Sodium in PDB 7y95: Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2

The structure of Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2, PDB code: 7y95 was solved by Q.Chen, Y.Yu, J.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.55 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.177, 39.096, 60.873, 90, 108.97, 90
R / Rfree (%)	15.1 / 19.1

The binding sites of Sodium atom in the Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2 (pdb code 7y95). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2, PDB code: 7y95:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2


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 Sdscam IG1 Domain, Isoform BETA6V2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:48.2 occ:1.00 HB3 A:ALA71 2.4 27.8 1.0 O A:TRP68 2.7 22.6 1.0 HB2 A:TRP68 2.8 32.5 1.0 HE3 A:TRP68 3.1 39.3 1.0 CB A:ALA71 3.2 23.2 1.0 O A:HOH256 3.3 29.4 1.0 HB2 A:ALA71 3.3 27.8 1.0 O A:HOH272 3.3 40.2 1.0 HA A:TRP68 3.4 29.0 1.0 C A:TRP68 3.5 20.2 1.0 HB1 A:ALA71 3.5 27.8 1.0 CB A:TRP68 3.6 27.1 1.0 CA A:TRP68 3.7 24.2 1.0 O A:HOH292 3.8 29.6 1.0 CE3 A:TRP68 4.0 32.8 1.0 H A:ALA71 4.1 23.9 1.0 HB3 A:TRP68 4.3 32.5 1.0 CA A:ALA71 4.4 21.2 1.0 CG A:TRP68 4.5 32.9 1.0 CD2 A:TRP68 4.6 34.8 1.0 HB A:VAL93 4.6 30.0 1.0 N A:ALA71 4.6 19.9 1.0 N A:GLU69 4.7 21.7 1.0 HA A:GLU69 4.8 28.2 1.0 O A:ALA71 4.9 22.8 1.0 H A:VAL93 4.9 26.3 1.0 C A:ALA71 4.9 19.1 1.0

Sodium binding site 2 out of 8 in the Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2


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 Sdscam IG1 Domain, Isoform BETA6V2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:51.8 occ:1.00 O A:HOH261 2.6 23.3 1.0 O B:HOH228 2.7 34.4 1.0 O A:HOH210 2.7 41.3 1.0 O B:HOH224 2.9 29.9 1.0 HA A:VAL22 3.0 20.0 1.0 HG13 B:ILE23 3.1 30.2 1.0 HD11 B:ILE23 3.2 35.2 1.0 O A:LYS21 3.2 17.8 1.0 O B:HOH289 3.3 21.4 1.0 HE22 B:GLN6 3.3 25.9 1.0 HE21 B:GLN6 3.3 25.9 1.0 HG12 B:ILE23 3.5 30.2 1.0 NE2 B:GLN6 3.5 21.5 1.0 CG1 B:ILE23 3.6 25.1 1.0 HG12 A:VAL22 3.7 26.3 1.0 CD1 B:ILE23 3.8 29.4 1.0 CA A:VAL22 4.0 16.7 1.0 H A:ILE23 4.0 18.8 1.0 O B:HOH280 4.0 30.0 1.0 C A:LYS21 4.2 15.8 1.0 O A:HOH215 4.2 43.3 1.0 O A:HOH273 4.2 35.9 1.0 HD12 B:ILE23 4.3 35.2 1.0 H B:ILE23 4.5 18.8 1.0 CG1 A:VAL22 4.5 21.9 1.0 O A:HOH286 4.5 44.6 1.0 O B:ILE23 4.5 16.7 1.0 N A:VAL22 4.5 14.7 1.0 OD1 B:ASN25 4.6 20.7 1.0 CD B:GLN6 4.6 16.1 1.0 HD13 B:ILE23 4.6 35.2 1.0 N A:ILE23 4.6 15.6 1.0 HG13 A:VAL22 4.7 26.3 1.0 HB3 B:PHE8 4.7 21.8 1.0 CB A:VAL22 4.7 17.1 1.0 C A:VAL22 4.7 15.1 1.0 HB A:VAL22 4.8 20.5 1.0 HB A:ILE23 4.9 24.9 1.0 HG12 A:ILE23 4.9 26.5 1.0 HG2 B:GLN6 4.9 20.4 1.0 HB2 A:LYS21 5.0 23.7 1.0

