Manganese in PDB 1z2w: Crystal Structure of Mouse VPS29 Complexed with MN2+

The structure of Crystal Structure of Mouse VPS29 Complexed with MN2+, PDB code: 1z2w was solved by B.M.Collins, C.F.Skinner, P.J.Watson, M.N.J.Seaman, D.J.Owen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.914, 68.953, 60.519, 90.00, 106.65, 90.00
R / Rfree (%)	17.6 / 23.7

The binding sites of Manganese atom in the Crystal Structure of Mouse VPS29 Complexed with MN2+ (pdb code 1z2w). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Mouse VPS29 Complexed with MN2+, PDB code: 1z2w:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Mouse VPS29 Complexed with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Mouse VPS29 Complexed with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:25.5 occ:1.00 NE2 A:HIS10 2.1 24.3 1.0 O A:HOH603 2.1 30.4 1.0 OD1 A:ASP8 2.2 25.6 1.0 NE2 A:HIS117 2.3 24.3 1.0 OD1 A:ASN39 2.4 28.4 1.0 CE1 A:HIS10 2.9 24.8 1.0 CG A:ASP8 3.1 22.1 1.0 CE1 A:HIS117 3.2 27.5 1.0 CD2 A:HIS10 3.2 24.9 1.0 CD2 A:HIS117 3.3 25.1 1.0 CG A:ASN39 3.3 24.3 1.0 MN A:MN602 3.4 27.1 1.0 O A:HOH632 3.5 34.0 1.0 CB A:ASN39 3.6 23.7 1.0 CB A:ASP8 3.7 21.9 1.0 O A:HIS115 4.0 25.4 1.0 OD2 A:ASP8 4.0 25.1 1.0 O A:HOH693 4.1 46.6 1.0 ND1 A:HIS10 4.1 22.2 1.0 CA A:ASP8 4.1 22.6 1.0 CG A:HIS10 4.2 24.9 1.0 ND1 A:HIS117 4.3 29.5 1.0 CE1 A:HIS86 4.3 20.6 1.0 CG A:HIS117 4.4 24.4 1.0 NE2 A:HIS86 4.5 19.8 1.0 CA A:HIS115 4.5 23.7 1.0 ND2 A:ASN39 4.6 17.9 1.0 C A:HIS115 4.7 24.9 1.0 NH1 A:ARG14 4.8 36.3 1.0 C A:ASP8 4.9 22.2 1.0 O A:ASP8 4.9 24.7 1.0 ND1 A:HIS115 5.0 25.9 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Mouse VPS29 Complexed with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Mouse VPS29 Complexed with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:27.1 occ:1.00 O A:HOH603 2.1 30.4 1.0 OD1 A:ASP62 2.2 30.7 1.0 ND1 A:HIS115 2.3 25.9 1.0 NE2 A:HIS86 2.4 19.8 1.0 OD1 A:ASN39 2.4 28.4 1.0 O A:HOH693 2.5 46.6 1.0 CE1 A:HIS115 2.9 32.6 1.0 CG A:ASP62 3.1 36.7 1.0 CE1 A:HIS86 3.3 20.6 1.0 OD2 A:ASP62 3.3 36.7 1.0 CD2 A:HIS86 3.3 19.3 1.0 CG A:ASN39 3.3 24.3 1.0 MN A:MN601 3.4 25.5 1.0 CG A:HIS115 3.4 19.6 1.0 ND2 A:ASN39 3.8 17.9 1.0 CA A:HIS115 3.9 23.7 1.0 CB A:HIS115 4.0 22.7 1.0 OD1 A:ASP8 4.1 25.6 1.0 O A:HIS115 4.1 25.4 1.0 NE2 A:HIS115 4.2 27.2 1.0 O A:HOH632 4.2 34.0 1.0 O A:HOH762 4.4 46.1 1.0 CD2 A:HIS115 4.4 27.1 1.0 ND1 A:HIS86 4.4 18.0 1.0 CG A:HIS86 4.5 21.3 1.0 C A:HIS115 4.5 24.9 1.0 CB A:ASP62 4.5 