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Sodium in PDB 2q3x: The RIM1ALPHA C2B Domain

Protein crystallography data

The structure of The RIM1ALPHA C2B Domain, PDB code: 2q3x was solved by R.Guan, H.Dai, D.R.Tomchick, M.Machius, T.C.Sudhof, J.Rizo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.40 / 1.73
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 62.037, 62.037, 145.180, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 21.5

Other elements in 2q3x:

The structure of The RIM1ALPHA C2B Domain also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The RIM1ALPHA C2B Domain (pdb code 2q3x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the The RIM1ALPHA C2B Domain, PDB code: 2q3x:

Sodium binding site 1 out of 1 in 2q3x

Go back to Sodium Binding Sites List in 2q3x
Sodium binding site 1 out of 1 in the The RIM1ALPHA C2B Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The RIM1ALPHA C2B Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:22.0
occ:1.00
OE2 B:GLU1535 3.0 30.2 1.0
O B:HOH118 3.2 45.3 1.0
N B:ASP1534 3.2 24.4 1.0
OE1 B:GLU1535 3.6 28.2 1.0
CD B:GLU1535 3.7 24.8 1.0
CB B:ALA1512 3.8 19.2 1.0
CB B:ASP1534 3.8 25.3 1.0
CA B:PHE1533 3.9 23.0 1.0
CG B:ASP1534 4.0 30.1 1.0
C B:PHE1533 4.0 24.3 1.0
CD1 B:PHE1533 4.1 23.0 1.0
CA B:ASP1534 4.1 24.9 1.0
CE B:LYS1514 4.1 38.2 1.0
OD2 B:ASP1534 4.1 31.1 1.0
CB B:PHE1533 4.3 21.5 1.0
CG B:PHE1533 4.6 21.8 1.0
OD1 B:ASP1534 4.7 28.9 1.0
O B:VAL1532 4.7 24.5 1.0
C B:ASP1534 4.9 24.6 1.0
CE1 B:PHE1533 5.0 25.3 1.0
O B:HOH143 5.0 39.0 1.0

Reference:

R.Guan, H.Dai, D.R.Tomchick, I.Dulubova, M.Machius, T.C.Sudhof, J.Rizo. Crystal Structure of the RIM1ALPHA C(2)B Domain at 1.7 A Resolution. Biochemistry V. 46 8988 2007.
ISSN: ISSN 0006-2960
PubMed: 17630786
DOI: 10.1021/BI700698A
Page generated: Tue Dec 15 05:54:21 2020

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