Sodium binding site 3 out of 8 in the Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:62.2 occ:1.00 HD22 A:ASN79 2.0 41.8 1.0 ND2 A:ASN79 2.7 34.9 1.0 O A:HOH222 2.7 22.9 1.0 HG11 A:VAL77 2.8 25.5 1.0 OD1 A:ASN79 2.9 31.4 1.0 HG12 A:VAL77 3.1 25.5 1.0 CG A:ASN79 3.1 29.0 1.0 CG1 A:VAL77 3.3 21.2 1.0 HB2 A:SER84 3.3 27.6 1.0 HD21 A:ASN79 3.4 41.8 1.0 HB3 A:SER84 3.5 27.6 1.0 HG13 A:VAL77 3.5 25.5 1.0 HG A:SER84 3.6 28.2 1.0 CB A:SER84 3.8 23.0 1.0 OG A:SER84 4.2 23.5 1.0 CB A:ASN79 4.6 23.7 1.0 O A:HOH249 4.7 25.6 1.0 CB A:VAL77 4.7 20.6 1.0 HB3 A:ASN79 4.8 28.4 1.0 HB A:VAL77 4.8 24.8 1.0

Sodium binding site 4 out of 8 in the Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:50.7 occ:1.00 HG A:LEU60 2.7 34.9 1.0 O B:HOH336 2.7 54.5 1.0 HB2 A:ASN62 2.8 21.4 1.0 HB3 A:ASN62 3.0 21.4 1.0 O A:LEU60 3.1 18.5 1.0 O A:ALA51 3.1 19.4 1.0 HB3 A:ALA51 3.2 29.4 1.0 HD23 A:LEU60 3.2 37.2 1.0 H A:ASN62 3.2 18.8 1.0 CB A:ASN62 3.3 17.8 1.0 H A:LYS53 3.3 22.9 1.0 HB3 A:LYS53 3.4 30.4 1.0 CG A:LEU60 3.5 29.1 1.0 N A:ASN62 3.5 15.7 1.0 C A:ALA51 3.5 18.4 1.0 HA A:VAL52 3.5 22.2 1.0 CD2 A:LEU60 3.6 31.0 1.0 HB1 A:ALA51 3.6 29.4 1.0 HD21 A:LEU60 3.7 37.2 1.0 N A:LYS53 3.7 19.1 1.0 HB3 A:LEU60 3.7 24.1 1.0 HB2 A:LYS53 3.7 30.4 1.0 C A:LEU60 3.7 17.0 1.0 CB A:ALA51 3.8 24.5 1.0 HA A:LEU61 3.9 17.2 1.0 CB A:LYS53 4.0 25.4 1.0 N A:VAL52 4.0 20.0 1.0 CA A:ASN62 4.0 15.9 1.0 C A:LEU61 4.1 15.0 1.0 CB A:LEU60 4.1 20.1 1.0 CA A:VAL52 4.1 18.5 1.0 C A:VAL52 4.1 19.3 1.0 CA A:LEU61 4.3 14.3 1.0 CA A:ALA51 4.3 22.2 1.0 N A:LEU61 4.3 16.0 1.0 CA A:LYS53 4.5 20.0 1.0 HE3 A:LYS21 4.5 33.0 1.0 CA A:LEU60 4.5 15.0 1.0 HD22 A:LEU60 4.6 37.2 1.0 CG A:ASN62 4.6 21.4 1.0 HA A:ASN62 4.6 19.1 1.0 H A:VAL52 4.6 24.1 1.0 HB2 A:ALA51 4.7 29.4 1.0 CD1 A:LEU60 4.7 31.3 1.0 HD11 A:LEU60 4.7 37.6 1.0 H A:ALA51 4.7 24.8 1.0 O B:HOH331 4.7 51.1 1.0 O A:LEU61 4.9 16.6 1.0 HD22 A:ASN62 4.9 30.9 1.0 HB2 A:LEU60 4.9 24.1 1.0 HD12 A:LEU60 5.0 37.6 1.0 H A:LEU61 5.0 19.2 1.0

Sodium binding site 5 out of 8 in the Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:59.1 occ:1.00 HD22 A:ASN73 3.1 41.3 1.0 HG21 A:THR88 3.1 24.6 1.0 HB3 A:ASN73 3.2 25.2 1.0 HB2 A:ASN73 3.3 25.2 1.0 O A:HOH206 3.6 29.3 1.0 CB A:ASN73 3.7 21.0 1.0 ND2 A:ASN73 3.7 34.5 1.0 CG2 A:THR88 4.0 20.5 1.0 HG23 A:THR88 4.1 24.6 1.0 CG A:ASN73 4.1 26.9 1.0 O A:HOH216 4.2 43.5 1.0 HD21 A:ASN73 4.3 41.3 1.0 HG A:SER75 4.5 25.6 1.0 HG22 A:THR88 4.5 24.6 1.0 OG A:SER75 4.6 21.4 1.0 OG1 A:THR88 4.6 19.9 1.0 HA A:ASP40 4.8 35.8 1.0 CB A:THR88 4.9 17.8 1.0

