Magnesium in PDB 3q5e: Crystal Structure of Human Atlastin-1 (Residues 1-447) Bound to Gdp, Crystal Form 2

The structure of Crystal Structure of Human Atlastin-1 (Residues 1-447) Bound to Gdp, Crystal Form 2, PDB code: 3q5e was solved by L.J.Byrnes, H.Sondermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.54 / 3.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.394, 133.549, 175.835, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 27.3

The binding sites of Magnesium atom in the Crystal Structure of Human Atlastin-1 (Residues 1-447) Bound to Gdp, Crystal Form 2 (pdb code 3q5e). 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 Human Atlastin-1 (Residues 1-447) Bound to Gdp, Crystal Form 2, PDB code: 3q5e:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human Atlastin-1 (Residues 1-447) Bound to Gdp, Crystal Form 2


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 Human Atlastin-1 (Residues 1-447) Bound to Gdp, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg448 b:72.1 occ:1.00 OD1 A:ASP146 2.6 80.2 1.0 O2B A:GDP3850 2.7 63.2 1.0 OG A:SER81 3.2 65.4 1.0 OE1 A:GLN148 3.3 0.6 1.0 N A:SER81 3.3 47.5 1.0 CG A:ASP146 3.5 75.4 1.0 CB A:SER81 3.6 47.8 1.0 CD A:GLN148 3.7 0.3 1.0 CB A:LYS80 3.7 44.5 1.0 CA A:SER81 3.8 48.5 1.0 OD2 A:ASP146 3.8 89.8 1.0 CE A:LYS80 3.9 50.6 1.0 CG A:GLN148 4.0 0.1 1.0 NZ A:LYS80 4.0 65.3 1.0 PB A:GDP3850 4.1 73.1 1.0 C A:LYS80 4.2 47.2 1.0 O1B A:GDP3850 4.4 88.6 1.0 NE2 A:GLN148 4.5 0.4 1.0 CA A:LYS80 4.5 42.8 1.0 CG A:LYS80 4.8 41.6 1.0 CB A:ASP146 4.9 58.1 1.0 OE2 A:GLU117 5.0 0.4 1.0 CD A:LYS80 5.0 41.5 1.0 O3B A:GDP3850 5.0 52.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human Atlastin-1 (Residues 1-447) Bound to Gdp, Crystal Form 2


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 Human Atlastin-1 (Residues 1-447) Bound to Gdp, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg448 b:71.0 occ:1.00 OG C:SER81 3.3 70.3 1.0 O2B C:GDP3850 3.9 57.3 1.0 CG C:GLU117 4.0 0.3 1.0 O1A C:GDP3850 4.1 48.0 1.0 CB C:SER81 4.1 56.2 1.0 O3B C:GDP3850 4.1 67.3 1.0 NE2 C:GLN148 4.6 0.3 1.0 CD C:GLU117 4.6 0.0 1.0 PB C:GDP3850 4.6 54.9 1.0 OE1 C:GLU117 4.6 0.7 1.0 CB C:GLU117 4.6 0.8 1.0 CB C:GLU119 4.8 0.8 1.0 O2A C:GDP3850 5.0 63.6 1.0 PA C:GDP3850 5.0 59.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human Atlastin-1 (Residues 1-447) Bound to Gdp, Crystal Form 2


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 Human Atlastin-1 (Residues 1-447) Bound to Gdp, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg448 b:68.4 occ:1.00 OG E:SER81 3.1 66.6 1.0 CB E:SER81 3.6 55.4 1.0 O1A E:GDP3850 3.9 39.5 1.0 CG E:ARG113 4.0 99.8 1.0 CA E:ARG113 4.1 89.5 1.0 CB E:ARG113 4.3 93.8 1.0 O2A E:GDP3850 4.7 48.8 1.0 N E:ARG113 4.7 82.5 1.0 O3B E:GDP3850 4.8 40.6 1.0 PA E:GDP3850 4.9 48.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human Atlastin-1 (Residues 1-447) Bound to Gdp, Crystal Form 2


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 Human Atlastin-1 (Residues 1-447) Bound to Gdp, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg448 b:70.9 occ:1.00 OD1 G:ASP146 3.1 66.4 1.0 OG G:SER81 3.3 57.9 1.0 NE2 G:GLN148 3.4 71.0 1.0 OE1 G:GLN124 3.5 72.2 1.0 CG G:ASP146 3.6 69.5 1.0 OE1 G:GLN148 3.7 91.5 1.0 OD2 G:ASP146 3.7 80.7 1.0 O2B G:GDP3850 3.7 69.3 1.0 CD G:GLN148 3.7 83.1 1.0 CD G:GLN124 4.6 67.5 1.0 CB G:ASP146 4.7 59.5 1.0 CB G:SER81 4.7 42.5 1.0 O3B G:GDP3850 4.7 55.0 1.0 PB G:GDP3850 4.8 58.4 1.0 CG G:GLN148 4.9 80.6 1.0 CB G:GLN148 5.0 67.5 1.0

L.J.Byrnes, H.Sondermann. Structural Basis For the Nucleotide-Dependent Dimerization of the Large G Protein Atlastin-1/SPG3A. Proc.Natl.Acad.Sci.Usa V. 108 2216 2011.
ISSN: ISSN 0027-8424
PubMed: 21220294
DOI: 10.1073/PNAS.1012792108