Zinc in PDB 5xch: Crystal Structure of Wild Type VPS29 Complexed with Zn+2 From Entamoeba Histolytica

The structure of Crystal Structure of Wild Type VPS29 Complexed with Zn+2 From Entamoeba Histolytica, PDB code: 5xch was solved by V.K.Srivastava, R.Yadav, P.Tomar, S.Gourinath, S.Datta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.90 / 2.85
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	47.310, 47.310, 148.000, 90.00, 90.00, 120.00
R / Rfree (%)	28.7 / 30.7

The binding sites of Zinc atom in the Crystal Structure of Wild Type VPS29 Complexed with Zn+2 From Entamoeba Histolytica (pdb code 5xch). 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 Wild Type VPS29 Complexed with Zn+2 From Entamoeba Histolytica, PDB code: 5xch:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Wild Type VPS29 Complexed with Zn+2 From Entamoeba Histolytica


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 Wild Type VPS29 Complexed with Zn+2 From Entamoeba Histolytica within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:38.3 occ:1.00 OD1 A:ASP62 2.3 33.3 1.0 ND1 A:HIS115 2.3 31.9 1.0 OD1 A:ASN39 2.4 32.0 1.0 ZN A:ZN202 2.5 38.4 1.0 CE1 A:HIS115 2.8 31.9 1.0 CG A:ASP62 3.2 43.7 1.0 NE2 A:HIS86 3.3 26.2 1.0 OD2 A:ASP62 3.4 44.0 1.0 OD1 A:ASP8 3.5 25.7 1.0 CG A:ASN39 3.5 24.4 1.0 CG A:HIS115 3.6 31.9 1.0 CD2 A:HIS86 4.1 23.7 1.0 NE2 A:HIS115 4.1 31.9 1.0 CA A:HIS115 4.1 26.6 1.0 CB A:ASN39 4.2 23.9 1.0 CB A:HIS115 4.2 31.9 1.0 CE1 A:HIS86 4.4 30.5 1.0 CD2 A:HIS115 4.5 31.9 1.0 CB A:ASP62 4.5 41.2 1.0 O A:HIS10 4.6 32.6 1.0 NE2 A:HIS117 4.6 36.8 1.0 ND2 A:ASN39 4.6 27.6 1.0 CG A:ASP8 4.7 22.5 1.0 N A:HIS115 4.8 31.1 1.0 N A:ASP62 4.9 41.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Wild Type VPS29 Complexed with Zn+2 From Entamoeba Histolytica


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 Wild Type VPS29 Complexed with Zn+2 From Entamoeba Histolytica within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:38.4 occ:1.00 ZN A:ZN201 2.5 38.3 1.0 NE2 A:HIS117 2.5 36.8 1.0 OD1 A:ASP8 2.6 25.7 1.0 CD2 A:HIS117 3.2 35.1 1.0 CB A:ASP8 3.3 21.5 1.0 CG A:ASP8 3.4 22.5 1.0 CE1 A:HIS117 3.6 41.5 1.0 OD1 A:ASN39 3.7 32.0 1.0 CA A:ASP8 3.7 28.3 1.0 O A:ASP8 3.7 33.8 1.0 C A:ASP8 4.0 31.4 1.0 O A:HIS10 4.0 32.6 1.0 ND1 A:HIS115 4.0 31.9 1.0 CA A:HIS115 4.1 26.6 1.0 CB A:ASN39 4.4 23.9 1.0 NE2 A:HIS86 4.4 26.2 1.0 CG A:ASN39 4.4 24.4 1.0 CG A:HIS117 4.5 37.9 1.0 N A:HIS115 4.5 31.1 1.0 OD2 A:ASP8 4.6 22.3 1.0 ND1 A:HIS117 4.6 45.3 1.0 OD1 A:ASP62 4.7 33.3 1.0 CE1 A:HIS115 4.8 31.9 1.0 CG1 A:VAL11 4.9 46.3 1.0 CG A:HIS115 4.9 31.9 1.0 C A:HIS115 4.9 26.0 1.0 CE1 A:HIS86 4.9 30.5 1.0 CB A:HIS115 5.0 31.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Wild Type VPS29 Complexed with Zn+2 From Entamoeba Histolytica


