Calcium in PDB 2zzv: Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate

The structure of Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate, PDB code: 2zzv was solved by N.Akiyama, K.Takeda, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.33 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.052, 77.335, 136.389, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 18.5

The binding sites of Calcium atom in the Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate (pdb code 2zzv). 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 A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate, PDB code: 2zzv:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate


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 A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:10.9 occ:1.00 O A:PHE217 2.3 12.2 1.0 OD1 A:ASN158 2.3 9.3 1.0 O2 A:LAC401 2.4 11.5 1.0 O1 A:LAC401 2.4 9.8 1.0 OE1 A:GLN247 2.4 9.7 1.0 OD2 A:ASP216 2.4 12.7 1.0 OD1 A:ASP216 2.6 12.5 1.0 CG A:ASP216 2.8 11.5 1.0 C1 A:LAC401 3.2 9.9 1.0 CG A:ASN158 3.2 8.7 1.0 CD A:GLN247 3.2 9.7 1.0 C2 A:LAC401 3.3 10.7 1.0 C A:PHE217 3.4 10.2 1.0 NE2 A:GLN247 3.6 9.6 1.0 CB A:ASN158 3.8 9.2 1.0 CA A:PHE217 3.9 9.8 1.0 N A:PHE217 4.1 11.2 1.0 ND2 A:ASN158 4.2 8.4 1.0 C3 A:LAC401 4.2 12.6 1.0 CD A:PRO180 4.3 9.5 1.0 CG A:PRO180 4.3 10.1 1.0 OD2 A:ASP250 4.3 9.4 1.0 CB A:ASP216 4.4 11.6 1.0 NH1 A:ARG178 4.4 9.4 1.0 OXT A:LAC401 4.4 10.2 1.0 CG A:GLN247 4.5 8.9 1.0 C A:ASP216 4.5 11.5 1.0 N A:VAL218 4.6 8.7 1.0 CB A:GLN247 4.7 8.5 1.0 NE2 A:HIS246 4.8 13.7 1.0 CG A:ASP250 4.8 7.9 1.0 CA A:VAL218 4.8 9.6 1.0 O A:ASP216 5.0 11.9 1.0 CD2 A:HIS246 5.0 14.3 1.0 CB A:PRO180 5.0 9.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate


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 A Periplasmic Substrate Binding Protein in Complex with Calcium and Lactate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:13.3 occ:1.00 OD1 B:ASN1158 2.3 11.4 1.0 O B:PHE1217 2.3 12.5 1.0 OE1 B:GLN1247 2.3 12.8 1.0 O1 B:LAC402 2.4 12.3 1.0 OD1 B:ASP1216 2.4 13.8 1.0 O2 B:LAC402 2.4 14.4 1.0 OD2 B:ASP1216 2.6 15.2 1.0 CG B:ASP1216 2.9 13.7 1.0 C1 B:LAC402 3.2 10.5 1.0 CG B:ASN1158 3.2 10.4 1.0 CD B:GLN1247 3.2 11.5 1.0 C2 B:LAC402 3.4 11.4 1.0 C B:PHE1217 3.4 13.5 1.0 NE2 B:GLN1247 3.7 10.8 1.0 CB B:ASN1158 3.8 9.4 1.0 CA B:PHE1217 3.9 12.1 1.0 N B:PHE1217 4.1 13.5 1.0 ND2 B:ASN1158 4.2 11.1 1.0 CD B:PRO1180 4.2 12.0 1.0 CG B:PRO1180 4.2 13.9 1.0 C3 B:LAC402 4.3 14.7 1.0 OD2 B:ASP1250 4.4 12.1 1.0 CB B:ASP1216 4.4 14.1 1.0 NH1 B:ARG1178 4.4 12.8 1.0 CG B:GLN1247 4.4 11.2 1.0 OXT B:LAC402 4.4 14.6 1.0 C B:ASP1216 4.5 14.3 1.0 N B:VAL1218 4.5 12.1 1.0 NE2 B:HIS1246 4.7 15.9 1.0 CB B:GLN1247 4.8 11.8 1.0 CA B:VAL1218 4.8 11.6 1.0 CG B:ASP1250 4.8 11.1 1.0 O B:ASP1216 4.9 14.6 1.0 CD2 B:HIS1246 5.0 15.1 1.0

N.Akiyama, K.Takeda, K.Miki. Crystal Structure of A Periplasmic Substrate-Binding Protein in Complex with Calcium Lactate J.Mol.Biol. V. 392 559 2009.
ISSN: ISSN 0022-2836
PubMed: 19631222
DOI: 10.1016/J.JMB.2009.07.043