Calcium in PDB 6hq5: Structure of Eal Enzyme BD1971 - Camp and Cyclic-Di-Gmp Bound Form

The structure of Structure of Eal Enzyme BD1971 - Camp and Cyclic-Di-Gmp Bound Form, PDB code: 6hq5 was solved by A.L.Lovering, I.T.Cadby, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.31 / 2.83
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	83.857, 83.857, 138.454, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 26.8

The binding sites of Calcium atom in the Structure of Eal Enzyme BD1971 - Camp and Cyclic-Di-Gmp Bound Form (pdb code 6hq5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Eal Enzyme BD1971 - Camp and Cyclic-Di-Gmp Bound Form, PDB code: 6hq5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of Eal Enzyme BD1971 - Camp and Cyclic-Di-Gmp Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Eal Enzyme BD1971 - Camp and Cyclic-Di-Gmp Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:70.9 occ:1.00 OE2 A:GLU277 2.3 0.6 1.0 O A:HOH901 2.3 59.0 1.0 O11 A:C2E801 2.3 69.7 1.0 OD1 A:ASN245 2.3 85.8 1.0 OD2 A:ASP306 2.3 98.4 1.0 OE2 A:GLU178 2.3 82.5 1.0 CG A:ASP306 3.2 96.3 1.0 CG A:ASN245 3.2 77.8 1.0 CD A:GLU277 3.3 0.9 1.0 P11 A:C2E801 3.4 79.0 1.0 ND2 A:ASN245 3.4 78.5 1.0 CD A:GLU178 3.5 81.8 1.0 O21 A:C2E801 3.7 86.2 1.0 CG A:GLU277 3.8 97.8 1.0 CB A:ASP306 3.9 95.5 1.0 OD1 A:ASP306 4.0 92.7 1.0 OE1 A:GLU178 4.1 82.3 1.0 O5A A:C2E801 4.3 80.4 1.0 OE1 A:GLU277 4.3 0.1 1.0 NZ A:LYS327 4.4 79.8 1.0 CB A:GLU277 4.6 92.8 1.0 CB A:ASN245 4.6 76.0 1.0 CG A:GLU178 4.6 80.9 1.0 O3' A:C2E801 4.8 74.0 1.0 C2' A:C2E801 4.9 71.5 1.0 OE2 A:GLU363 5.0 88.8 1.0 C5A A:C2E801 5.0 80.0 1.0

Calcium binding site 2 out of 4 in the Structure of Eal Enzyme BD1971 - Camp and Cyclic-Di-Gmp Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Eal Enzyme BD1971 - Camp and Cyclic-Di-Gmp Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca804 b:85.3 occ:1.00 OD1 A:ASP329 2.3 97.8 1.0 OD1 A:ASP307 2.3 0.4 1.0 O21 A:C2E801 2.3 86.2 1.0 OE1 A:GLU363 2.3 93.2 1.0 OD1 A:ASP306 2.9 92.7 1.0 OE2 A:GLU363 3.0 88.8 1.0 CD A:GLU363 3.0 87.8 1.0 CG A:ASP307 3.4 0.3 1.0 P11 A:C2E801 3.6 79.0 1.0 O5A A:C2E801 3.6 80.4 1.0 CG A:ASP329 3.6 89.3 1.0 CG A:ASP306 3.6 96.3 1.0 OD2 A:ASP306 3.6 98.4 1.0 O A:HOH901 4.0 59.0 1.0 OD2 A:ASP307 4.0 0.1 1.0 N A:ASP307 4.3 99.7 1.0 OD2 A:ASP329 4.4 87.9 1.0 CB A:ASP329 4.5 87.4 1.0 CG A:GLU363 4.5 86.3 1.0 CA A:ASP307 4.5 0.2 1.0 O3' A:C2E801 4.5 74.0 1.0 CB A:ASP307 4.6 0.8 1.0 O11 A:C2E801 4.6 69.7 1.0 CA A:ASP329 4.7 86.5 1.0 NE A:ARG330 4.9 0.3 1.0 C5A A:C2E801 4.9 80.0 1.0 N A:ARG330 4.9 89.3 1.0

