Sodium in PDB 6u9u: Structure of GM9_TH8SEQ732127 Fab

The structure of Structure of GM9_TH8SEQ732127 Fab, PDB code: 6u9u was solved by S.Singh, T.J.Liban, M.Pancera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.78 / 2.26
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	147.709, 147.709, 63.200, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25

The binding sites of Sodium atom in the Structure of GM9_TH8SEQ732127 Fab (pdb code 6u9u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of GM9_TH8SEQ732127 Fab, PDB code: 6u9u:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Structure of GM9_TH8SEQ732127 Fab


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of GM9_TH8SEQ732127 Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:70.8 occ:1.00 O H:HOH418 2.3 55.8 1.0 OE1 H:GLU156 3.0 61.9 1.0 O H:HOH427 3.3 45.6 1.0 HD21 H:LEU116 3.3 65.7 1.0 HB2 H:GLU156 3.4 66.6 1.0 HH H:TYR184 3.7 81.2 1.0 HG3 H:GLU156 3.7 68.2 1.0 OH H:TYR184 3.7 67.5 1.0 CD H:GLU156 3.8 54.4 1.0 HD11 H:LEU116 4.0 68.8 1.0 CG H:GLU156 4.1 56.7 1.0 CD2 H:LEU116 4.2 54.6 1.0 CB H:GLU156 4.2 55.4 1.0 HD22 H:LEU116 4.2 65.7 1.0 CZ H:TYR184 4.3 62.8 1.0 HG21 H:THR91 4.5 45.6 1.0 HG1 H:THR118 4.5 65.0 1.0 HB3 H:GLU156 4.6 66.6 1.0 HE2 H:TYR184 4.6 79.8 1.0 H H:GLU156 4.6 54.2 1.0 CE2 H:TYR184 4.7 66.3 1.0 HD23 H:LEU116 4.7 65.7 1.0 HG22 H:THR91 4.8 45.6 1.0 CD1 H:LEU116 4.9 57.2 1.0 OE2 H:GLU156 4.9 52.1 1.0 HG23 H:THR118 4.9 84.4 1.0 CE1 H:TYR184 4.9 64.2 1.0 CG2 H:THR91 5.0 37.9 1.0 HG23 H:THR91 5.0 45.6 1.0 HE1 H:TYR184 5.0 77.2 1.0

Sodium binding site 2 out of 6 in the Structure of GM9_TH8SEQ732127 Fab


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of GM9_TH8SEQ732127 Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:78.0 occ:1.00 HG1 L:THR178 2.1 60.4 1.0 OG1 L:THR178 2.9 50.2 1.0 O L:HOH437 3.0 51.2 1.0 OG H:SER187 3.2 84.3 1.0 HG H:SER187 3.3 0.4 1.0 HA H:LEU186 3.3 53.6 1.0 HD11 H:LEU149 3.5 0.3 1.0 HG21 L:THR178 3.6 71.2 1.0 OG H:SER185 3.6 69.6 1.0 HG H:SER185 3.7 83.7 1.0 O L:HOH407 3.7 45.5 1.0 HD13 H:LEU149 3.7 0.3 1.0 HD12 H:LEU149 3.7 0.3 1.0 CD1 H:LEU149 3.8 90.2 1.0 HB L:THR178 3.8 78.6 1.0 CB L:THR178 3.9 65.4 1.0 HG L:SER176 3.9 0.2 1.0 C H:LEU186 3.9 71.5 1.0 CA H:LEU186 4.0 44.6 1.0 N H:SER187 4.0 48.1 1.0 H H:SER187 4.1 57.8 1.0 CG2 L:THR178 4.2 59.2 1.0 O H:LEU186 4.3 55.4 1.0 O H:SER185 4.3 50.8 1.0 N H:LEU186 4.3 45.8 1.0 CB H:SER187 4.4 96.9 1.0 C H:SER185 4.4 49.0 1.0 OG L:SER176 4.5 92.5 1.0 HB2 H:SER187 4.5 0.4 1.0 HG22 L:VAL133 4.7 78.7 1.0 HB H:VAL177 4.7 82.4 1.0 HG23 L:THR178 4.8 71.2 1.0 CA H:SER187 4.8 58.6 1.0 H H:LEU186 4.8 55.1 1.0 HG22 L:THR178 4.9 71.2 1.0 CB H:SER185 4.9 51.2 1.0 HG21 H:VAL177 5.0 91.2 1.0

Sodium binding site 3 out of 6 in the Structure of GM9_TH8SEQ732127 Fab


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of GM9_TH8SEQ732127 Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Na301 b:44.2 occ:1.00 OD2 L:ASP91 2.3 48.9 1.0 O H:TYR104 2.4 61.6 1.0 OE1 L:GLU32 2.4 35.9 1.0 O L:ASP91 2.5 45.8 1.0 O L:HOH412 2.5 55.3 1.0 O1 L:FMT305 2.8 0.6 1.0 HB2 L:ASP91 3.0 58.3 1.0 HA H:PHE105 3.1 52.5 1.0 HB3 L:GLU32 3.1 53.4 1.0 CG L:ASP91 3.2 59.2 1.0 C L:ASP91 3.3 55.9 1.0 CD L:GLU32 3.4 38.9 1.0 CB L:ASP91 3.5 48.4 1.0 H H:PHE106 3.5 56.5 1.0 C H:TYR104 3.5 48.4 1.0 HB3 H:PHE106 3.6 50.0 1.0 C L:FMT305 3.8 95.5 1.0 N H:PHE106 3.8 46.9 1.0 HA L:TYR92 3.8 62.9 1.0 CA H:PHE105 3.8 43.6 1.0 HG2 L:GLU32 3.9 79.8 1.0 CB L:GLU32 3.9 44.4 1.0 CG L:GLU32 3.9 66.3 1.0 CA L:ASP91 4.0 34.1 1.0 HB2 H:PHE106 4.0 50.0 1.0 N H:PHE105 4.1 51.6 1.0 C H:PHE105 4.1 52.3 1.0 N L:TYR92 4.2 37.0 1.0 CB H:PHE106 4.2 41.5 1.0 HO2 L:FMT305 4.2 0.5 1.0 OD1 L:ASP91 4.3 39.2 1.0 OE2 L:GLU32 4.3 42.4 1.0 HB3 L:ASP91 4.3 58.3 1.0 HB2 L:GLU32 4.4 53.4 1.0 O2 L:FMT305 4.4 92.8 1.0 CA L:TYR92 4.4 52.3 1.0 H L:FMT305 4.4 0.8 1.0 HB3 H:TYR104 4.5 39.0 1.0 HA L:ASP91 4.6 41.0 1.0 O L:HOH449 4.6 43.4 1.0 CA H:PHE106 4.7 44.0 1.0 HA H:TYR104 4.7 62.6 1.0 O L:TYR92 4.7 44.6 1.0 CA H:TYR104 4.7 52.1 1.0 HE1 L:TYR96 4.8 67.4 1.0 HE1 H:TRP101 4.8 43.7 1.0 C L:TYR92 4.9 46.5 1.0 HG3 L:GLU32 4.9 79.8 1.0 H L:ASP91 4.9 57.3 1.0 H H:PHE105 4.9 62.1 1.0 H L:TYR92 4.9 44.6 1.0 HA L:GLU32 4.9 69.9 1.0 HD1 H:PHE105 5.0 48.3 1.0

Sodium binding site 4 out of 6 in the Structure of GM9_TH8SEQ732127 Fab


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of GM9_TH8SEQ732127 Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Na302 b:72.9 occ:1.00 HA L:LEU11 3.5 68.8 1.0 HG L:SER10 3.6 85.5 1.0 OG L:SER10 3.6 71.2 1.0 OG L:SER12 3.8 78.6 1.0 HB2 L:SER10 3.8 59.4 1.0 HG L:SER12 3.9 94.5 1.0 C L:LEU11 3.9 68.9 1.0 HB2 L:SER12 3.9 65.8 1.0 CA L:LEU11 4.0 57.2 1.0 N L:LEU11 4.1 53.7 1.0 N L:SER12 4.1 52.6 1.0 H L:SER12 4.1 63.3 1.0 C L:SER10 4.2 44.6 1.0 CB L:SER10 4.2 49.4 1.0 O L:SER10 4.3 36.7 1.0 CB L:SER12 4.3 54.7 1.0 O L:LEU11 4.3 49.0 1.0 H L:LEU11 4.4 64.6 1.0 HG3 L:GLU105 4.8 0.7 1.0 CA L:SER12 4.8 69.8 1.0 CA L:SER10 4.9 51.8 1.0

