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Sodium in PDB 2v1q: Atomic-Resolution Structure of the Yeast SLA1 SH3 Domain 3

Protein crystallography data

The structure of Atomic-Resolution Structure of the Yeast SLA1 SH3 Domain 3, PDB code: 2v1q was solved by I.Kursula, P.Kursula, P.Zou, F.Lehmann, Y.H.Song, M.Wilmanns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 46.940, 55.250, 85.290, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 18.8

Other elements in 2v1q:

The structure of Atomic-Resolution Structure of the Yeast SLA1 SH3 Domain 3 also contains other interesting chemical elements:

Platinum (Pt) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Atomic-Resolution Structure of the Yeast SLA1 SH3 Domain 3 (pdb code 2v1q). 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 Atomic-Resolution Structure of the Yeast SLA1 SH3 Domain 3, PDB code: 2v1q:

Sodium binding site 1 out of 1 in 2v1q

Go back to Sodium Binding Sites List in 2v1q
Sodium binding site 1 out of 1 in the Atomic-Resolution Structure of the Yeast SLA1 SH3 Domain 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Atomic-Resolution Structure of the Yeast SLA1 SH3 Domain 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1061

b:39.9
occ:1.00
O A:HOH2050 1.8 19.7 1.0
O A:SER35 2.3 18.0 1.0
O A:ASP32 2.5 12.8 1.0
CA A:LYS36 2.5 17.6 1.0
C A:SER35 2.7 14.5 1.0
N A:LYS36 2.7 17.6 1.0
NE1 A:TRP39 3.1 12.7 1.0
C A:ASP32 3.4 11.4 1.0
CG A:LYS36 3.5 20.9 1.0
CB A:LYS36 3.5 19.3 1.0
C A:LYS36 3.6 18.3 1.0
CD1 A:TRP39 3.8 12.2 1.0
O A:LYS36 4.0 20.7 1.0
CA A:SER35 4.1 15.5 1.0
CA A:ASP32 4.1 11.4 1.0
CE2 A:TRP39 4.3 15.2 1.0
O A:HOH2055 4.3 21.7 1.0
N A:SER35 4.3 14.9 1.0
O A:HOH2065 4.4 14.0 1.0
CB A:ASP32 4.4 12.4 1.0
N A:LYS33 4.4 12.1 1.0
N A:ASP37 4.4 17.2 1.0
O A:HOH2060 4.6 34.1 1.0
CA A:LYS33 4.6 11.9 1.0
CZ2 A:TRP39 4.8 16.5 1.0
C A:LYS33 4.9 12.4 1.0
CD A:LYS36 4.9 24.8 1.0

Reference:

P.Kursula, I.Kursula, N.Pinotsis, F.Lehmann, P.Zou, Y.H.Song, M.Wilmanns. Structural Genomics of Yeast SH3 Domains To Be Published.
Page generated: Tue Dec 15 05:56:14 2020

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