Sodium in PDB 8srx: Crystal Structure of Bak-Bax Heterodimer with Lysopc

Protein crystallography data

The structure of Crystal Structure of Bak-Bax Heterodimer with Lysopc, PDB code: 8srx was solved by J.M.Brouwer, P.E.Czabotar, P.M.Colman, M.S.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.71 / 2.09
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.166, 45.562, 43.714, 90, 101.76, 90
R / Rfree (%) 21.6 / 26.5

Other elements in 8srx:

The structure of Crystal Structure of Bak-Bax Heterodimer with Lysopc also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Bak-Bax Heterodimer with Lysopc (pdb code 8srx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Bak-Bax Heterodimer with Lysopc, PDB code: 8srx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8srx

Go back to Sodium Binding Sites List in 8srx
Sodium binding site 1 out of 2 in the Crystal Structure of Bak-Bax Heterodimer with Lysopc


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Bak-Bax Heterodimer with Lysopc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:68.7
occ:1.00
OE1 A:GLN98 2.3 76.9 1.0
CD A:GLN98 3.3 72.4 1.0
CG A:GLN98 3.8 66.2 1.0
NE2 A:GLN98 4.4 62.2 1.0

Sodium binding site 2 out of 2 in 8srx

Go back to Sodium Binding Sites List in 8srx
Sodium binding site 2 out of 2 in the Crystal Structure of Bak-Bax Heterodimer with Lysopc


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Bak-Bax Heterodimer with Lysopc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:47.7
occ:1.00
O B:HOH301 2.8 46.4 1.0
CD B:LYS57 3.5 40.2 1.0
NZ B:LYS57 4.0 51.4 1.0
CG B:LYS57 4.1 40.0 1.0
OG B:SER55 4.2 50.0 1.0
CE B:LYS57 4.3 39.9 1.0
CB B:LYS57 4.3 32.2 1.0
CB B:SER55 4.8 51.8 1.0

Reference:

M.S.Miller, A.D.Cowan, J.M.Brouwer, S.T.Smyth, L.Peng, A.Z.Wardak, R.T.Uren, C.Luo, M.J.Roy, S.Shah, Z.Tan, G.E.Reid, P.M.Colman, P.E.Czabotar. Sequence Differences Between Bax and Bak Core Domains Manifest As Differences in Their Interactions with Lipids. Febs J. 2023.
ISSN: ISSN 1742-464X
PubMed: 38088212
DOI: 10.1111/FEBS.17031
Page generated: Wed Oct 9 13:33:32 2024

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