Magnesium in PDB 8vgb: Crystal Structure of Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) From Oryza Sativa in Complex with Gdp

The structure of Crystal Structure of Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) From Oryza Sativa in Complex with Gdp, PDB code: 8vgb was solved by S.G.Lee, J.M.Jez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.37 / 2.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.393, 68.419, 167.977, 90, 89.91, 90
R / Rfree (%)	26.6 / 30.6

The binding sites of Magnesium atom in the Crystal Structure of Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) From Oryza Sativa in Complex with Gdp (pdb code 8vgb). 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 Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) From Oryza Sativa in Complex with Gdp, PDB code: 8vgb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) From Oryza Sativa in Complex with Gdp


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 Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) From Oryza Sativa in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:98.2 occ:1.00 O2B A:GDP500 2.0 82.6 1.0 O3B A:GDP500 2.2 93.0 1.0 PB A:GDP500 2.5 88.3 1.0 O1B A:GDP500 3.2 83.0 1.0 OG A:SER53 3.6 83.3 1.0 CE A:LYS52 3.8 76.6 1.0 O1A A:GDP500 3.9 82.7 1.0 O3A A:GDP500 3.9 80.7 1.0 NZ A:LYS52 4.1 77.8 1.0 CB A:SER53 4.1 79.9 1.0 CG A:LYS52 4.1 73.0 1.0 PA A:GDP500 4.4 78.6 1.0 OG1 A:THR194 4.5 94.5 1.0 N A:SER53 4.5 74.8 1.0 CD A:LYS52 4.5 68.7 1.0 O A:GLY48 4.5 96.4 1.0 O A:VAL220 4.8 129.9 1.0 O2A A:GDP500 4.8 79.5 1.0 OD2 A:ASP219 4.8 76.9 1.0 CA A:SER53 4.9 77.5 1.0 OD1 A:ASP219 5.0 83.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) From Oryza Sativa in Complex with Gdp


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 Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) From Oryza Sativa in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:81.0 occ:1.00 O1B B:GDP401 1.9 87.4 1.0 OG B:SER53 2.0 84.0 1.0 O2B B:GDP401 2.1 83.2 1.0 PB B:GDP401 2.4 87.3 1.0 CB B:SER53 3.4 82.5 1.0 O3A B:GDP401 3.4 84.7 1.0 O3B B:GDP401 3.7 83.3 1.0 N B:SER53 3.8 78.2 1.0 CE B:LYS52 4.1 83.6 1.0 O2A B:GDP401 4.1 87.5 1.0 CA B:SER53 4.2 77.8 1.0 PA B:GDP401 4.2 85.9 1.0 OD2 B:ASP219 4.3 92.5 1.0 O B:GLY48 4.6 90.3 1.0 O1A B:GDP401 4.6 91.4 1.0 NZ B:LYS52 4.7 85.6 1.0 CB B:LYS52 4.9 83.4 1.0 C B:LYS52 4.9 80.1 1.0 OG1 B:THR194 4.9 105.3 1.0 N B:LYS52 4.9 76.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) From Oryza Sativa in Complex with Gdp


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 Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) From Oryza Sativa in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:83.7 occ:1.00 O1B C:GDP401 2.0 84.3 1.0 O3B C:GDP401 2.1 82.3 1.0 PB C:GDP401 2.4 104.3 1.0 O2B C:GDP401 2.9 87.9 1.0 CE C:LYS52 3.8 78.7 1.0 CG2 C:THR194 3.8 128.2 1.0 O3A C:GDP401 3.9 90.6 1.0 OG C:SER53 4.0 77.6 1.0 O2A C:GDP401 4.0 95.0 1.0 NZ C:LYS52 4.0 77.8 1.0 CG C:LYS52 4.2 84.2 1.0 O C:GLY48 4.2 83.2 1.0 NH1 C:ARG191 4.5 107.1 1.0 PA C:GDP401 4.5 111.6 1.0 CB C:SER53 4.6 72.9 1.0 CD C:LYS52 4.6 77.7 1.0 NH2 C:ARG191 4.7 104.2 1.0 N C:SER53 4.9 77.3 1.0 OD2 C:ASP219 4.9 72.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) From Oryza Sativa in Complex with Gdp


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 Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) From Oryza Sativa in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:85.0 occ:1.00 O2B D:GDP401 2.0 79.2 1.0 OG D:SER53 2.0 80.0 1.0 O3B D:GDP401 2.1 88.8 1.0 PB D:GDP401 2.3 87.9 1.0 O1B D:GDP401 2.9 82.3 1.0 N D:SER53 3.0 79.9 1.0 CB D:SER53 3.2 77.9 1.0 CE D:LYS52 3.5 79.2 1.0 CA D:SER53 3.6 77.6 1.0 OD2 D:ASP219 3.8 80.7 1.0 CB D:LYS52 3.8 81.5 1.0 O3A D:GDP401 3.8 86.5 1.0 C D:LYS52 3.9 81.3 1.0 OD1 D:ASP219 4.1 74.3 1.0 N D:LYS52 4.1 78.4 1.0 CA D:LYS52 4.2 80.8 1.0 CD D:LYS52 4.3 75.0 1.0 O2A D:GDP401 4.3 82.7 1.0 CG D:ASP219 4.4 76.4 1.0 CG D:LYS52 4.5 78.5 1.0 PA D:GDP401 4.6 70.8 1.0 NZ D:LYS52 4.6 77.6 1.0 O1A D:GDP401 4.9 74.7 1.0 O D:VAL220 4.9 76.5 1.0 O D:LYS52 5.0 84.6 1.0

M.D.Torres-Rodriguez, S.G.Lee, S.Roy Choudhury, R.Paul, B.Selvam, D.Shukla, J.M.Jez, S.Pandey. Structure-Function Analysis of Plant G-Protein Regulatory Mechanisms Identifies Key G Alpha-Rgs Protein Interactions. J.Biol.Chem. V. 300 07252 2024.
ISSN: ESSN 1083-351X
PubMed: 38569936
DOI: 10.1016/J.JBC.2024.107252