34.4 1.0 CB A:ASN39 4.6 23.7 1.0 N A:ASP62 4.6 32.4 1.0 CB A:HIS88 4.8 34.7 1.0 CE1 A:HIS10 4.8 24.8 1.0 N A:HIS115 4.8 23.3 1.0 NE2 A:HIS10 4.9 24.3 1.0 O A:ASP62 4.9 37.6 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Mouse VPS29 Complexed with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Mouse VPS29 Complexed with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn701 b:25.3 occ:1.00 O B:HOH703 2.0 22.5 1.0 OD1 B:ASP8 2.1 23.9 1.0 NE2 B:HIS10 2.2 23.2 1.0 NE2 B:HIS117 2.3 25.5 1.0 OD1 B:ASN39 2.3 27.0 1.0 CG B:ASP8 3.1 20.3 1.0 CD2 B:HIS10 3.1 22.6 1.0 CE1 B:HIS10 3.2 22.7 1.0 CD2 B:HIS117 3.3 20.9 1.0 CE1 B:HIS117 3.3 20.8 1.0 CG B:ASN39 3.3 24.3 1.0 MN B:MN702 3.3 25.0 1.0 O B:HOH780 3.5 39.1 1.0 CB B:ASN39 3.6 23.5 1.0 CB B:ASP8 3.7 20.7 1.0 O B:HOH770 3.8 35.5 1.0 OD2 B:ASP8 4.1 22.3 1.0 O B:HIS115 4.1 23.4 1.0 CA B:ASP8 4.2 20.6 1.0 CE1 B:HIS86 4.3 23.8 1.0 ND1 B:HIS10 4.3 24.4 1.0 NE2 B:HIS86 4.3 19.2 1.0 CG B:HIS10 4.3 24.9 1.0 ND1 B:HIS117 4.4 21.8 1.0 CG B:HIS117 4.4 19.2 1.0 CA B:HIS115 4.5 20.9 1.0 ND2 B:ASN39 4.6 21.8 1.0 NH1 B:ARG14 4.7 24.9 1.0 C B:HIS115 4.7 22.1 1.0 ND1 B:HIS115 4.8 27.1 1.0 C B:ASP8 5.0 21.4 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Mouse VPS29 Complexed with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Mouse VPS29 Complexed with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn702 b:25.0 occ:1.00 O B:HOH703 2.0 22.5 1.0 OD2 B:ASP62 2.1 27.8 1.0 ND1 B:HIS115 2.3 27.1 1.0 NE2 B:HIS86 2.3 19.2 1.0 OD1 B:ASN39 2.3 27.0 1.0 O B:HOH770 2.4 35.5 1.0 CE1 B:HIS115 3.1 27.9 1.0 CG B:ASP62 3.1 35.8 1.0 CD2 B:HIS86 3.2 22.8 1.0 CE1 B:HIS86 3.3 23.8 1.0 MN B:MN701 3.3 25.3 1.0 CG B:HIS115 3.4 23.0 1.0 CG B:ASN39 3.4 24.3 1.0 OD1 B:ASP62 3.4 36.5 1.0 CB B:HIS115 3.8 22.2 1.0 ND2 B:ASN39 3.8 21.8 1.0 CA B:HIS115 3.8 20.9 1.0 O B:HOH780 4.0 39.1 1.0 OD1 B:ASP8 4.1 23.9 1.0 O B:HIS115 4.2 23.4 1.0 NE2 B:HIS115 4.3 25.4 1.0 CG B:HIS86 4.4 19.8 1.0 ND1 B:HIS86 4.4 19.6 1.0 CD2 B:HIS115 4.4 31.7 1.0 O B:HOH733 4.5 37.8 1.0 CB B:ASP62 4.5 34.9 1.0 N B:ASP62 4.6 34.2 1.0 C B:HIS115 4.6 22.1 1.0 CB B:ASN39 4.7 23.5 1.0 CB B:HIS88 4.8 30.5 1.0 O B:ASP62 4.8 37.6 1.0 NE2 B:HIS10 4.8 23.2 1.0 N B:HIS115 4.9 19.1 1.0

B.M.Collins, C.F.Skinner, P.J.Watson, M.N.J.Seaman, D.J.Owen. VPS29 Has A Phosphoesterase Fold That Acts As A Protein Interaction Scaffold For Retromer Assembly Nat.Struct.Mol.Biol. V. 12 594 2005.
ISSN: ISSN 1545-9993
PubMed: 15965486
DOI: 10.1038/NSMB954