Sodium in PDB 6ef9: Gspb Siglec Domain

The structure of Gspb Siglec Domain, PDB code: 6ef9 was solved by T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.22 / 1.30
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	92.083, 92.083, 143.928, 90.00, 90.00, 120.00
R / Rfree (%)	13.1 / 14.4

The binding sites of Sodium atom in the Gspb Siglec Domain (pdb code 6ef9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Gspb Siglec Domain, PDB code: 6ef9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Gspb Siglec Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Gspb Siglec Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:17.5 occ:1.00 O A:GLU401 2.3 21.3 1.0 OD2 A:ASP490 2.3 20.6 1.0 OD1 A:ASP427 2.4 16.9 1.0 O2 A:FMT610 2.4 51.9 1.0 OD2 A:ASP427 2.5 15.1 1.0 C A:FMT610 2.6 52.0 1.0 CG A:ASP427 2.8 15.0 1.0 O1 A:FMT610 2.8 51.2 1.0 O1 A:FMT611 3.0 45.8 1.0 H A:FMT610 3.1 62.3 1.0 C A:GLU401 3.2 21.6 1.0 HD22 A:ASN494 3.3 22.3 1.0 CG A:ASP490 3.4 16.9 1.0 HA A:GLU401 3.5 32.7 1.0 H A:SER429 3.6 17.9 1.0 HB3 A:ASP490 3.7 18.2 1.0 HB3 A:SER429 3.8 17.2 1.0 HB2 A:ASP490 3.8 18.2 1.0 H A:ASN428 3.8 18.3 1.0 CB A:ASP490 3.9 15.1 1.0 CA A:GLU401 3.9 27.3 1.0 HD3 A:PRO403 3.9 16.7 1.0 HB2 A:ASN494 4.1 20.7 1.0 ND2 A:ASN494 4.1 18.6 1.0 HG A:SER429 4.1 17.1 1.0 C A:FMT611 4.2 46.1 1.0 HA A:ARG402 4.2 20.7 1.0 N A:ARG402 4.2 18.8 1.0 CB A:ASP427 4.3 14.8 1.0 OG A:SER429 4.3 14.3 1.0 C A:ARG402 4.3 15.7 1.0 O A:HOH776 4.4 22.6 1.0 N A:SER429 4.4 14.9 1.0 HD21 A:ASN494 4.4 22.3 1.0 CB A:SER429 4.5 14.4 1.0 N A:ASN428 4.5 15.2 1.0 CA A:ARG402 4.5 17.3 1.0 CB A:GLU401 4.5 27.3 1.0 N A:PRO403 4.5 14.1 1.0 OD1 A:ASP490 4.5 16.2 1.0 CD A:PRO403 4.6 13.9 1.0 HB3 A:ASP427 4.7 17.8 1.0 HA A:ASP427 4.7 16.5 1.0 HB2 A:ASP427 4.7 17.8 1.0 O A:ARG402 4.7 16.9 1.0 HA A:PRO403 4.8 16.2 1.0 H A:FMT611 4.9 55.4 1.0 CB A:ASN494 4.9 17.3 1.0 O2 A:FMT611 4.9 45.5 1.0 O A:THR400 4.9 40.9 1.0 CG A:ASN494 4.9 19.1 1.0 CA A:ASP427 5.0 13.8 1.0 HB3 A:PRO403 5.0 16.1 1.0 H A:ARG402 5.0 22.5 1.0

Sodium binding site 2 out of 6 in the Gspb Siglec Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Gspb Siglec Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:21.2 occ:1.00 O A:HOH854 2.4 27.6 1.0 O A:HOH853 2.4 20.2 1.0 OD1 A:ASN406 2.5 16.3 1.0 O A:HOH758 2.5 17.9 1.0 O A:HOH911 2.5 33.9 1.0 O A:HOH834 2.6 14.3 1.0 HA A:ASN406 3.2 14.3 1.0 CG A:ASN406 3.5 15.0 1.0 NA A:NA606 3.6 49.1 1.0 HB2 A:ASN406 3.9 16.0 1.0 CA A:ASN406 4.0 11.9 1.0 H A:VAL407 4.1 14.0 1.0 CB A:ASN406 4.1 13.3 1.0 O A:HOH782 4.2 16.1 1.0 O A:VAL405 4.3 13.1 1.0 O A:HOH724 4.5 16.3 1.0 O A:HOH868 4.5 37.3 1.0 O A:HOH808 4.5 15.8 1.0 O A:HOH890 4.6 30.4 1.0 O A:HOH900 4.6 32.4 1.0 ND2 A:ASN406 4.6 16.5 1.0 N A:VAL407 4.7 11.6 1.0 HD21 A:ASN406 4.8 19.8 1.0 O A:HOH828 4.8 30.9 1.0 C A:ASN406 4.9 11.5 1.0

