Atomistry » Barium » PDB 2y5y-4e60 » 3ns4
Atomistry »
  Barium »
    PDB 2y5y-4e60 »
      3ns4 »

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: Wed Jul 10 15:15:08 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy