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Magnesium in PDB 3n1e: VPS54 C-Terminal Domain

Protein crystallography data

The structure of VPS54 C-Terminal Domain, PDB code: 3n1e was solved by F.J.Perez-Victoria, G.Abascal-Palacios, I.Tascon, A.Kajava, E.P.Pioro, J.S.Bonifacino, A.Hierro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.36 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 29.760, 77.064, 120.057, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the VPS54 C-Terminal Domain (pdb code 3n1e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the VPS54 C-Terminal Domain, PDB code: 3n1e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3n1e

Go back to Magnesium Binding Sites List in 3n1e
Magnesium binding site 1 out of 5 in the VPS54 C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of VPS54 C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg977

b:16.0
occ:1.00
O A:HOH279 3.0 47.0 1.0
O A:HOH13 3.1 12.0 1.0
N A:GLN941 3.3 11.0 1.0
CB A:GLN941 3.5 9.4 0.5
CB A:GLN941 3.6 9.6 0.5
CD A:PRO940 3.6 13.6 1.0
CG A:GLN941 3.7 10.8 0.5
N A:PRO940 3.7 11.5 1.0
CA A:GLN941 4.0 10.3 0.5
CA A:GLN941 4.0 10.3 0.5
O A:HOH102 4.0 20.8 1.0
C A:GLY939 4.1 10.3 1.0
CG A:PRO940 4.1 18.9 1.0
C A:PRO940 4.2 10.7 1.0
CA A:GLY939 4.3 11.4 1.0
CB A:PRO940 4.3 17.9 1.0
CA A:PRO940 4.3 10.5 1.0
O A:HOH20 4.5 16.8 1.0
OE1 A:GLN941 4.7 12.0 0.5
CG A:GLN941 4.7 12.8 0.5
O A:GLY939 4.8 10.6 1.0
N A:ASN942 4.9 9.9 1.0
CD A:GLN941 4.9 18.0 0.5

Magnesium binding site 2 out of 5 in 3n1e

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Magnesium binding site 2 out of 5 in the VPS54 C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of VPS54 C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:42.6
occ:1.00
O B:HOH245 2.7 42.2 1.0
OG1 B:THR946 3.0 13.1 1.0
O B:HOH270 3.2 36.5 1.0
NE1 B:TRP973 3.3 17.7 1.0
O B:HOH239 3.6 27.1 1.0
CA B:THR946 3.6 11.3 1.0
CB B:THR946 3.8 14.6 1.0
CZ2 B:TRP973 4.0 19.2 1.0
CE2 B:TRP973 4.0 16.9 1.0
CG2 B:THR946 4.1 13.5 1.0
O B:HOH3 4.3 12.4 1.0
N B:THR946 4.3 9.3 1.0
CD1 B:ILE972 4.4 9.8 1.0
CD1 B:TRP973 4.4 19.6 1.0
CB B:VAL949 4.7 7.6 1.0
OD1 B:ASN942 4.8 17.3 1.0
O B:HOH265 4.8 35.6 1.0
C B:THR946 4.8 8.9 1.0
CG1 B:VAL949 4.8 10.8 1.0
O B:HOH271 4.8 46.5 1.0
C B:VAL945 4.8 8.6 1.0
CG2 B:VAL949 4.9 10.5 1.0
O B:THR946 4.9 9.0 1.0
O B:VAL945 4.9 8.6 1.0
CG1 B:VAL945 5.0 10.3 1.0

Magnesium binding site 3 out of 5 in 3n1e

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Magnesium binding site 3 out of 5 in the VPS54 C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of VPS54 C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg975

b:30.8
occ:1.00
O B:HOH292 3.1 40.9 1.0
O B:HOH30 4.2 18.8 1.0

Magnesium binding site 4 out of 5 in 3n1e

Go back to Magnesium Binding Sites List in 3n1e
Magnesium binding site 4 out of 5 in the VPS54 C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of VPS54 C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg976

b:40.8
occ:1.00
N B:GLN836 3.2 25.6 1.0
O B:HOH235 3.4 19.7 1.0
CB B:ASP835 3.5 28.2 1.0
CB B:GLN836 3.7 24.2 1.0
CG B:GLN836 3.7 30.1 1.0
CA B:GLN836 4.0 29.1 1.0
CA B:ASP835 4.1 24.1 1.0
C B:ASP835 4.2 23.5 1.0
CD B:GLN836 4.4 39.7 1.0
CG B:ASP835 4.4 33.5 1.0
NE2 B:GLN836 4.4 30.1 1.0
O B:HOH88 4.7 30.1 1.0
OD2 B:ASP835 4.8 28.9 1.0
N B:TRP837 5.0 25.1 1.0

Magnesium binding site 5 out of 5 in 3n1e

Go back to Magnesium Binding Sites List in 3n1e
Magnesium binding site 5 out of 5 in the VPS54 C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of VPS54 C-Terminal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg977

b:21.5
occ:1.00
O B:HOH31 2.9 18.1 1.0
N B:GLN941 3.3 11.7 1.0
CD B:PRO940 3.5 14.3 1.0
CG B:GLN941 3.6 19.4 1.0
N B:PRO940 3.6 14.1 1.0
CB B:GLN941 3.6 13.8 1.0
CG B:PRO940 3.6 16.9 1.0
O B:HOH148 3.9 39.2 1.0
C B:GLY939 4.0 18.5 1.0
CA B:GLN941 4.0 11.6 1.0
CA B:GLY939 4.1 15.1 1.0
O B:HOH67 4.1 25.7 1.0
C B:PRO940 4.2 13.5 1.0
CA B:PRO940 4.3 13.7 1.0
OE1 B:GLN941 4.3 34.6 1.0
CD B:GLN941 4.3 30.2 1.0
CB B:PRO940 4.5 17.2 1.0
O B:GLY939 4.7 14.4 1.0
OD1 B:ASP937 4.8 22.3 1.0
N B:ASN942 4.8 12.7 1.0

Reference:

F.J.Perez-Victoria, G.Abascal-Palacios, I.Tascon, A.Kajava, J.G.Magadan, E.P.Pioro, J.S.Bonifacino, A.Hierro. Structural Basis For the Wobbler Mouse Neurodegenerative Disorder Caused By Mutation in the VPS54 Subunit of the Garp Complex. Proc.Natl.Acad.Sci.Usa V. 107 12860 2010.
ISSN: ISSN 0027-8424
PubMed: 20615984
DOI: 10.1073/PNAS.1004756107
Page generated: Mon Dec 14 08:27:25 2020

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