Sodium in PDB 7ugd: Asp-Bound Gltph Rsmr Mutant in Ifs-A1 State

The structure of Asp-Bound Gltph Rsmr Mutant in Ifs-A1 State also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Sodium atom in the Asp-Bound Gltph Rsmr Mutant in Ifs-A1 State (pdb code 7ugd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Asp-Bound Gltph Rsmr Mutant in Ifs-A1 State, PDB code: 7ugd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Asp-Bound Gltph Rsmr Mutant in Ifs-A1 State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Asp-Bound Gltph Rsmr Mutant in Ifs-A1 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:123.7 occ:1.00 O A:ASN310 2.0 120.9 1.0 O A:GLY306 2.7 128.8 1.0 OD2 A:ASP405 2.9 127.8 1.0 O A:ASN401 2.9 117.6 1.0 C A:ASN310 3.2 120.9 1.0 OD1 A:ASP405 3.4 127.8 1.0 CG A:ASP405 3.5 127.8 1.0 C A:ASN401 3.6 117.6 1.0 C A:GLY306 3.9 128.8 1.0 CB A:ASN401 3.9 117.6 1.0 CA A:ASN310 4.0 120.9 1.0 CB A:ASN310 4.0 120.9 1.0 ND2 A:ASN310 4.1 120.9 1.0 CA A:ASN401 4.1 117.6 1.0 CA A:ALA307 4.2 125.3 1.0 N A:MET311 4.2 116.5 1.0 N A:ASN310 4.2 120.9 1.0 CG A:MET311 4.3 116.5 1.0 C A:ALA307 4.3 125.3 1.0 CG A:ASN310 4.4 120.9 1.0 O A:ALA307 4.4 125.3 1.0 CA A:MET311 4.4 116.5 1.0 N A:VAL402 4.5 121.1 1.0 N A:ALA307 4.5 125.3 1.0 CA A:VAL402 4.8 121.1 1.0 CB A:ASP405 4.8 127.8 1.0 CG A:ASN401 4.9 117.6 1.0 OG A:SER278 4.9 125.4 1.0 N A:THR308 4.9 120.8 1.0 CB A:MET311 4.9 116.5 1.0

Sodium binding site 2 out of 3 in the Asp-Bound Gltph Rsmr Mutant in Ifs-A1 State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Asp-Bound Gltph Rsmr Mutant in Ifs-A1 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:120.9 occ:1.00 O A:THR308 2.5 120.8 1.0 O A:SER349 2.5 110.7 1.0 O A:THR352 2.5 110.7 1.0 SD A:MET311 2.8 116.5 1.0 O A:ILE350 3.0 110.7 1.0 C A:THR308 3.2 120.8 1.0 C A:THR352 3.4 110.7 1.0 CG A:MET311 3.4 116.5 1.0 CE A:MET311 3.4 116.5 1.0 C A:ILE350 3.5 110.7 1.0 N A:THR352 3.5 110.7 1.0 C A:SER349 3.6 110.7 1.0 CA A:THR352 3.7 110.7 1.0 CB A:THR352 3.8 110.7 1.0 CA A:ILE350 3.9 110.7 1.0 N A:ILE309 4.0 119.5 1.0 CA A:THR308 4.0 120.8 1.0 CA A:ILE309 4.2 119.5 1.0 N A:ILE350 4.2 110.7 1.0 C A:GLY351 4.3 110.7 1.0 N A:GLY351 4.3 110.7 1.0 O A:ILE309 4.4 119.5 1.0 C A:ILE309 4.4 119.5 1.0 CB A:MET311 4.5 116.5 1.0 OG1 A:THR352 4.5 110.7 1.0 N A:ALA353 4.6 112.3 1.0 CA A:GLY351 4.7 110.7 1.0 CB A:THR308 4.8 120.8 1.0 CA A:SER349 4.8 110.7 1.0 CG2 A:THR352 5.0 110.7 1.0

Sodium binding site 3 out of 3 in the Asp-Bound Gltph Rsmr Mutant in Ifs-A1 State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Asp-Bound Gltph Rsmr Mutant in Ifs-A1 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:131.7 occ:1.00 OG A:SER93 2.4 120.8 1.0 OG1 A:THR92 2.4 123.5 1.0 OD1 A:ASN310 2.4 120.9 1.0 OD1 A:ASP312 2.4 119.4 1.0 O A:TYR89 2.6 127.9 1.0 N A:SER93 2.9 120.8 1.0 CB A:THR92 3.4 123.5 1.0 CB A:SER93 3.4 120.8 1.0 CA A:SER93 3.4 120.8 1.0 C A:THR92 3.5 123.5 1.0 C A:TYR89 3.6 127.9 1.0 CG A:ASP312 3.6 119.4 1.0 CG A:ASN310 3.6 120.9 1.0 CA A:TYR89 3.9 127.9 1.0 CA A:THR92 3.9 123.5 1.0 OD2 A:ASP312 4.1 119.4 1.0 CA A:ASN310 4.2 120.9 1.0 CB A:ASN310 4.3 120.9 1.0 N A:THR92 4.3 123.5 1.0 O A:THR92 4.3 123.5 1.0 N A:MET311 4.5 116.5 1.0 CB A:TYR89 4.5 127.9 1.0 ND2 A:ASN310 4.6 120.9 1.0 O A:TYR88 4.7 130.2 1.0 CG2 A:THR92 4.7 123.5 1.0 C A:ASN310 4.7 120.9 1.0 N A:ASP312 4.7 119.4 1.0 CB A:ASP312 4.8 119.4 1.0 N A:LEU90 4.8 125.3 1.0 CA A:ASP312 4.9 119.4 1.0 C A:SER93 4.9 120.8 1.0 C A:MET311 5.0 116.5 1.0

Y.Huang, K.Reddy, B.Qiu, C.Bracken, W.Zhan, D.Eliezer, O.Boudker. An Environmentally Ultrasensitive Fluorine Probe to Resolve Protein Conformational Ensembles By 19F uc(Nmr) and Cryo-Em To Be Published.