Sodium binding site 5 out of 6 in the Structure of GM9_TH8SEQ732127 Fab


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of GM9_TH8SEQ732127 Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Na303 b:80.7 occ:1.00 HE22 L:GLN3 2.4 88.8 1.0 O L:HOH405 2.4 41.9 1.0 O L:ASP1 2.8 70.8 1.0 NE2 L:GLN3 3.2 73.9 1.0 HG L:SER26 3.3 62.1 1.0 H2 L:ASP1 3.5 0.3 1.0 HE21 L:GLN3 3.7 88.8 1.0 HE21 L:GLN27 3.8 61.1 1.0 OE1 L:GLN3 4.0 0.5 1.0 C L:ASP1 4.0 77.0 1.0 CD L:GLN3 4.1 96.0 1.0 OG L:SER26 4.1 51.6 1.0 HB2 L:SER26 4.3 64.2 1.0 N L:ASP1 4.3 86.8 1.0 HE22 L:GLN27 4.4 61.1 1.0 NE2 L:GLN27 4.4 50.8 1.0 HA L:ILE2 4.4 62.5 1.0 H3 L:ASP1 4.6 0.3 1.0 CB L:SER26 4.7 53.4 1.0 CA L:ASP1 4.7 77.7 1.0 H1 L:ASP1 4.8 0.3 1.0 HB2 L:ASP1 4.9 82.5 1.0 HB3 L:SER26 5.0 64.2 1.0 H L:GLN3 5.0 47.8 1.0

Sodium binding site 6 out of 6 in the Structure of GM9_TH8SEQ732127 Fab


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of GM9_TH8SEQ732127 Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Na304 b:90.5 occ:1.00 H L:ASP122 2.5 98.5 1.0 HB2 L:ASP122 3.0 0.0 1.0 N L:ASP122 3.3 82.0 1.0 HA L:SER121 3.4 89.5 1.0 HG2 H:PRO131 3.6 59.5 1.0 HB2 L:SER121 3.7 0.2 1.0 H L:GLU123 3.8 68.5 1.0 CB L:ASP122 3.9 99.0 1.0 OD1 L:ASP122 3.9 98.1 1.0 HG3 H:PRO131 4.0 59.5 1.0 CA L:SER121 4.1 74.4 1.0 CA L:ASP122 4.2 74.6 1.0 C L:SER121 4.2 58.8 1.0 CG H:PRO131 4.2 49.4 1.0 CG L:ASP122 4.4 94.5 1.0 CB L:SER121 4.4 86.7 1.0 N L:GLU123 4.6 56.9 1.0 HB3 L:ASP122 4.6 0.0 1.0 HD2 H:PRO131 4.7 65.8 1.0 HB3 L:SER121 4.9 0.2 1.0 C L:ASP122 4.9 66.5 1.0 HA L:ASP122 5.0 89.7 1.0

G.E.Phad, P.Pushparaj, K.Tran, V.Dubrovskaya, M.Adori, P.Martinez-Murillo, N.Vazquez Bernat, S.Singh, G.Dionne, S.O'dell, K.Bhullar, S.Narang, C.Sorini, E.J.Villablanca, C.Sundling, B.Murrell, J.R.Mascola, L.Shapiro, M.Pancera, M.Martin, M.Corcoran, R.T.Wyatt, G.B.Karlsson Hedestam. Extensive Dissemination and Intraclonal Maturation of Hiv Env Vaccine-Induced B Cell Responses. J.Exp.Med. 2019.
ISSN: ESSN 1540-9538
PubMed: 31704807
DOI: 10.1084/JEM.20191155