Zinc in PDB 1vix: Crystal Structure of A Putative Peptidase T

All present enzymatic activity of Crystal Structure of A Putative Peptidase T:
3.4.11.14;

The structure of Crystal Structure of A Putative Peptidase T, PDB code: 1vix was solved by Structural Genomix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.69 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	115.270, 145.787, 77.121, 90.00, 90.00, 90.00
R / Rfree (%)	25.6 / 30.3

The binding sites of Zinc atom in the Crystal Structure of A Putative Peptidase T (pdb code 1vix). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Putative Peptidase T, PDB code: 1vix:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Putative Peptidase T


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 Putative Peptidase T within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn419 b:56.7 occ:1.00 NE2 A:HIS78 2.1 31.5 1.0 OD2 A:ASP140 2.1 40.0 1.0 OD1 A:ASP196 2.1 45.7 1.0 OD2 A:ASP196 2.2 44.3 1.0 CG A:ASP196 2.5 42.8 1.0 ZN A:ZN420 3.0 97.1 1.0 CE1 A:HIS78 3.0 31.2 1.0 CG A:ASP140 3.0 37.3 1.0 CD2 A:HIS78 3.1 31.6 1.0 OD1 A:ASP140 3.2 39.2 1.0 OE1 A:GLU174 3.5 59.0 1.0 OE1 A:GLU173 3.6 53.1 1.0 CB A:ASP141 3.9 31.7 1.0 CB A:ASP196 4.0 41.3 1.0 ND1 A:HIS78 4.1 30.4 1.0 CG A:HIS78 4.2 31.9 1.0 CD A:GLU173 4.3 53.4 1.0 CG A:ASP141 4.3 30.5 1.0 CB A:ASP140 4.4 34.9 1.0 O A:ASP196 4.5 41.1 1.0 OD2 A:ASP141 4.7 29.4 1.0 OE2 A:GLU173 4.7 53.9 1.0 CA A:ASP140 4.8 34.7 1.0 OD1 A:ASP141 4.8 28.0 1.0 CD A:GLU174 4.8 57.1 1.0 CA A:ASP196 4.8 40.7 1.0 CA A:ASP141 4.8 31.8 1.0 C A:ASP140 4.9 33.8 1.0 N A:ASP141 4.9 33.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Putative Peptidase T


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 Putative Peptidase T within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn420 b:97.1 occ:1.00 OE1 A:GLU174 2.0 59.0 1.0 OD1 A:ASP140 2.2 39.2 1.0 NE2 A:HIS379 2.5 55.0 1.0 ZN A:ZN419 3.0 56.7 1.0 CG A:ASP140 3.0 37.3 1.0 CD A:GLU174 3.1 57.1 1.0 CE1 A:HIS379 3.1 55.4 1.0 OD2 A:ASP140 3.1 40.0 1.0 OE2 A:GLU174 3.4 58.2 1.0 CD2 A:HIS379 3.8 54.3 1.0 OE1 A:GLU173 4.0 53.1 1.0 NE2 A:HIS78 4.3 31.5 1.0 CB A:ASP140 4.4 34.9 1.0 ND1 A:HIS379 4.4 55.1 1.0 CG A:GLU174 4.4 54.6 1.0 OD2 A:ASP196 4.5 44.3 1.0 CE1 A:HIS78 4.5 31.2 1.0 OD1 A:ASP196 4.7 45.7 1.0 CG A:HIS379 4.7 53.8 1.0 CD A:GLU173 4.9 53.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Putative Peptidase T


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Putative Peptidase T within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn419 b:59.5 occ:1.00 NE2 B:HIS78 2.1 38.4 1.0 OD1 B:ASP196 2.2 45.2 1.0 OD2 B:ASP196 2.4 44.9 1.0 OD1 B:ASP140 2.6 50.6 1.0 OD2 B:ASP140 2.6 48.8 1.0 CG B:ASP196 2.7 44.2 1.0 CG B:ASP140 2.9 47.4 1.0 CE1 B:HIS78 2.9 38.0 1.0 ZN B:ZN420 3.1 0.1 1.0 OE1 B:GLU173 3.2 52.4 1.0 CD2 B:HIS78 3.3 38.1 1.0 CB B:ASP141 3.8 42.2 1.0 ND1 B:HIS78 4.1 37.6 1.0 CB B:ASP196 4.2 42.9 1.0 CD B:GLU173 4.2 51.9 1.0 CB B:ASP140 4.3 44.3 1.0 CG B:HIS78 4.3 38.3 1.0 CG B:ASP141 4.4 42.1 1.0 OE1 B:GLU174 4.4 53.5 1.0 O B:ASP196 4.5 42.5 1.0 OD1 B:ASP141 4.7 44.7 1.0 CA B:ASP140 4.7 43.6 1.0 CA B:ASP141 4.7 41.9 1.0 N B:ASP141 4.7 42.7 1.0 OE2 B:GLU174 4.7 51.9 1.0 C B:ASP140 4.7 43.4 1.0 CD B:GLU174 4.7 51.5 1.0 OE2 B:GLU173 4.9 53.1 1.0 CA B:ASP196 4.9 42.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Putative Peptidase T


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Putative Peptidase T within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn420 b:0.1 occ:1.00 OD2 B:ASP140 2.0 48.8 1.0 NE2 B:HIS379 2.5 56.7 1.0 OE2 B:GLU174 2.8 51.9 1.0 ZN B:ZN419 3.1 59.5 1.0 CG B:ASP140 3.1 47.4 1.0 OE1 B:GLU174 3.1 53.5 1.0 CD B:GLU174 3.3 51.5 1.0 CD2 B:HIS379 3.5 56.3 1.0 CE1 B:HIS379 3.5 56.0 1.0 OD1 B:ASP140 3.6 50.6 1.0 OE1 B:GLU173 4.0 52.4 1.0 CB B:ASP140 4.3 44.3 1.0 ND1 B:HIS379 4.6 56.6 1.0 NE2 B:HIS78 4.6 38.4 1.0 CG B:HIS379 4.6 56.1 1.0 CE1 B:HIS78 4.7 38.0 1.0 CG B:GLU174 4.7 50.9 1.0 OD2 B:ASP196 4.9 44.9 1.0 OD1 B:ASP196 4.9 45.2 1.0 CB B:TYR378 5.0 53.8 1.0

J.Badger, J.M.Sauder, J.M.Adams, S.Antonysamy, K.Bain, M.G.Bergseid, S.G.Buchanan, M.D.Buchanan, Y.Batiyenko, J.A.Christopher, S.Emtage, A.Eroshkina, I.Feil, E.B.Furlong, K.S.Gajiwala, X.Gao, D.He, J.Hendle, A.Huber, K.Hoda, P.Kearins, C.Kissinger, B.Laubert, H.A.Lewis, J.Lin, K.Loomis, D.Lorimer, G.Louie, M.Maletic, C.D.Marsh, I.Miller, J.Molinari, H.J.Muller-Dieckmann, J.M.Newman, B.W.Noland, B.Pagarigan, F.Park, T.S.Peat, K.W.Post, S.Radojicic, A.Ramos, R.Romero, M.E.Rutter, W.E.Sanderson, K.D.Schwinn, J.Tresser, J.Winhoven, T.A.Wright, L.Wu, J.Xu, T.J.Harris. Structural Analysis of A Set of Proteins Resulting From A Bacterial Genomics Project Proteins V. 60 787 2005.
ISSN: ISSN 0887-3585
PubMed: 16021622
DOI: 10.1002/PROT.20541