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Calcium in PDB 4by6: Yeast NOT1-NOT2-NOT5 Complex

Protein crystallography data

The structure of Yeast NOT1-NOT2-NOT5 Complex, PDB code: 4by6 was solved by V.Bhaskar, J.Basquin, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.904 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 110.452, 109.174, 133.622, 90.00, 94.70, 90.00
R / Rfree (%) 18.12 / 22.58

Calcium Binding Sites:

The binding sites of Calcium atom in the Yeast NOT1-NOT2-NOT5 Complex (pdb code 4by6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Yeast NOT1-NOT2-NOT5 Complex, PDB code: 4by6:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4by6

Go back to Calcium Binding Sites List in 4by6
Calcium binding site 1 out of 2 in the Yeast NOT1-NOT2-NOT5 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Yeast NOT1-NOT2-NOT5 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3080

b:61.0
occ:1.00
O A:ASP1915 2.5 56.3 1.0
OD1 A:ASP1918 2.5 88.3 1.0
OD2 A:ASP1918 2.5 69.6 1.0
OD2 A:ASP1931 2.6 63.9 1.0
CG A:ASP1918 2.9 74.6 1.0
CG A:ASP1931 3.7 55.3 1.0
C A:ASP1915 3.7 50.9 1.0
CB A:ASP1931 4.1 42.5 1.0
CA A:ASP1915 4.4 49.9 1.0
CB A:ASP1918 4.4 63.5 1.0
CB A:ASP1915 4.7 52.0 1.0
N A:THR1916 4.8 37.5 1.0
OD1 A:ASP1931 4.8 57.9 1.0
CA A:THR1916 4.9 41.6 1.0

Calcium binding site 2 out of 2 in 4by6

Go back to Calcium Binding Sites List in 4by6
Calcium binding site 2 out of 2 in the Yeast NOT1-NOT2-NOT5 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Yeast NOT1-NOT2-NOT5 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca3079

b:61.4
occ:1.00
OD2 D:ASP1918 2.5 73.3 1.0
OD2 D:ASP1931 2.5 60.1 1.0
O D:ASP1915 2.6 63.1 1.0
OD1 D:ASP1918 2.6 81.7 1.0
CG D:ASP1918 2.9 71.4 1.0
CG D:ASP1931 3.7 59.5 1.0
C D:ASP1915 3.8 59.5 1.0
CB D:ASP1931 4.1 52.4 1.0
CB D:ASP1918 4.4 68.1 1.0
CA D:ASP1915 4.5 58.5 1.0
OD1 D:ASP1931 4.7 67.5 1.0
N D:THR1916 4.8 50.3 1.0
CB D:ASP1915 4.9 59.5 1.0
CA D:THR1916 5.0 50.1 1.0
CD2 D:LEU1934 5.0 52.1 1.0

Reference:

V.Bhaskar, V.Roudko, J.Basquin, K.Sharma, H.Urlaub, B.Seraphin, E.Conti. Structure and Rna-Binding Properties of the NOT1-NOT2-NOT5 Module of the Yeast CCR4-Not Complex Nat.Struct.Mol.Biol. V. 20 1281 2013.
ISSN: ISSN 1545-9993
PubMed: 24121231
DOI: 10.1038/NSMB.2686
Page generated: Sat Dec 12 04:41:45 2020

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