Zinc in PDB 3pso: Crystal Structure of Mouse VPS29 Complexed with ZN2+

The structure of Crystal Structure of Mouse VPS29 Complexed with ZN2+, PDB code: 3pso was solved by J.Swarbrick, D.Shaw, S.Chhabra, R.Ghai, E.Valkov, S.Norwood, B.Collins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.26 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.268, 68.643, 62.537, 90.00, 105.72, 90.00
R / Rfree (%)	18.5 / 24.2

The binding sites of Zinc atom in the Crystal Structure of Mouse VPS29 Complexed with ZN2+ (pdb code 3pso). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Mouse VPS29 Complexed with ZN2+, PDB code: 3pso:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of Mouse VPS29 Complexed with ZN2+


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 Mouse VPS29 Complexed with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:86.5 occ:1.00 NE2 A:HIS117 2.2 84.6 1.0 NE2 A:HIS10 2.4 95.2 1.0 OD1 A:ASP8 2.5 70.7 1.0 CE1 A:HIS117 2.9 84.7 1.0 OD1 A:ASN39 2.9 80.1 1.0 CD2 A:HIS10 3.0 93.0 1.0 ZN A:ZN602 3.3 81.7 1.0 CD2 A:HIS117 3.3 83.4 1.0 CG A:ASP8 3.4 73.8 1.0 CE1 A:HIS10 3.6 99.0 1.0 CB A:ASP8 3.7 83.8 1.0 CG A:ASN39 3.8 83.8 1.0 CA A:ASP8 4.0 82.3 1.0 CB A:ASN39 4.0 82.1 1.0 ND1 A:HIS117 4.0 80.9 1.0 CG A:HIS10 4.2 99.5 1.0 CG A:HIS117 4.3 73.4 1.0 O A:HIS115 4.4 63.6 1.0 CA A:HIS115 4.4 65.8 1.0 CE1 A:HIS86 4.4 76.9 1.0 ND1 A:HIS10 4.4 96.2 1.0 NH1 A:ARG14 4.6 0.5 1.0 OD2 A:ASP8 4.6 75.7 1.0 C A:ASP8 4.6 80.6 1.0 NE2 A:HIS86 4.6 76.7 1.0 O A:ASP8 4.7 75.3 1.0 C A:HIS115 4.8 67.0 1.0 OD1 A:ASP62 4.8 75.5 1.0 ND2 A:ASN39 5.0 84.8 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of Mouse VPS29 Complexed with ZN2+


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 Mouse VPS29 Complexed with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:81.7 occ:1.00 OD2 A:ASP62 2.2 85.4 1.0 NE2 A:HIS86 2.3 76.7 1.0 ND1 A:HIS115 2.3 64.3 1.0 OD1 A:ASN39 2.7 80.1 1.0 CE1 A:HIS86 2.8 76.9 1.0 OD1 A:ASP62 2.8 75.5 1.0 CG A:ASP62 2.8 83.4 1.0 CG A:HIS115 3.1 70.5 1.0 CB A:HIS115 3.2 67.9 1.0 ZN A:ZN601 3.3 86.5 1.0 CA A:HIS115 3.4 65.8 1.0 CE1 A:HIS115 3.4 64.0 1.0 CD2 A:HIS86 3.5 75.0 1.0 OD1 A:ASP8 3.7 70.7 1.0 CG A:ASN39 3.9 83.8 1.0 ND1 A:HIS86 4.0 69.5 1.0 O A:HIS115 4.1 63.6 1.0 C A:HIS115 4.2 67.0 1.0 CB A:ASP62 4.3 81.4 1.0 CG A:HIS86 4.3 71.5 1.0 CD2 A:HIS115 4.3 63.6 1.0 N A:HIS115 4.4 68.1 1.0 NE2 A:HIS115 4.5 70.3 1.0 NE2 A:HIS117 4.5 84.6 1.0 ND2 A:ASN39 4.6 84.8 1.0 NE2 A:HIS10 4.6 95.2 1.0 CB A:HIS88 4.7 64.4 1.0 N A:ASP62 4.7 86.1 1.0 CG A:ASP8 4.9 73.8 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of Mouse VPS29 Complexed with ZN2+


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 Mouse VPS29 Complexed with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:0.7 occ:1.00 NE2 A:HIS57 2.2 79.6 1.0 OD2 A:ASP55 2.5 76.2 1.0 OD1 A:ASP55 2.8 70.3 1.0 CD2 A:HIS57 2.9 61.6 1.0 CD2 A:HIS33 2.9 66.5 1.0 CG A:ASP55 3.0 71.7 1.0 NE2 A:HIS33 3.3 87.0 1.0 CE1 A:HIS57 3.4 83.8 1.0 CG1 A:VAL75 3.5 73.5 1.0 CG A:HIS57 4.2 62.1 1.0 CG A:HIS33 4.2 69.5 1.0 ND1 A:HIS57 4.4 76.9 1.0 CB A:ASP55 4.5 68.7 1.0 CE1 A:HIS33 4.5 87.0 1.0 O A:THR76 4.7 66.0 1.0 CB A:VAL75 5.0 55.8 1.0 ND1 A:HIS33 5.0 69.4 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of Mouse VPS29 Complexed with ZN2+


