Zinc in PDB 1lfw: Crystal Structure of Pepv

All present enzymatic activity of Crystal Structure of Pepv:
3.4.13.3;

The structure of Crystal Structure of Pepv, PDB code: 1lfw was solved by D.Jozic, G.Bourenkow, H.Bartunik, H.Scholze, V.Dive, B.Henrich, R.Huber, W.Bode, K.Maskos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	11.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.151, 77.025, 89.955, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / n/a

The binding sites of Zinc atom in the Crystal Structure of Pepv (pdb code 1lfw). 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 Pepv, PDB code: 1lfw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Pepv


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 Pepv within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:7.4 occ:1.00 OD1 A:ASP119 1.9 7.9 1.0 OE2 A:GLU154 1.9 8.7 1.0 NE2 A:HIS439 1.9 5.5 1.0 O2P A:AEP683 2.0 6.9 1.0 CD A:GLU154 2.6 10.0 1.0 OE1 A:GLU154 2.6 9.5 1.0 O1P A:AEP683 2.8 7.2 1.0 CG A:ASP119 2.9 8.6 1.0 P A:AEP683 2.9 8.3 1.0 CD2 A:HIS439 2.9 7.8 1.0 CE1 A:HIS439 3.0 8.3 1.0 O A:HOH1164 3.1 39.2 1.0 OD2 A:ASP119 3.2 8.2 1.0 ZN A:ZN1002 3.8 11.0 1.0 O A:HOH1008 3.9 7.4 1.0 CG A:GLU154 4.0 8.2 1.0 ND1 A:HIS439 4.0 6.9 1.0 CG A:HIS439 4.0 6.7 1.0 C1 A:AEP683 4.1 10.3 1.0 N A:AEP683 4.1 9.9 1.0 NE2 A:HIS269 4.1 10.8 1.0 C4 A:AEP683 4.1 9.8 1.0 CB A:ASP119 4.2 7.0 1.0 C6 A:AEP683 4.3 11.9 1.0 CD2 A:HIS269 4.3 9.7 1.0 CG1 A:VAL91 4.5 8.4 1.0 CE1 A:HIS87 4.6 5.9 1.0 C2 A:AEP683 4.6 12.6 1.0 ND2 A:ASN217 4.7 7.8 1.0 NE2 A:HIS87 4.7 5.1 1.0 OE2 A:GLU153 4.7 11.7 1.0 O A:HOH1063 4.9 8.5 1.0 C7 A:AEP683 4.9 14.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Pepv


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 Pepv within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:11.0 occ:1.00 OD2 A:ASP119 2.0 8.2 1.0 NE2 A:HIS87 2.1 5.1 1.0 OD2 A:ASP177 2.1 9.7 1.0 O1P A:AEP683 2.1 7.2 1.0 N A:AEP683 2.2 9.9 1.0 OD1 A:ASP177 2.3 8.2 1.0 CG A:ASP177 2.5 8.4 1.0 C1 A:AEP683 3.0 10.3 1.0 P A:AEP683 3.0 8.3 1.0 CE1 A:HIS87 3.0 5.9 1.0 CD2 A:HIS87 3.1 6.0 1.0 CG A:ASP119 3.1 8.6 1.0 OD1 A:ASP119 3.6 7.9 1.0 OE2 A:GLU153 3.7 11.7 1.0 CB A:ASP120 3.8 7.8 1.0 ZN A:ZN1001 3.8 7.4 1.0 O2P A:AEP683 3.9 6.9 1.0 CB A:ASP177 4.0 9.1 1.0 OE2 A:GLU154 4.0 8.7 1.0 O A:ASP177 4.1 8.2 1.0 ND1 A:HIS87 4.1 5.2 1.0 CG A:HIS87 4.2 5.8 1.0 C4 A:AEP683 4.2 9.8 1.0 CD A:GLU153 4.2 11.9 1.0 O A:HOH1021 4.3 7.2 1.0 OE1 A:GLU153 4.3 14.1 1.0 CB A:ASP119 4.3 7.0 1.0 C2 A:AEP683 4.4 12.6 1.0 CG A:ASP120 4.4 5.9 1.0 CA A:ASP119 4.5 8.1 1.0 O A:HOH1164 4.6 39.2 1.0 C A:ASP119 4.7 7.8 1.0 CD A:GLU154 4.8 10.0 1.0 O A:HOH1109 4.8 34.6 1.0 CA A:ASP177 4.8 7.2 1.0 C A:ASP177 4.9 8.6 1.0 CA A:ASP120 4.9 9.6 1.0 N A:ASP120 4.9 9.6 1.0 OD2 A:ASP120 4.9 7.7 1.0 OD1 A:ASP120 5.0 7.4 1.0

D.Jozic, G.Bourenkow, H.Bartunik, H.Scholze, V.Dive, B.Henrich, R.Huber, W.Bode, K.Maskos. Crystal Structure of the Dinuclear Zinc Aminopeptidase Pepv From Lactobacillus Delbrueckii Unravels Its Preference For Dipeptides Structure V. 10 1097 2002.
ISSN: ISSN 0969-2126
PubMed: 12176387
DOI: 10.1016/S0969-2126(02)00805-5