Calcium binding site 3 out of 4 in the Structure of Eal Enzyme BD1971 - Camp and Cyclic-Di-Gmp Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Eal Enzyme BD1971 - Camp and Cyclic-Di-Gmp Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:73.1 occ:1.00 OD2 B:ASP306 2.3 0.8 1.0 OE2 B:GLU277 2.3 91.6 1.0 OD1 B:ASN245 2.3 81.4 1.0 OE2 B:GLU178 2.3 81.9 1.0 O B:HOH901 2.3 78.6 1.0 O11 B:C2E801 2.3 63.1 1.0 CG B:ASP306 3.1 95.8 1.0 CG B:ASN245 3.2 76.3 1.0 CD B:GLU277 3.3 93.2 1.0 ND2 B:ASN245 3.4 79.9 1.0 CD B:GLU178 3.5 75.7 1.0 P11 B:C2E801 3.6 80.1 1.0 CG B:GLU277 3.8 90.6 1.0 CB B:ASP306 3.8 92.2 1.0 OD1 B:ASP306 3.9 91.5 1.0 O21 B:C2E801 4.1 81.1 1.0 OE1 B:GLU178 4.1 74.3 1.0 OE1 B:GLU277 4.3 98.3 1.0 O5A B:C2E801 4.3 77.0 1.0 NZ B:LYS327 4.4 80.5 1.0 CB B:ASN245 4.6 74.0 1.0 CB B:GLU277 4.6 86.7 1.0 CG B:GLU178 4.6 75.5 1.0 O3' B:C2E801 4.9 73.3 1.0 C2' B:C2E801 5.0 67.8 1.0 OE1 B:GLU363 5.0 89.3 1.0

Calcium binding site 4 out of 4 in the Structure of Eal Enzyme BD1971 - Camp and Cyclic-Di-Gmp Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Eal Enzyme BD1971 - Camp and Cyclic-Di-Gmp Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca804 b:87.5 occ:1.00 OD1 B:ASP307 2.3 0.9 1.0 O21 B:C2E801 2.3 81.1 1.0 OD1 B:ASP329 2.3 92.2 1.0 OE1 B:GLU363 2.3 89.3 1.0 OD1 B:ASP306 2.6 91.5 1.0 OE2 B:GLU363 2.8 86.4 1.0 CD B:GLU363 2.9 83.5 1.0 CG B:ASP307 3.4 0.3 1.0 CG B:ASP306 3.4 95.8 1.0 OD2 B:ASP306 3.5 0.8 1.0 CG B:ASP329 3.6 86.0 1.0 P11 B:C2E801 3.6 80.1 1.0 O5A B:C2E801 3.8 77.0 1.0 O B:HOH901 3.9 78.6 1.0 N B:ASP307 4.0 97.5 1.0 OD2 B:ASP307 4.0 1.0 1.0 CA B:ASP307 4.3 0.9 1.0 CB B:ASP329 4.4 84.4 1.0 O11 B:C2E801 4.4 63.1 1.0 CG B:GLU363 4.4 82.9 1.0 CB B:ASP307 4.5 0.9 1.0 OD2 B:ASP329 4.5 85.5 1.0 CA B:ASP329 4.5 82.5 1.0 O3' B:C2E801 4.7 73.3 1.0 CB B:ASP306 4.8 92.2 1.0 N B:ARG330 5.0 80.2 1.0 C B:ASP306 5.0 92.1 1.0

I.T.Cadby, S.M.Basford, R.Nottingham, R.Meek, R.Lowry, C.Lambert, M.Tridgett, R.Till, R.Ahmad, R.Fung, L.Hobley, W.S.Hughes, P.J.Moynihan, R.E.Sockett, A.L.Lovering. Nucleotide Signaling Pathway Convergence in A Camp-Sensing Bacterial C-Di-Gmp Phosphodiesterase. Embo J. V. 38 00772 2019.
ISSN: ESSN 1460-2075
PubMed: 31355487
DOI: 10.15252/EMBJ.2018100772