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 Mouse VPS29 Complexed with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:0.1 occ:1.00 ND1 A:HIS10 2.0 96.2 1.0 SG A:CYS41 2.4 0.1 1.0 CE1 A:HIS10 2.8 99.0 1.0 CG A:HIS10 3.1 99.5 1.0 CB A:HIS10 3.5 92.0 1.0 CB A:CYS41 3.7 99.1 1.0 CA A:HIS10 3.8 0.4 1.0 NE2 A:HIS10 4.0 95.2 1.0 CB A:HIS13 4.0 0.4 1.0 CG A:HIS13 4.1 0.3 1.0 CD2 A:HIS10 4.1 93.0 1.0 CD2 A:HIS13 4.2 0.9 1.0 C A:HIS10 4.5 0.9 1.0 ND1 A:HIS13 4.6 0.3 1.0 CZ A:ARG14 4.7 0.1 1.0 O A:HIS10 4.8 1.0 1.0 NH1 A:ARG14 4.8 0.5 1.0 CG A:ARG14 4.8 0.4 1.0 NE2 A:HIS13 4.9 0.6 1.0 NE A:ARG14 5.0 0.3 1.0 N A:HIS10 5.0 93.1 1.0 NH2 A:ARG14 5.0 0.4 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of Mouse VPS29 Complexed with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Mouse VPS29 Complexed with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:70.6 occ:1.00 NE2 B:HIS117 2.2 87.7 1.0 NE2 B:HIS10 2.5 96.9 1.0 OD1 B:ASP8 2.5 69.3 1.0 CE1 B:HIS117 2.9 86.2 1.0 OD1 B:ASN39 2.9 74.6 1.0 CD2 B:HIS10 3.0 92.8 1.0 CD2 B:HIS117 3.3 86.3 1.0 ZN B:ZN702 3.3 66.2 1.0 CG B:ASP8 3.5 72.1 1.0 CE1 B:HIS10 3.6 0.8 1.0 CB B:ASP8 3.7 84.0 1.0 CG B:ASN39 3.8 81.1 1.0 CA B:ASP8 4.0 80.3 1.0 CB B:ASN39 4.0 82.7 1.0 ND1 B:HIS117 4.0 81.6 1.0 CG B:HIS10 4.2 0.2 1.0 CG B:HIS117 4.3 73.3 1.0 O B:HIS115 4.4 61.2 1.0 CE1 B:HIS86 4.4 76.9 1.0 CA B:HIS115 4.4 65.1 1.0 ND1 B:HIS10 4.5 98.3 1.0 NH1 B:ARG14 4.5 0.5 1.0 NE2 B:HIS86 4.6 77.2 1.0 C B:ASP8 4.6 80.6 1.0 OD2 B:ASP8 4.6 72.3 1.0 O B:ASP8 4.7 76.3 1.0 C B:HIS115 4.8 65.8 1.0 OD1 B:ASP62 4.8 77.8 1.0 ND2 B:ASN39 5.0 82.7 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of Mouse VPS29 Complexed with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Mouse VPS29 Complexed with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:66.2 occ:1.00 OD2 B:ASP62 2.2 89.8 1.0 NE2 B:HIS86 2.2 77.2 1.0 ND1 B:HIS115 2.4 61.9 1.0 OD1 B:ASN39 2.7 74.6 1.0 OD1 B:ASP62 2.7 77.8 1.0 CG B:ASP62 2.8 85.1 1.0 CE1 B:HIS86 2.8 76.9 1.0 CG B:HIS115 3.1 71.3 1.0 CB B:HIS115 3.2 67.6 1.0 ZN B:ZN701 3.3 70.6 1.0 CD2 B:HIS86 3.4 75.5 1.0 CA B:HIS115 3.4 65.1 1.0 CE1 B:HIS115 3.5 61.7 1.0 OD1 B:ASP8 3.7 69.3 1.0 CG B:ASN39 3.9 81.1 1.0 ND1 B:HIS86 3.9 68.5 1.0 O B:HIS115 4.1 61.2 1.0 CB B:ASP62 4.2 78.9 1.0 CG B:HIS86 4.3 71.0 1.0 C B:HIS115 4.3 65.8 1.0 CD2 B:HIS115 4.4 63.5 1.0 N B:HIS115 4.4 67.0 1.0 NE2 B:HIS115 4.5 66.8 1.0 ND2 B:ASN39 4.5 82.7 1.0 NE2 B:HIS117 4.6 87.7 1.0 N B:ASP62 4.6 82.6 1.0 NE2 B:HIS10 4.7 96.9 1.0 CB B:HIS88 4.7 63.9 1.0 CG B:ASP8 5.0 72.1 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of Mouse VPS29 Complexed with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Mouse VPS29 Complexed with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn703 b:0.1 occ:1.00 NE2 B:HIS57 2.3 79.6 1.0 OD2 B:ASP55 2.4 76.4 1.0 ND1 B:HIS33 2.6 68.6 1.0 CE1 B:HIS33 2.7 85.7 1.0 OD1 B:ASP55 2.7 74.3 1.0 CG B:ASP55 2.9 71.5 1.0 CD2 B:HIS57 3.0 60.6 1.0 CE1 B:HIS57 3.5 81.9 1.0 CG1 B:VAL75 3.6 74.2 1.0 NE2 B:HIS33 3.9 88.3 1.0 CG B:HIS33 4.0 70.3 1.0 CG B:HIS57 4.2 60.0 1.0 CB B:ASP55 4.4 67.3 1.0 ND1 B:HIS57 4.5 75.0 1.0 CD2 B:HIS33 4.6 69.7 1.0 O B:THR76 4.8 66.7 1.0 CB B:HIS33 4.9 62.6 1.0

J.Swarbrick, D.Shaw, S.Chhabra, R.Ghai, E.Valkov, S.Norwood, B.Collins. Conformational Dynamics and Biomolecular Interactions of VPS29 Studied By uc(Nmr) and X-Ray Crystallography To Be Published.