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Barium in PDB 3nkv: Crystal Structure of RAB1B Covalently Modified with Amp at Y77

Protein crystallography data

The structure of Crystal Structure of RAB1B Covalently Modified with Amp at Y77, PDB code: 3nkv was solved by M.P.Mueller, H.Peters, W.Blankenfeldt, R.S.Goody, A.Itzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.80 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.970, 100.589, 45.071, 90.00, 102.43, 90.00
R / Rfree (%) 15 / 18.7

Other elements in 3nkv:

The structure of Crystal Structure of RAB1B Covalently Modified with Amp at Y77 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of RAB1B Covalently Modified with Amp at Y77 (pdb code 3nkv). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 2 binding sites of Barium where determined in the Crystal Structure of RAB1B Covalently Modified with Amp at Y77, PDB code: 3nkv:
Jump to Barium binding site number: 1; 2;

Barium binding site 1 out of 2 in 3nkv

Go back to Barium Binding Sites List in 3nkv
Barium binding site 1 out of 2 in the Crystal Structure of RAB1B Covalently Modified with Amp at Y77


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of RAB1B Covalently Modified with Amp at Y77 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba175

b:28.4
occ:0.30
O A:HOH261 2.6 26.6 1.0
OD1 A:ASP44 2.9 57.5 1.0
O A:VAL43 2.9 37.9 1.0
O A:ILE41 2.9 34.5 1.0
C A:VAL43 3.8 36.3 1.0
N A:VAL43 3.8 33.0 1.0
C A:ILE41 4.1 30.5 1.0
CG A:ASP44 4.2 50.4 1.0
CA A:VAL43 4.5 28.7 1.0
O A:HOH236 4.5 26.9 1.0
N A:ASP44 4.5 34.0 1.0
C A:GLY42 4.5 33.3 1.0
CA A:GLY42 4.6 32.5 1.0
CA A:ASP44 4.7 32.5 1.0
N A:GLY42 4.9 33.9 1.0
OD2 A:ASP44 4.9 55.8 1.0

Barium binding site 2 out of 2 in 3nkv

Go back to Barium Binding Sites List in 3nkv
Barium binding site 2 out of 2 in the Crystal Structure of RAB1B Covalently Modified with Amp at Y77


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of RAB1B Covalently Modified with Amp at Y77 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba175

b:18.7
occ:0.80
O B:HOH301 2.5 21.3 1.0
O B:HOH187 2.6 37.9 1.0
OG1 B:THR134 2.7 26.1 1.0
OD2 B:ASP132 2.8 33.2 1.0
O B:HOH228 2.9 28.5 1.0
OD1 B:ASP132 2.9 30.9 1.0
CG B:ASP132 3.3 30.1 1.0
CB B:THR134 3.7 29.7 1.0
OD1 B:ASN133 4.6 31.5 1.0
N B:THR134 4.6 22.6 1.0
CG2 B:THR134 4.6 29.5 1.0
CA B:THR134 4.7 24.8 1.0
CB B:ASP132 4.8 31.7 1.0

Reference:

M.P.Muller, H.Peters, J.Blumer, W.Blankenfeldt, R.S.Goody, A.Itzen. The Legionella Effector Protein Drra Ampylates the Membrane Traffic Regulator RAB1B. Science V. 329 946 2010.
ISSN: ISSN 0036-8075
PubMed: 20651120
DOI: 10.1126/SCIENCE.1192276
Page generated: Tue Oct 27 17:00:45 2020

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