Magnesium in PDB 4cym: Complex of Human Varp-ANKRD1 with RAB32-Gppcp

All present enzymatic activity of Complex of Human Varp-ANKRD1 with RAB32-Gppcp:
3.6.5.2;

The structure of Complex of Human Varp-ANKRD1 with RAB32-Gppcp, PDB code: 4cym was solved by I.Perez-Dorado, I.B.Schaefer, A.J.Mccoy, D.J.Owen, P.R.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	125.09 / 2.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	144.445, 144.445, 135.680, 90.00, 90.00, 120.00
R / Rfree (%)	19.205 / 24.565

The binding sites of Magnesium atom in the Complex of Human Varp-ANKRD1 with RAB32-Gppcp (pdb code 4cym). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Complex of Human Varp-ANKRD1 with RAB32-Gppcp, PDB code: 4cym:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Complex of Human Varp-ANKRD1 with RAB32-Gppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex of Human Varp-ANKRD1 with RAB32-Gppcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1199 b:32.9 occ:1.00 OG1 A:THR57 2.1 39.3 1.0 O2B A:GCP1198 2.1 35.6 1.0 O3G A:GCP1198 2.1 37.6 1.0 OG1 A:THR39 2.1 35.0 1.0 O A:HOH2003 2.1 38.2 1.0 O A:HOH2004 2.2 32.9 1.0 CB A:THR57 3.0 44.4 1.0 PG A:GCP1198 3.0 34.3 1.0 CB A:THR39 3.2 36.2 1.0 O1G A:GCP1198 3.3 34.9 1.0 PB A:GCP1198 3.3 38.0 1.0 N A:THR57 3.7 46.2 1.0 C3B A:GCP1198 3.7 36.1 1.0 CA A:THR57 3.9 45.6 1.0 OD2 A:ASP81 4.0 41.8 1.0 O A:HOH2008 4.0 54.1 1.0 CG2 A:THR57 4.0 45.5 1.0 N A:THR39 4.1 40.2 1.0 OD1 A:ASP81 4.2 47.7 1.0 CA A:THR39 4.2 39.8 1.0 O1B A:GCP1198 4.2 38.1 1.0 CG2 A:THR39 4.2 34.2 1.0 O2A A:GCP1198 4.3 39.7 1.0 O2G A:GCP1198 4.4 42.5 1.0 O3A A:GCP1198 4.4 39.5 1.0 CG A:ASP81 4.5 43.9 1.0 O A:ARG55 4.5 65.0 1.0 PA A:GCP1198 4.6 43.7 1.0 O1A A:GCP1198 4.7 44.9 1.0 C A:ALA56 4.7 50.6 1.0

Magnesium binding site 2 out of 3 in the Complex of Human Varp-ANKRD1 with RAB32-Gppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complex of Human Varp-ANKRD1 with RAB32-Gppcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1199 b:45.0 occ:1.00 O3G B:GCP1198 1.9 47.5 1.0 O2B B:GCP1198 2.0 42.2 1.0 OG1 B:THR57 2.2 54.7 1.0 O B:HOH2004 2.2 52.6 1.0 O B:HOH2003 2.2 53.2 1.0 OG1 B:THR39 2.2 55.6 1.0 PG B:GCP1198 3.0 46.4 1.0 CB B:THR57 3.1 61.3 1.0 CB B:THR39 3.2 58.0 1.0 O1G B:GCP1198 3.2 45.8 1.0 PB B:GCP1198 3.2 44.7 1.0 C3B B:GCP1198 3.7 46.2 1.0 N B:THR57 3.8 66.0 1.0 O2A B:GCP1198 3.9 46.8 1.0 O B:HOH2006 4.0 58.9 1.0 CA B:THR57 4.0 59.9 1.0 N B:THR39 4.0 52.8 1.0 OD2 B:ASP81 4.1 65.8 1.0 O1B B:GCP1198 4.1 43.3 1.0 CG2 B:THR57 4.2 65.3 1.0 CA B:THR39 4.2 55.3 1.0 OD1 B:ASP81 4.2 62.7 1.0 CG2 B:THR39 4.3 59.2 1.0 O3A B:GCP1198 4.3 48.1 1.0 O2G B:GCP1198 4.4 55.4 1.0 PA B:GCP1198 4.5 48.3 1.0 O B:ARG55 4.5 62.9 1.0 CG B:ASP81 4.6 61.1 1.0 O1A B:GCP1198 4.7 57.5 1.0 C B:ALA56 4.8 63.1 1.0 NZ B:LYS38 5.0 61.4 1.0

Magnesium binding site 3 out of 3 in the Complex of Human Varp-ANKRD1 with RAB32-Gppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Complex of Human Varp-ANKRD1 with RAB32-Gppcp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1199 b:44.6 occ:1.00 OG1 C:THR57 2.1 50.4 1.0 O C:HOH2004 2.1 49.5 1.0 O C:HOH2003 2.1 43.7 1.0 O3G C:GCP1198 2.2 48.1 1.0 OG1 C:THR39 2.2 49.9 1.0 O2B C:GCP1198 2.2 48.5 1.0 CB C:THR57 3.0 55.2 1.0 PG C:GCP1198 3.1 46.9 1.0 CB C:THR39 3.2 52.4 1.0 C3B C:GCP1198 3.2 44.8 1.0 PB C:GCP1198 3.3 47.4 1.0 O1G C:GCP1198 3.6 43.6 1.0 N C:THR57 3.7 51.8 1.0 CA C:THR57 4.0 53.7 1.0 N C:THR39 4.0 53.7 1.0 OD2 C:ASP81 4.1 54.9 1.0 CG2 C:THR57 4.1 59.3 1.0 CA C:THR39 4.2 51.8 1.0 CG2 C:THR39 4.2 53.7 1.0 OD1 C:ASP81 4.3 57.6 1.0 O1B C:GCP1198 4.3 45.4 1.0 O2A C:GCP1198 4.3 46.5 1.0 O1A C:GCP1198 4.4 55.0 1.0 O3A C:GCP1198 4.4 52.8 1.0 PA C:GCP1198 4.5 56.8 1.0 O C:ARG55 4.5 69.6 1.0 O2G C:GCP1198 4.5 48.8 1.0 CG C:ASP81 4.6 54.5 1.0 C C:ALA56 4.7 55.5 1.0 CA C:ALA56 5.0 56.4 1.0

G.G.Hesketh, I.Perez-Dorado, L.P.Jackson, L.Wartosch, I.B.Schefer, S.R.Gray, A.J.Mccoy, O.B.Zeldin, E.F.Garman, M.E.Harbour, P.R.Evans, M.N.Seaman, J.P.Luzio, D.J.Owen. Varp Is Recruited on to Endosomes By Direct Interaction with Retromer, Where Together They Function in Export to the Cell Surface. Dev.Cell V. 29 591 2014.
ISSN: ISSN 1534-5807
PubMed: 24856514
DOI: 10.1016/J.DEVCEL.2014.04.010