Sodium binding site 6 out of 8 in the Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:67.4 occ:1.00 O A:HOH270 2.3 36.7 1.0 O A:HOH215 2.5 43.3 1.0 O B:HOH216 2.5 34.3 1.0 HA A:PRO11 3.2 27.7 1.0 O A:PHE9 3.3 19.2 1.0 O A:PHE10 3.5 19.6 1.0 C A:PHE10 3.6 18.4 1.0 HB2 A:PHE9 3.6 16.5 1.0 HD2 B:PHE9 3.6 31.0 1.0 N A:PRO11 3.8 19.9 1.0 C A:PHE9 3.8 16.3 1.0 CA A:PRO11 3.9 23.1 1.0 HE2 B:PHE9 3.9 34.5 1.0 O A:HOH210 4.1 41.3 1.0 O B:PRO7 4.2 21.8 1.0 O B:HOH224 4.2 29.9 1.0 HD3 A:PRO11 4.3 23.3 1.0 HB3 A:PRO11 4.3 31.0 1.0 HA A:PHE10 4.3 18.6 1.0 N A:PHE10 4.3 14.7 1.0 CA A:PHE10 4.3 15.5 1.0 CB A:PHE9 4.4 13.8 1.0 CD2 B:PHE9 4.4 25.8 1.0 O A:HOH283 4.4 41.2 1.0 O B:HOH310 4.5 46.2 1.0 HB3 A:PHE9 4.5 16.5 1.0 CE2 B:PHE9 4.5 28.7 1.0 CD A:PRO11 4.6 19.4 1.0 CB A:PRO11 4.7 25.8 1.0 CA A:PHE9 4.7 14.6 1.0 H A:PHE9 4.7 20.3 1.0 O A:HOH273 4.7 35.9 1.0 HE21 B:GLN6 4.8 25.9 1.0 HZ3 A:LYS12 4.8 46.1 1.0 HE2 A:LYS12 4.8 47.2 1.0 HA B:PHE8 4.9 21.3 1.0 O B:HOH280 4.9 30.0 1.0 H A:PHE10 5.0 17.6 1.0 HB2 B:PRO7 5.0 24.9 1.0

Sodium binding site 7 out of 8 in the Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:53.8 occ:1.00 HD23 B:LEU60 3.2 31.9 1.0 O A:HOH207 3.3 28.6 1.0 HG2 B:LYS53 3.4 47.9 1.0 HE1 A:TYR58 3.6 21.7 1.0 HB2 B:LYS53 3.6 34.6 1.0 HD21 B:LEU60 3.8 31.9 1.0 CD2 B:LEU60 3.9 26.6 1.0 HB3 B:LYS53 3.9 34.6 1.0 CB B:LYS53 4.1 28.9 1.0 CG B:LYS53 4.1 40.0 1.0 HD22 B:LEU60 4.1 31.9 1.0 CE1 A:TYR58 4.4 18.1 1.0 O B:HOH309 4.5 44.7 1.0 HD3 B:LYS53 4.6 53.0 1.0 HG3 B:LYS53 4.8 47.9 1.0 HE3 B:LYS21 4.9 26.9 1.0 CD B:LYS53 5.0 44.1 1.0

Sodium binding site 8 out of 8 in the Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Sdscam IG1 Domain, Isoform BETA6V2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na104 b:67.2 occ:1.00 HG1 B:THR42 2.1 33.2 1.0 O B:HOH240 2.1 44.5 1.0 OG1 B:THR42 2.7 27.7 1.0 O B:ASP40 2.7 22.8 1.0 HA3 B:GLY41 3.3 25.9 1.0 C B:GLY41 3.5 21.2 1.0 N B:THR42 3.6 21.1 1.0 C B:ASP40 3.7 21.6 1.0 CA B:GLY41 3.8 21.6 1.0 CB B:THR42 3.8 22.6 1.0 H B:THR42 3.8 25.4 1.0 O B:GLY41 3.8 23.2 1.0 HB B:THR42 4.0 27.1 1.0 O B:HOH246 4.0 25.2 1.0 CA B:THR42 4.2 21.5 1.0 N B:GLY41 4.2 21.4 1.0 O B:HOH271 4.2 48.7 1.0 HA B:THR42 4.3 25.8 1.0 HA2 B:GLY41 4.7 25.9 1.0 O B:HOH304 4.7 45.9 1.0 HB3 B:ASP40 4.7 27.0 1.0 HB2 B:ASP40 4.8 27.0 1.0 O B:LYS39 4.8 18.0 1.0

J.Cheng, Y.Yu, X.Wang, X.Zheng, T.Liu, D.Hu, Y.Jin, Y.Lai, T.M.Fu, Q.Chen. Structural Basis For the Self-Recognition of Sdscam in Chelicerata. Nat Commun V. 14 2522 2023.
ISSN: ESSN 2041-1723
PubMed: 37130844
DOI: 10.1038/S41467-023-38205-1