Calcium in PDB 3gfx: Klebsiella Pneumoniae BLRP1 pH 4.5 Calcium/Cy-Digmp Complex

The structure of Klebsiella Pneumoniae BLRP1 pH 4.5 Calcium/Cy-Digmp Complex, PDB code: 3gfx 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)	15.00 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.000, 96.900, 128.500, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 27.7

The binding sites of Calcium atom in the Klebsiella Pneumoniae BLRP1 pH 4.5 Calcium/Cy-Digmp Complex (pdb code 3gfx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Klebsiella Pneumoniae BLRP1 pH 4.5 Calcium/Cy-Digmp Complex, PDB code: 3gfx:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Klebsiella Pneumoniae BLRP1 pH 4.5 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 4.5 Calcium/Cy-Digmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:18.9 occ:1.00 O2P A:C2E501 2.2 16.9 1.0 OD2 A:ASP302 2.3 28.0 1.0 OE2 A:GLU272 2.4 28.7 1.0 OE2 A:GLU188 2.4 24.8 1.0 OD1 A:ASN239 2.4 24.8 1.0 O A:HOH423 2.6 20.2 1.0 CG A:ASP302 3.2 27.4 1.0 P1 A:C2E501 3.3 16.6 1.0 CG A:ASN239 3.4 24.8 1.0 CD A:GLU188 3.5 24.4 1.0 CD A:GLU272 3.6 28.5 1.0 O1P A:C2E501 3.6 17.3 1.0 ND2 A:ASN239 3.7 24.6 1.0 O A:HOH412 3.8 21.3 1.0 OD1 A:ASP302 3.8 28.0 1.0 O A:HOH462 3.9 31.8 1.0 OE1 A:GLU188 4.0 24.9 1.0 O A:HOH406 4.1 14.2 1.0 CB A:ASP302 4.2 26.8 1.0 O5' A:C2E501 4.3 16.6 1.0 OE1 A:GLU272 4.3 29.0 1.0 NZ A:LYS323 4.4 24.5 1.0 C2A A:C2E501 4.4 16.3 1.0 O2A A:C2E501 4.5 15.9 1.0 CB A:GLU272 4.5 27.5 1.0 O3A A:C2E501 4.6 16.5 1.0 CG A:GLU272 4.6 27.9 1.0 CG A:GLU188 4.6 24.2 1.0 CB A:ASN239 4.8 24.9 1.0 OE1 A:GLU359 4.8 25.7 1.0 C5' A:C2E501 4.9 15.8 1.0 C3A A:C2E501 5.0 16.2 1.0

Calcium binding site 2 out of 2 in the Klebsiella Pneumoniae BLRP1 pH 4.5 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 4.5 Calcium/Cy-Digmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:19.9 occ:1.00 OE2 B:GLU272 2.2 27.3 1.0 O2P B:C2E501 2.3 18.8 1.0 OD1 B:ASP302 2.3 28.5 1.0 OE2 B:GLU188 2.3 25.1 1.0 O B:HOH445 2.4 18.2 1.0 OD1 B:ASN239 2.5 25.5 1.0 CG B:ASP302 3.2 28.0 1.0 CD B:GLU188 3.3 24.9 1.0 CD B:GLU272 3.4 26.6 1.0 CG B:ASN239 3.4 25.4 1.0 P1 B:C2E501 3.5 18.5 1.0 OD2 B:ASP302 3.6 28.9 1.0 ND2 B:ASN239 3.8 25.0 1.0 O1P B:C2E501 3.8 18.9 1.0 OE1 B:GLU188 3.8 25.1 1.0 O B:HOH414 4.0 16.8 1.0 OE1 B:GLU272 4.1 27.2 1.0 CB B:GLU272 4.3 26.1 1.0 O5' B:C2E501 4.4 19.0 1.0 NZ B:LYS323 4.4 24.9 1.0 CB B:ASP302 4.4 27.4 1.0 CG B:GLU188 4.5 24.2 1.0 CG B:GLU272 4.5 26.4 1.0 O B:HOH427 4.5 17.1 1.0 C2A B:C2E501 4.6 18.2 1.0 O3A B:C2E501 4.7 18.7 1.0 O2A B:C2E501 4.8 18.1 1.0 C5' B:C2E501 4.8 18.6 1.0 CB B:ASN239 4.8 25.5 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