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Magnesium in PDB 3hyt: Structural Basis of Gdp Release and Gating in G Protein Coupled FE2+ Transport

Protein crystallography data

The structure of Structural Basis of Gdp Release and Gating in G Protein Coupled FE2+ Transport, PDB code: 3hyt was solved by M.J.Maher, M.Jormakka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.08 / 2.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.000, 46.410, 120.070, 90.00, 94.95, 90.00
R / Rfree (%) 22.7 / 29.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Basis of Gdp Release and Gating in G Protein Coupled FE2+ Transport (pdb code 3hyt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structural Basis of Gdp Release and Gating in G Protein Coupled FE2+ Transport, PDB code: 3hyt:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3hyt

Go back to Magnesium Binding Sites List in 3hyt
Magnesium binding site 1 out of 3 in the Structural Basis of Gdp Release and Gating in G Protein Coupled FE2+ Transport


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis of Gdp Release and Gating in G Protein Coupled FE2+ Transport within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:36.7
occ:1.00
O1G A:AGO801 2.0 45.4 1.0
OG1 A:THR17 2.0 35.1 1.0
O2B A:AGO801 2.5 43.9 1.0
O A:HOH314 2.6 26.9 1.0
O A:HOH306 3.0 55.9 1.0
PG A:AGO801 3.3 45.6 1.0
CB A:THR17 3.4 35.0 1.0
PB A:AGO801 3.7 43.5 1.0
N3B A:AGO801 3.9 44.6 1.0
N A:THR17 3.9 34.4 1.0
OD2 A:ASP56 4.0 42.4 1.0
OD1 A:ASP56 4.1 42.9 1.0
O2G A:AGO801 4.1 45.7 1.0
CA A:THR17 4.1 35.0 1.0
CG2 A:THR17 4.3 34.9 1.0
NZ A:LYS16 4.3 33.1 1.0
CG A:ASP56 4.4 42.4 1.0
O1B A:AGO801 4.4 43.9 1.0
O3G A:AGO801 4.5 46.0 1.0
CB A:LYS16 4.6 33.7 1.0
O2A A:AGO801 4.7 45.0 1.0
C A:LYS16 4.9 34.1 1.0
O3A A:AGO801 4.9 44.2 1.0

Magnesium binding site 2 out of 3 in 3hyt

Go back to Magnesium Binding Sites List in 3hyt
Magnesium binding site 2 out of 3 in the Structural Basis of Gdp Release and Gating in G Protein Coupled FE2+ Transport


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis of Gdp Release and Gating in G Protein Coupled FE2+ Transport within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:38.2
occ:1.00
O1G B:AGO801 2.0 41.5 0.8
O2B B:AGO801 2.2 41.4 0.8
OG1 B:THR17 2.2 29.1 1.0
O B:HOH307 2.4 19.9 1.0
PG B:AGO801 3.1 41.4 0.8
PB B:AGO801 3.3 41.7 0.8
N3B B:AGO801 3.4 41.8 0.8
CB B:THR17 3.5 29.2 1.0
O2A B:AGO801 3.8 43.2 0.8
N B:THR17 4.1 29.4 1.0
OD2 B:ASP56 4.2 33.9 1.0
O2G B:AGO801 4.2 41.8 0.8
O3G B:AGO801 4.3 41.5 0.8
O1B B:AGO801 4.3 41.8 0.8
CA B:THR17 4.4 29.3 1.0
O3A B:AGO801 4.4 42.2 0.8
CG2 B:THR17 4.5 29.0 1.0
PA B:AGO801 4.6 43.0 0.8
OD1 B:ASP56 4.7 34.3 1.0
CB B:LYS16 4.7 29.9 1.0
CG B:ASP56 4.9 33.8 1.0
O1A B:AGO801 5.0 43.1 0.8

Magnesium binding site 3 out of 3 in 3hyt

Go back to Magnesium Binding Sites List in 3hyt
Magnesium binding site 3 out of 3 in the Structural Basis of Gdp Release and Gating in G Protein Coupled FE2+ Transport


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis of Gdp Release and Gating in G Protein Coupled FE2+ Transport within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:30.8
occ:0.50
O2B C:AGO801 1.7 29.2 0.5
O1G C:AGO801 2.1 29.8 0.5
N3B C:AGO801 2.3 29.6 0.5
OG1 C:THR17 2.3 58.2 1.0
PB C:AGO801 2.4 29.3 0.5
PG C:AGO801 2.4 29.9 0.5
O2A C:AGO801 3.1 28.9 0.5
O2G C:AGO801 3.2 30.4 0.5
O1B C:AGO801 3.4 29.2 0.5
NZ C:LYS16 3.6 58.1 1.0
CB C:THR17 3.6 58.3 1.0
O3A C:AGO801 3.6 29.1 0.5
N C:THR17 3.9 58.2 1.0
PA C:AGO801 3.9 28.9 0.5
O3G C:AGO801 3.9 29.8 0.5
CA C:THR17 4.3 58.4 1.0
CB C:LYS16 4.4 57.9 1.0
O1A C:AGO801 4.7 28.6 0.5
CG2 C:THR17 4.7 58.3 1.0
CE C:LYS16 4.8 58.0 1.0
C C:LYS16 4.8 58.0 1.0
CG C:LYS16 4.9 57.9 1.0
OD2 C:ASP56 4.9 52.4 1.0

Reference:

A.Guilfoyle, M.J.Maher, M.Rapp, R.Clarke, S.Harrop, M.Jormakka. Structural Basis of Gdp Release and Gating in G Protein Coupled Fe(2+) Transport. Embo J. 2009.
ISSN: ESSN 1460-2075
PubMed: 19629046
DOI: 10.1038/EMBOJ.2009.208
Page generated: Mon Dec 14 08:15:13 2020

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