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

Protein crystallography data

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

Magnesium Binding Sites:

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 3q5e

Go back to Magnesium Binding Sites List in 3q5e
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 3q5e

Go back to Magnesium Binding Sites List in 3q5e
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 3q5e

Go back to Magnesium Binding Sites List in 3q5e
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 3q5e

Go back to Magnesium Binding Sites List in 3q5e
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

Reference:

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
Page generated: Thu Aug 15 09:56:04 2024

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