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

The structure of Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Zinc and Lactate, PDB code: 2zzw 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)	28.38 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.701, 84.986, 113.531, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 19.1

The binding sites of Zinc atom in the Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Zinc and Lactate (pdb code 2zzw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Zinc and Lactate, PDB code: 2zzw:
Jump to Zinc binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Zinc and Lactate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn362 b:12.6 occ:1.00 OD1 A:ASN158 2.1 11.1 1.0 O2 A:LAC401 2.1 14.7 1.0 OD2 A:ASP216 2.2 12.7 1.0 O1 A:LAC401 2.2 10.2 1.0 O A:PHE217 2.2 8.3 1.0 OE1 A:GLN247 2.2 8.7 1.0 CG A:ASP216 3.0 13.0 1.0 OD1 A:ASP216 3.0 12.0 1.0 C1 A:LAC401 3.0 13.2 1.0 CD A:GLN247 3.1 5.9 1.0 C2 A:LAC401 3.1 14.8 1.0 CG A:ASN158 3.1 7.5 1.0 C A:PHE217 3.3 8.5 1.0 NE2 A:GLN247 3.5 6.3 1.0 CB A:ASN158 3.8 8.0 1.0 CA A:PHE217 3.9 7.9 1.0 N A:PHE217 4.1 10.8 1.0 C3 A:LAC401 4.1 26.2 1.0 ND2 A:ASN158 4.1 5.7 1.0 OD2 A:ASP250 4.2 7.5 1.0 CD A:PRO180 4.2 6.9 1.0 CG A:PRO180 4.3 4.8 1.0 OXT A:LAC401 4.3 9.9 1.0 CG A:GLN247 4.3 6.0 1.0 NH1 A:ARG178 4.4 6.0 1.0 CB A:ASP216 4.4 13.0 1.0 N A:VAL218 4.5 7.2 1.0 C A:ASP216 4.5 9.9 1.0 CG A:ASP250 4.6 8.4 1.0 CB A:GLN247 4.7 8.7 1.0 CA A:VAL218 4.7 7.3 1.0 NE2 A:HIS246 4.8 7.8 1.0 OD1 A:ASP250 4.9 7.5 1.0 O A:ASP216 4.9 10.0 1.0 CD2 A:HIS246 4.9 7.2 1.0 CB A:PRO180 5.0 4.3 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Periplasmic Substrate Binding Protein in Complex with Zinc and Lactate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn362 b:18.6 occ:1.00 O2 B:LAC402 2.1 20.1 1.0 OE1 B:GLN247 2.2 10.0 1.0 OD1 B:ASN158 2.2 14.5 1.0 O1 B:LAC402 2.2 18.3 1.0 OD2 B:ASP216 2.2 16.4 1.0 O B:PHE217 2.2 11.2 1.0 CG B:ASP216 3.0 17.6 1.0 OD1 B:ASP216 3.0 16.9 1.0 C1 B:LAC402 3.0 18.3 1.0 C2 B:LAC402 3.1 22.7 1.0 CG B:ASN158 3.1 13.3 1.0 CD B:GLN247 3.1 11.1 1.0 C B:PHE217 3.3 11.9 1.0 NE2 B:GLN247 3.6 8.9 1.0 CA B:PHE217 3.8 13.2 1.0 CB B:ASN158 3.8 12.7 1.0 N B:PHE217 4.0 15.7 1.0 C3 B:LAC402 4.0 28.4 1.0 ND2 B:ASN158 4.1 9.3 1.0 CD B:PRO180 4.2 14.1 1.0 CG B:PRO180 4.2 14.9 1.0 OD2 B:ASP250 4.3 9.6 1.0 OXT B:LAC402 4.3 16.6 1.0 NH1 B:ARG178 4.4 9.3 1.0 CG B:GLN247 4.4 8.4 1.0 CB B:ASP216 4.5 15.0 1.0 N B:VAL218 4.5 11.1 1.0 C B:ASP216 4.5 15.4 1.0 CG B:ASP250 4.7 9.6 1.0 CB B:GLN247 4.7 8.2 1.0 CA B:VAL218 4.8 11.3 1.0 OD1 B:ASP250 4.8 8.9 1.0 NE2 B:HIS246 4.9 11.9 1.0 CB B:PRO180 4.9 11.9 1.0 O B:ASP216 5.0 17.7 1.0 CD2 B:HIS246 5.0 13.4 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