Calcium in PDB 2w27: Crystal Structure of the Bacillus Subtilis Ykui Protein, with An Eal Domain, in Complex with Substrate C-Di-Gmp and Calcium

The structure of Crystal Structure of the Bacillus Subtilis Ykui Protein, with An Eal Domain, in Complex with Substrate C-Di-Gmp and Calcium, PDB code: 2w27 was solved by S.Padavattan, W.F.Anderson, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.167, 124.521, 168.751, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 27.5

The binding sites of Calcium atom in the Crystal Structure of the Bacillus Subtilis Ykui Protein, with An Eal Domain, in Complex with Substrate C-Di-Gmp and Calcium (pdb code 2w27). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Bacillus Subtilis Ykui Protein, with An Eal Domain, in Complex with Substrate C-Di-Gmp and Calcium, PDB code: 2w27:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Bacillus Subtilis Ykui Protein, with An Eal Domain, in Complex with Substrate C-Di-Gmp and Calcium


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 the Bacillus Subtilis Ykui Protein, with An Eal Domain, in Complex with Substrate C-Di-Gmp and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:50.4 occ:1.00 OE1 A:GLU122 2.0 43.0 1.0 O1P A:5GP501 2.2 39.0 1.0 OE1 A:GLU33 2.3 39.0 1.0 ND2 A:ASN88 2.5 46.9 1.0 CD A:GLU122 3.1 38.8 1.0 OD1 A:ASN88 3.2 40.9 1.0 CG A:ASN88 3.2 41.4 1.0 P A:5GP501 3.4 35.9 1.0 OD2 A:ASP152 3.4 53.5 1.0 CD A:GLU33 3.5 38.7 1.0 O2P A:5GP501 3.7 46.0 1.0 OE2 A:GLU122 3.7 38.9 1.0 NZ A:LYS173 3.9 40.7 1.0 OD1 A:ASP152 3.9 52.2 1.0 OE2 A:GLU33 4.1 42.1 1.0 CG A:ASP152 4.1 47.3 1.0 O5' A:5GP501 4.2 38.7 1.0 CB A:GLU122 4.3 36.5 1.0 CG A:GLU122 4.3 37.9 1.0 OE2 A:GLU209 4.5 41.4 1.0 O3' A:5GP502 4.6 39.2 1.0 CG A:GLU33 4.7 37.2 1.0 CB A:ASN88 4.7 38.8 1.0 CD A:LYS173 4.7 39.2 1.0 CE A:LYS173 4.8 40.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Bacillus Subtilis Ykui Protein, with An Eal Domain, in Complex with Substrate C-Di-Gmp and Calcium


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 the Bacillus Subtilis Ykui Protein, with An Eal Domain, in Complex with Substrate C-Di-Gmp and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:50.1 occ:1.00 OE1 B:GLU122 2.1 43.1 1.0 O1P B:5GP501 2.1 38.6 1.0 ND2 B:ASN88 2.3 47.0 1.0 OE1 B:GLU33 2.5 39.1 1.0 CG B:ASN88 3.1 41.3 1.0 OD1 B:ASN88 3.2 40.4 1.0 CD B:GLU122 3.3 38.9 1.0 OD2 B:ASP152 3.4 53.8 1.0 P B:5GP501 3.4 35.6 1.0 CD B:GLU33 3.6 38.8 1.0 O2P B:5GP501 3.8 45.9 1.0 OD1 B:ASP152 3.9 51.9 1.0 OE2 B:GLU122 4.0 39.3 1.0 CG B:ASP152 4.1 47.2 1.0 NZ B:LYS173 4.1 40.9 1.0 OE2 B:GLU33 4.2 42.2 1.0 O5' B:5GP501 4.2 38.7 1.0 CB B:GLU122 4.3 36.2 1.0 CG B:GLU122 4.4 37.8 1.0 O3' B:5GP502 4.5 39.2 1.0 CB B:ASN88 4.6 39.2 1.0 OE2 B:GLU209 4.6 41.2 1.0 CD B:LYS173 4.8 39.4 1.0 CG B:GLU33 4.8 37.6 1.0 CE B:LYS173 5.0 40.9 1.0 C2' B:5GP502 5.0 38.7 1.0 C3' B:5GP502 5.0 38.6 1.0

G.Minasov, S.Padavattan, L.Shuvalova, J.S.Brunzelle, D.J.Miller, A.Basle, C.Massa, F.R.Collart, T.Schirmer, W.F.Anderson. Crystal Structures of Ykui and Its Complex with Second Messenger C-Di-Gmp Suggests Catalytic Mechanism of Phosphodiester Bond Cleavage By Eal Domains. J.Biol.Chem. V. 284 13174 2009.
ISSN: ISSN 0021-9258
PubMed: 19244251
DOI: 10.1074/JBC.M808221200