Magnesium in PDB 3qof: Crystal Structure of the Cytosolic Domain of Human Atlastin-1 in Complex with Gdp, Orthorhombic Form

The structure of Crystal Structure of the Cytosolic Domain of Human Atlastin-1 in Complex with Gdp, Orthorhombic Form, PDB code: 3qof was solved by X.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.742, 133.445, 176.266, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 26.7

The binding sites of Magnesium atom in the Crystal Structure of the Cytosolic Domain of Human Atlastin-1 in Complex with Gdp, Orthorhombic Form (pdb code 3qof). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Cytosolic Domain of Human Atlastin-1 in Complex with Gdp, Orthorhombic Form, PDB code: 3qof:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Cytosolic Domain of Human Atlastin-1 in Complex with Gdp, Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Cytosolic Domain of Human Atlastin-1 in Complex with Gdp, Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg595 b:68.6 occ:1.00 OG A:SER81 2.6 71.0 1.0 O2B A:GDP593 2.8 61.0 1.0 OD2 A:ASP146 3.2 88.8 1.0 O3B A:GDP593 3.4 66.0 1.0 PB A:GDP593 3.6 75.0 1.0 CB A:SER81 3.8 63.1 1.0 CG A:ASP146 4.0 84.3 1.0 N A:SER81 4.0 60.9 1.0 OD1 A:ASP146 4.1 77.3 1.0 CA A:SER81 4.2 60.8 1.0 CG A:GLN148 4.3 95.2 1.0 NZ A:LYS80 4.3 64.7 1.0 O1B A:GDP593 4.4 69.2 1.0 CB A:LYS80 4.5 61.9 1.0 O2A A:GDP593 4.6 68.9 1.0 OE1 A:GLN148 4.9 96.6 1.0 CD A:GLN148 4.9 94.8 1.0 C A:LYS80 4.9 57.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Cytosolic Domain of Human Atlastin-1 in Complex with Gdp, Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Cytosolic Domain of Human Atlastin-1 in Complex with Gdp, Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg595 b:70.6 occ:1.00 O2B B:GDP593 2.5 70.8 1.0 OG B:SER81 3.0 65.3 1.0 OD2 B:ASP146 3.1 72.6 1.0 CG B:GLN148 3.6 82.5 1.0 O3B B:GDP593 3.7 76.1 1.0 PB B:GDP593 3.7 72.8 1.0 CG B:ASP146 4.0 65.3 1.0 OE1 B:GLN148 4.0 87.8 1.0 OD1 B:ASP146 4.2 60.8 1.0 CD B:GLN148 4.3 94.7 1.0 CB B:SER81 4.4 58.3 1.0 N B:SER81 4.5 52.8 1.0 O3A B:GDP593 4.6 59.5 1.0 O1B B:GDP593 4.7 46.2 1.0 CA B:SER81 4.8 55.4 1.0 CD B:LYS80 4.8 51.9 1.0 NZ B:LYS80 4.8 67.5 1.0 CB B:LYS80 4.9 47.7 1.0 CB B:GLN148 4.9 70.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Cytosolic Domain of Human Atlastin-1 in Complex with Gdp, Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Cytosolic Domain of Human Atlastin-1 in Complex with Gdp, Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg595 b:57.2 occ:1.00 O2B C:GDP593 2.7 61.3 1.0 OG C:SER81 2.8 64.9 1.0 OD2 C:ASP146 3.1 67.1 1.0 O C:HOH474 3.1 56.0 1.0 O3B C:GDP593 3.4 52.0 1.0 PB C:GDP593 3.7 45.7 1.0 CG C:ASP146 3.8 62.3 1.0 CB C:SER81 3.9 62.0 1.0 OD1 C:ASP146 4.1 57.2 1.0 NZ C:LYS80 4.3 46.6 1.0 N C:SER81 4.4 50.2 1.0 CB C:LYS80 4.5 45.8 1.0 O3A C:GDP593 4.6 54.9 1.0 CA C:SER81 4.7 55.2 1.0 CB C:GLN148 4.7 79.6 1.0 O1B C:GDP593 4.8 38.7 1.0 CB C:ASP146 4.8 57.8 1.0 CA C:GLN148 5.0 79.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Cytosolic Domain of Human Atlastin-1 in Complex with Gdp, Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Cytosolic Domain of Human Atlastin-1 in Complex with Gdp, Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg595 b:70.0 occ:1.00 O2B D:GDP593 2.9 69.1 1.0 OG D:SER81 3.0 69.8 1.0 OD2 D:ASP146 3.1 69.9 1.0 NH1 D:ARG113 3.1 0.7 1.0 OD1 D:ASP146 3.2 75.0 1.0 OE1 D:GLN148 3.4 97.1 1.0 CG D:GLN148 3.4 94.3 1.0 CG D:ASP146 3.5 72.8 1.0 CD D:GLN148 3.5 95.6 1.0 CZ D:ARG113 4.0 0.6 1.0 PB D:GDP593 4.3 56.1 1.0 CB D:SER81 4.3 59.9 1.0 NE2 D:GLN148 4.4 85.5 1.0 CD D:ARG113 4.4 0.2 1.0 NE D:ARG113 4.5 0.1 1.0 N D:SER81 4.6 51.5 1.0 O3B D:GDP593 4.6 69.8 1.0 CA D:SER81 4.7 52.2 1.0 CB D:GLN148 4.8 93.6 1.0 NH2 D:ARG113 4.8 0.9 1.0 CB D:ASP146 4.9 65.5 1.0 O3A D:GDP593 4.9 59.1 1.0 CB D:LYS80 5.0 49.4 1.0

X.Bian, R.W.Klemm, T.Y.Liu, M.Zhang, S.Sun, X.Sui, X.Liu, T.A.Rapoport, J.Hu. Structures of the Atlastin Gtpase Provide Insight Into Homotypic Fusion of Endoplasmic Reticulum Membranes. Proc.Natl.Acad.Sci.Usa V. 108 3976 2011.
ISSN: ISSN 0027-8424
PubMed: 21368113
DOI: 10.1073/PNAS.1101643108