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 Wild Type VPS29 Complexed with Zn+2 From Entamoeba Histolytica within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:47.6 occ:1.00 OD2 B:ASP62 2.0 36.7 1.0 ND1 B:HIS115 2.2 33.7 1.0 NE2 B:HIS86 2.6 27.7 1.0 CG B:ASP62 2.8 36.7 1.0 ZN B:ZN202 2.9 46.9 1.0 OD1 B:ASP62 3.1 36.7 1.0 CE1 B:HIS115 3.1 33.7 1.0 CG B:HIS115 3.3 33.7 1.0 CE1 B:HIS86 3.3 28.9 1.0 OD1 B:ASN39 3.5 35.0 1.0 CD2 B:HIS86 3.6 21.7 1.0 CB B:HIS115 3.6 33.7 1.0 CA B:HIS115 3.7 24.8 1.0 OD1 B:ASP8 3.7 21.3 1.0 CG B:ASN39 3.8 27.0 1.0 ND2 B:ASN39 4.1 29.6 1.0 CB B:ASP62 4.1 36.7 1.0 NE2 B:HIS115 4.3 33.7 1.0 CD2 B:HIS115 4.4 33.7 1.0 N B:HIS115 4.4 26.7 1.0 N B:ASP62 4.4 51.5 1.0 NE2 B:HIS117 4.4 35.2 1.0 ND1 B:HIS86 4.5 24.6 1.0 O B:HOH305 4.5 9.5 1.0 CB B:ASN39 4.6 23.2 1.0 CG B:HIS86 4.6 21.0 1.0 C B:HIS115 4.8 28.8 1.0 O B:HIS115 4.8 36.1 1.0 CG B:ASP8 4.9 21.3 1.0 CA B:ASP62 5.0 51.5 1.0 CD2 B:HIS117 5.0 28.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Wild Type VPS29 Complexed with Zn+2 From Entamoeba Histolytica


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 Wild Type VPS29 Complexed with Zn+2 From Entamoeba Histolytica within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:46.9 occ:1.00 NE2 B:HIS117 2.1 35.2 1.0 OD1 B:ASN39 2.2 35.0 1.0 OD1 B:ASP8 2.8 21.3 1.0 CE1 B:HIS117 2.9 34.2 1.0 ZN B:ZN201 2.9 47.6 1.0 CG B:ASN39 3.1 27.0 1.0 CD2 B:HIS117 3.2 28.1 1.0 CB B:ASN39 3.6 23.2 1.0 CG B:ASP8 3.7 21.3 1.0 OD2 B:ASP62 3.8 36.7 1.0 CB B:ASP8 3.8 21.3 1.0 ND1 B:HIS117 4.1 37.2 1.0 CA B:ASP8 4.1 21.3 1.0 ND2 B:ASN39 4.2 29.6 1.0 O B:HIS10 4.2 31.6 1.0 CG B:HIS117 4.2 30.7 1.0 O B:HOH305 4.5 9.5 1.0 CE1 B:HIS86 4.6 28.9 1.0 ND1 B:HIS115 4.6 33.7 1.0 C B:ASP8 4.6 21.3 1.0 NE2 B:HIS86 4.7 27.7 1.0 CA B:HIS115 4.7 24.8 1.0 O B:ASP8 4.8 21.3 1.0 OD2 B:ASP8 4.9 21.3 1.0 CG B:ASP62 4.9 36.7 1.0

V.K.Srivastava, R.Yadav, N.Watanabe, P.Tomar, M.Mukherjee, S.Gourinath, K.Nakada-Tsukui, T.Nozaki, S.Datta. Structural and Thermodynamic Characterization of Metal Binding in VPS29 From Entamoeba Histolytica: Implication in Retromer Function. Mol. Microbiol. V. 106 562 2017.
ISSN: ESSN 1365-2958
PubMed: 28898487
DOI: 10.1111/MMI.13836