Sodium in PDB 6xd4: Cdc-Like Protein

The structure of Cdc-Like Protein, PDB code: 6xd4 was solved by C.J.Morton, M.W.Parker, S.L.Lawrence, B.A.Johnstone, R.K.Tweten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.04 / 2.10
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	121.74, 121.74, 88.91, 90, 90, 90
R / Rfree (%)	20.2 / 24.7

The binding sites of Sodium atom in the Cdc-Like Protein (pdb code 6xd4). 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 Cdc-Like Protein, PDB code: 6xd4:

Sodium binding site 1 out of 1 in the Cdc-Like Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cdc-Like Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:41.0 occ:1.00 O A:VAL90 2.1 34.6 1.0 OD1 A:ASN92 2.2 38.5 1.0 O A:PRO344 2.3 39.5 1.0 OD1 A:ASN95 2.4 38.6 1.0 HA A:ASN92 2.7 60.8 1.0 HG12 A:VAL90 3.0 44.0 1.0 HG11 A:VAL310 3.1 43.6 1.0 HG13 A:VAL310 3.1 43.6 1.0 C A:VAL90 3.1 36.5 1.0 HB A:VAL90 3.1 48.4 1.0 CG A:ASN92 3.3 46.7 1.0 HD22 A:ASN95 3.4 56.3 1.0 CG A:ASN95 3.4 46.3 1.0 CA A:ASN92 3.4 50.6 1.0 HG22 A:VAL343 3.5 46.7 1.0 CG1 A:VAL310 3.5 36.3 1.0 C A:LEU91 3.5 43.2 1.0 N A:ASN92 3.5 38.5 1.0 C A:PRO344 3.6 40.1 1.0 O A:LEU91 3.6 45.1 1.0 HA A:ILE345 3.7 43.1 1.0 HG12 A:VAL310 3.7 43.6 1.0 CG1 A:VAL90 3.7 36.6 1.0 CB A:VAL90 3.7 40.2 1.0 ND2 A:ASN95 3.8 46.8 1.0 HB2 A:PRO344 3.8 40.5 1.0 H A:ASN92 3.9 46.3 1.0 CB A:ASN92 4.0 41.1 1.0 CA A:VAL90 4.0 35.1 1.0 HG11 A:VAL90 4.0 44.0 1.0 N A:LEU91 4.0 44.2 1.0 HA A:LEU91 4.1 50.9 1.0 CA A:LEU91 4.1 42.4 1.0 HD2 A:PRO344 4.3 45.8 1.0 ND2 A:ASN92 4.3 47.8 1.0 HD22 A:ASN92 4.4 57.5 1.0 CG2 A:VAL343 4.4 38.8 1.0 N A:ILE345 4.4 36.0 1.0 H A:VAL90 4.5 41.5 1.0 CA A:ILE345 4.5 35.9 1.0 HG13 A:VAL90 4.5 44.0 1.0 CA A:PRO344 4.5 35.7 1.0 HB3 A:ASN92 4.6 49.4 1.0 CB A:PRO344 4.6 33.6 1.0 HB2 A:ASN92 4.6 49.4 1.0 HD21 A:ASN95 4.6 56.3 1.0 N A:PRO344 4.7 39.1 1.0 HG22 A:ILE345 4.7 44.2 1.0 HB A:VAL343 4.7 53.5 1.0 HA A:ASN95 4.7 50.3 1.0 HG21 A:VAL343 4.7 46.7 1.0 C A:ASN92 4.7 46.5 1.0 N A:VAL90 4.7 34.5 1.0 HA A:VAL90 4.8 42.2 1.0 CB A:ASN95 4.8 37.9 1.0 H A:LEU91 4.9 53.2 1.0 CB A:VAL310 4.9 38.5 1.0 CD A:PRO344 4.9 38.1 1.0 HG23 A:VAL343 5.0 46.7 1.0 HG21 A:VAL310 5.0 47.6 1.0 HG23 A:ILE345 5.0 44.2 1.0

J.C.Evans, B.A.Johnstone, S.L.Lawrence, C.J.Morton, M.P.Christie, M.W.Parker, R.K.Tweten. A Key Motif in the Cholesterol-Dependent Cytolysins Reveals A Large Family of Related Proteins. Mbio V. 11 2020.
ISSN: ESSN 2150-7511
PubMed: 32994330
DOI: 10.1128/MBIO.02351-20