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Barium in PDB 3ns4: Structure of A C-Terminal Fragment of Its VPS53 Subunit Suggests Similarity of Garp to A Family of Tethering Complexes

Protein crystallography data

The structure of Structure of A C-Terminal Fragment of Its VPS53 Subunit Suggests Similarity of Garp to A Family of Tethering Complexes, PDB code: 3ns4 was solved by N.Vasan, K.M.Reinisch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.40 / 2.90
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 127.236, 127.236, 81.658, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 22.1

Barium Binding Sites:

The binding sites of Barium atom in the Structure of A C-Terminal Fragment of Its VPS53 Subunit Suggests Similarity of Garp to A Family of Tethering Complexes (pdb code 3ns4). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 3 binding sites of Barium where determined in the Structure of A C-Terminal Fragment of Its VPS53 Subunit Suggests Similarity of Garp to A Family of Tethering Complexes, PDB code: 3ns4:
Jump to Barium binding site number: 1; 2; 3;

Barium binding site 1 out of 3 in 3ns4

Go back to Barium Binding Sites List in 3ns4
Barium binding site 1 out of 3 in the Structure of A C-Terminal Fragment of Its VPS53 Subunit Suggests Similarity of Garp to A Family of Tethering Complexes


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Structure of A C-Terminal Fragment of Its VPS53 Subunit Suggests Similarity of Garp to A Family of Tethering Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1

b:0.3
occ:1.00
OD1 A:ASN620 3.1 64.6 1.0
CG A:ASN620 3.7 58.5 1.0
O A:HOH17 4.0 2.0 1.0
ND2 A:ASN620 4.2 72.3 1.0
OE2 A:GLU623 4.6 74.3 1.0
CB A:ASN620 4.7 47.9 1.0
CA A:ASN620 4.9 43.8 1.0

Barium binding site 2 out of 3 in 3ns4

Go back to Barium Binding Sites List in 3ns4
Barium binding site 2 out of 3 in the Structure of A C-Terminal Fragment of Its VPS53 Subunit Suggests Similarity of Garp to A Family of Tethering Complexes


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Structure of A C-Terminal Fragment of Its VPS53 Subunit Suggests Similarity of Garp to A Family of Tethering Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba2

b:0.7
occ:1.00
O A:SER644 2.7 0.2 1.0
O A:GLU641 2.9 59.0 1.0
C A:SER644 3.9 0.8 1.0
C A:GLU641 4.0 50.5 1.0
N A:SER644 4.6 77.4 1.0
CA A:GLU641 4.7 53.9 1.0
CA A:SER644 4.7 84.9 1.0
CB A:GLU641 4.8 56.1 1.0
N A:ASN645 4.8 0.4 1.0
CA A:ASN645 5.0 0.2 1.0

Barium binding site 3 out of 3 in 3ns4

Go back to Barium Binding Sites List in 3ns4
Barium binding site 3 out of 3 in the Structure of A C-Terminal Fragment of Its VPS53 Subunit Suggests Similarity of Garp to A Family of Tethering Complexes


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Structure of A C-Terminal Fragment of Its VPS53 Subunit Suggests Similarity of Garp to A Family of Tethering Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3

b:74.8
occ:1.00
O A:ASN727 2.9 56.8 1.0
OD1 A:ASN727 2.9 67.8 1.0
O A:THR730 3.0 55.9 1.0
CG A:ASN727 3.5 57.1 1.0
C A:ASN727 3.7 52.2 1.0
C A:THR730 3.7 54.6 1.0
ND2 A:ASN727 3.9 70.5 1.0
CA A:ASN727 4.3 50.9 1.0
N A:LEU728 4.5 53.6 1.0
CB A:ASN727 4.6 52.7 1.0
N A:THR730 4.6 53.8 1.0
CA A:LEU728 4.7 54.3 1.0
CA A:THR730 4.7 54.9 1.0
C A:LEU728 4.8 56.0 1.0
O A:LEU728 4.9 57.9 1.0

Reference:

N.Vasan, A.Hutagalung, P.Novick, K.M.Reinisch. Structure of A C-Terminal Fragment of Its VPS53 Subunit Suggests Similarity of Golgi-Associated Retrograde Protein (Garp) Complex to A Family of Tethering Complexes. Proc.Natl.Acad.Sci.Usa V. 107 14176 2010.
ISSN: ISSN 0027-8424
PubMed: 20660722
DOI: 10.1073/PNAS.1009419107
Page generated: Sat Dec 12 01:55:50 2020

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