Sodium binding site 3 out of 6 in the Gspb Siglec Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Gspb Siglec Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:15.8 occ:1.00 O A:HOH914 2.4 23.1 1.0 O A:HOH887 2.4 13.6 1.0 O A:HOH903 2.4 17.6 1.0 O A:HOH883 2.4 14.4 1.0 O A:HOH912 2.4 17.5 1.0 O A:HOH886 2.6 12.8 1.0 O A:HOH750 3.9 12.9 1.0 O A:HOH915 4.0 25.7 1.0 O A:HOH727 4.1 12.1 1.0 O A:HOH874 4.1 20.2 1.0 O A:HOH794 4.1 12.7 1.0 O A:HOH711 4.3 15.7 1.0 O A:HOH774 4.3 14.1 1.0 O A:HOH837 4.4 38.1 1.0 O A:HOH894 4.5 16.0 1.0 O A:HOH895 4.5 26.8 0.5 O A:HOH869 4.6 25.4 1.0 O A:HOH775 4.6 12.8 1.0 O A:HOH907 4.7 29.6 1.0

Sodium binding site 4 out of 6 in the Gspb Siglec Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Gspb Siglec Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:24.9 occ:1.00 OD1 A:ASN430 2.4 17.2 1.0 O A:ASP427 2.4 14.8 1.0 O A:HOH744 2.5 15.0 1.0 O A:HOH850 2.6 27.4 1.0 HA A:ASN428 3.3 20.4 1.0 C A:ASP427 3.3 14.9 1.0 H A:ASP427 3.4 16.5 1.0 CG A:ASN430 3.6 16.3 1.0 O A:HOH732 3.7 24.2 1.0 H A:ASN430 3.7 16.5 1.0 HB3 A:ASN463 3.8 21.8 1.0 HA A:ASN430 3.8 16.8 1.0 CA A:ASN428 4.0 17.0 1.0 N A:ASN428 4.0 15.2 1.0 N A:ASP427 4.1 13.7 1.0 C A:ASN428 4.2 16.1 1.0 O A:ASN428 4.2 17.1 1.0 N A:ASN430 4.2 13.8 1.0 O A:HOH708 4.3 27.8 1.0 HD21 A:ASN430 4.3 20.7 1.0 HB A:THR426 4.3 19.5 1.0 CA A:ASN430 4.4 14.0 1.0 CA A:ASP427 4.4 13.8 1.0 ND2 A:ASN430 4.4 17.3 1.0 CB A:ASN430 4.5 14.7 1.0 O A:ASN463 4.5 16.0 1.0 HB2 A:ASN463 4.6 21.8 1.0 CB A:ASN463 4.6 18.2 1.0 HD22 A:ASN463 4.8 29.3 1.0 N A:SER429 4.9 14.9 1.0 HB3 A:ASN430 4.9 17.7 1.0 H A:ASN428 4.9 18.3 1.0

Sodium binding site 5 out of 6 in the Gspb Siglec Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Gspb Siglec Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:32.5 occ:1.00 O A:HOH823 2.1 29.6 1.0 O A:HOH839 2.3 32.2 1.0 O A:HOH904 2.3 41.0 1.0 OG A:SER418 2.4 15.2 1.0 O A:HOH812 2.6 40.6 1.0 HB3 A:SER418 3.3 16.9 1.0 CB A:SER418 3.4 14.1 1.0 O A:HOH712 3.9 13.6 1.0 HB2 A:SER418 3.9 16.9 1.0 H A:SER418 3.9 15.1 1.0 O A:HOH851 4.2 17.6 1.0 N A:SER418 4.6 12.6 1.0 CA A:SER418 4.6 12.5 1.0 OD1 A:ASN472 4.7 25.4 1.0

Sodium binding site 6 out of 6 in the Gspb Siglec Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Gspb Siglec Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:49.1 occ:1.00 O A:HOH853 2.4 20.2 1.0 O A:HOH854 2.5 27.6 1.0 NA A:NA602 3.6 21.2 1.0 OD1 A:ASN406 4.2 16.3 1.0 O A:HOH911 4.2 33.9 1.0 O A:HOH782 4.6 16.1 1.0 O A:HOH900 4.7 32.4 1.0

T.M.Iverson, T.M.Iverson. N/A N/A.