Calcium in PDB 3gg1: Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex

The structure of Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex, PDB code: 3gg1 was solved by T.Barends, E.Hartmann, J.Griese, T.Beitlich, N.Kirienko, D.Ryjenkov, J.Reinstein, R.Shoeman, M.Gomelsky, I.Schlichting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.850, 96.690, 127.040, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 29.6

The binding sites of Calcium atom in the Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex (pdb code 3gg1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex, PDB code: 3gg1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:17.6 occ:1.00 OE2 A:GLU272 2.2 27.6 1.0 OD1 A:ASN239 2.2 22.9 1.0 OD2 A:ASP302 2.3 30.5 1.0 O2P A:C2E501 2.3 24.0 1.0 OE2 A:GLU188 2.3 25.0 1.0 O A:HOH406 2.4 11.0 1.0 CG A:ASN239 3.2 23.8 1.0 CG A:ASP302 3.3 30.7 1.0 CD A:GLU188 3.4 24.9 1.0 CD A:GLU272 3.4 29.1 1.0 ND2 A:ASN239 3.6 22.9 1.0 P1 A:C2E501 3.6 23.5 1.0 OE1 A:GLU188 3.8 24.1 1.0 OD1 A:ASP302 3.9 30.1 1.0 CB A:GLU272 4.0 29.3 1.0 O5' A:C2E501 4.1 23.3 1.0 O A:HOH481 4.2 33.3 1.0 O1P A:C2E501 4.2 23.2 1.0 OE1 A:GLU272 4.3 28.4 1.0 CB A:ASP302 4.3 30.7 1.0 CG A:GLU272 4.3 29.2 1.0 OE2 A:GLU359 4.5 26.1 1.0 NZ A:LYS323 4.5 26.1 1.0 O A:HOH425 4.6 40.5 1.0 CG A:GLU188 4.6 25.0 1.0 CB A:ASN239 4.6 24.3 1.0 C2A A:C2E501 4.8 23.2 1.0 O3A A:C2E501 4.8 23.1 1.0 CA A:CA503 4.9 30.8 1.0

Calcium binding site 2 out of 4 in the Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:30.8 occ:1.00 OD1 A:ASP303 2.3 33.5 1.0 OE1 A:GLU359 2.3 26.0 1.0 O1P A:C2E501 2.3 23.2 1.0 OD1 A:ASP302 2.8 30.1 1.0 CD A:GLU359 2.9 24.9 1.0 OE2 A:GLU359 3.0 26.1 1.0 CG A:ASP303 3.5 33.3 1.0 CG A:ASP302 3.5 30.7 1.0 OD2 A:ASP302 3.7 30.5 1.0 P1 A:C2E501 3.7 23.5 1.0 N A:ASP303 4.0 32.1 1.0 O A:HOH406 4.1 11.0 1.0 O A:HOH481 4.2 33.3 1.0 O2P A:C2E501 4.2 24.0 1.0 CA A:ASP303 4.2 33.0 1.0 OD2 A:ASP303 4.3 34.4 1.0 CG A:GLU359 4.4 24.7 1.0 OD1 A:ASP325 4.4 30.0 1.0 CB A:ASP303 4.5 33.0 1.0 O5' A:C2E501 4.6 23.3 1.0 O3A A:C2E501 4.7 23.1 1.0 C5' A:C2E501 4.7 23.2 1.0 CB A:ASP302 4.8 30.7 1.0 CA A:CA502 4.9 17.6 1.0 CB A:GLU359 5.0 23.9 1.0

Calcium binding site 3 out of 4 in the Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:18.9 occ:1.00 OD1 B:ASP302 2.2 30.4 1.0 O2P B:C2E501 2.2 24.4 1.0 OE2 B:GLU188 2.2 24.5 1.0 OE2 B:GLU272 2.3 28.3 1.0 O B:HOH483 2.4 22.9 1.0 OD1 B:ASN239 2.4 22.1 1.0 CG B:ASP302 3.1 31.1 1.0 CD B:GLU188 3.3 24.8 1.0 CG B:ASN239 3.3 23.5 1.0 OD2 B:ASP302 3.3 30.9 1.0 CD B:GLU272 3.5 29.2 1.0 P1 B:C2E501 3.6 24.3 1.0 ND2 B:ASN239 3.6 22.0 1.0 OE1 B:GLU188 3.9 23.9 1.0 O B:HOH429 4.0 28.7 1.0 CB B:GLU272 4.0 29.5 1.0 NZ B:LYS323 4.1 26.6 1.0 O5' B:C2E501 4.2 23.8 1.0 CG B:GLU272 4.3 29.4 1.0 O1P B:C2E501 4.4 24.1 1.0 OE1 B:GLU272 4.4 29.2 1.0 CB B:ASP302 4.4 31.1 1.0 CG B:GLU188 4.4 24.5 1.0 CB B:ASN239 4.7 24.2 1.0 OE2 B:GLU359 4.8 26.2 1.0 O3A B:C2E501 4.8 23.9 1.0 C2A B:C2E501 4.8 23.9 1.0 CD B:LYS323 4.8 27.2 1.0 CE B:LYS323 5.0 26.8 1.0

Calcium binding site 4 out of 4 in the Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Klebsiella Pneumoniae BLRP1 pH 8.0 Calcium/Cy-Digmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:35.0 occ:1.00 OD1 B:ASP303 2.3 33.8 1.0 O1P B:C2E501 2.3 24.1 1.0 OD1 B:ASP325 2.6 29.0 1.0 OE1 B:GLU359 2.7 26.8 1.0 CD B:GLU359 3.2 25.7 1.0 CG B:ASP303 3.4 33.6 1.0 OE2 B:GLU359 3.6 26.2 1.0 CG B:ASP325 3.8 28.5 1.0 P1 B:C2E501 3.8 24.3 1.0 CG B:GLU359 4.1 24.7 1.0 CA B:ASP303 4.2 33.2 1.0 OD2 B:ASP303 4.2 34.5 1.0 OD2 B:ASP302 4.3 30.9 1.0 CB B:ASP303 4.3 33.2 1.0 O3A B:C2E501 4.5 23.9 1.0 N B:ASP303 4.5 32.4 1.0 OD2 B:ASP325 4.6 28.8 1.0 O2P B:C2E501 4.6 24.4 1.0 CB B:ASP325 4.7 28.0 1.0 CA B:ASP325 4.7 28.0 1.0 O B:HOH483 4.7 22.9 1.0 N B:ALA326 4.8 28.2 1.0 C5' B:C2E501 4.8 23.8 1.0 O5' B:C2E501 4.8 23.8 1.0 O B:HOH429 4.9 28.7 1.0

T.R.Barends, E.Hartmann, J.J.Griese, T.Beitlich, N.V.Kirienko, D.A.Ryjenkov, J.Reinstein, R.L.Shoeman, M.Gomelsky, I.Schlichting. Structure and Mechanism of A Bacterial Light-Regulated Cyclic Nucleotide Phosphodiesterase. Nature V. 459 1015 2009.
ISSN: ISSN 0028-0836
PubMed: 19536266
DOI: 10.1038/NATURE07966