48.7 1.0 OD2 C:ASP443 3.3 38.2 1.0 OD1 C:ASP51 3.5 54.1 1.0 OE1 A:GLU464 3.8 56.9 1.0 OE2 A:GLU464 4.0 64.7 1.0 C C:GLY49 4.0 51.6 1.0 O A:GLU463 4.0 54.6 1.0 CD A:GLU464 4.2 59.6 1.0 CG C:ASP51 4.3 60.6 1.0 OD2 C:ASP51 4.4 66.4 1.0 CA C:GLY49 4.5 55.6 1.0 CG A:ARG544 4.6 62.2 1.0 CB C:ASP443 4.8 47.5 1.0 C A:GLU463 4.9 52.6 1.0

Calcium binding site 3 out of 4 in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1556 b:46.8 occ:1.00 OD1 D:ASP443 2.6 40.0 1.0 OD1 D:ASP51 2.7 61.7 1.0 O D:GLY49 3.3 48.4 1.0 OE2 E:GLU464 3.5 56.3 1.0 CG D:ASP51 3.5 66.9 1.0 OD2 D:ASP51 3.6 66.4 1.0 CG D:ASP443 3.7 59.8 1.0 CD E:GLU464 4.1 65.3 1.0 OE1 E:GLU464 4.2 64.3 1.0 OD2 D:ASP443 4.3 53.9 1.0 CG E:ARG544 4.3 64.7 1.0 O E:GLU463 4.3 49.8 1.0 C D:GLY49 4.5 53.9 1.0 OE1 E:GLU463 4.6 89.3 1.0 CB D:ASP51 5.0 54.7 1.0

Calcium binding site 4 out of 4 in the Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Unusual, Dual Endo- and Exo-Nuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1558 b:63.0 occ:1.00 OD1 E:ASP443 2.5 63.3 1.0 O E:GLY49 3.2 67.6 1.0 OE2 D:GLU464 3.4 50.8 1.0 CG E:ASP443 3.5 64.8 1.0 OE1 D:GLU464 3.7 43.2 1.0 OD2 E:ASP443 3.8 58.9 1.0 CD D:GLU464 4.0 52.2 1.0 C E:GLY49 4.0 53.1 1.0 CG D:ARG544 4.1 84.1 1.0 CA E:GLY49 4.3 57.3 1.0 OD1 E:ASP51 4.3 60.6 1.0 O D:GLU463 4.3 51.8 1.0 CD D:ARG544 4.7 60.9 1.0 N E:GLY444 4.7 67.7 1.0 OD2 E:ASP51 4.8 68.4 1.0 CB E:ASP443 4.9 55.0 1.0 CG E:ASP51 4.9 66.5 1.0

J.A.Newman, L.Hewitt, C.Rodrigues, A.Solovyova, C.R.Harwood, R.J.Lewis. Unusual, Dual Endo- and Exonuclease Activity in the Degradosome Explained By Crystal Structure Analysis of Rnase J1. Structure V. 19 1241 2011.
ISSN: ISSN 0969-2126
PubMed: 21893285
DOI: 10.1016/J.STR.2011.06.017