Sodium in PDB 8g8a: Crystal Structure of DH1317.8 Fab in Complex with Hiv Proximal Mper Peptide

The structure of Crystal Structure of DH1317.8 Fab in Complex with Hiv Proximal Mper Peptide, PDB code: 8g8a was solved by B.M.Janus, A.Astavans, G.Ofek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.89 / 2.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	164.976, 63.84, 111.971, 90, 101.06, 90
R / Rfree (%)	22.2 / 25.6

The binding sites of Sodium atom in the Crystal Structure of DH1317.8 Fab in Complex with Hiv Proximal Mper Peptide (pdb code 8g8a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of DH1317.8 Fab in Complex with Hiv Proximal Mper Peptide, PDB code: 8g8a:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of DH1317.8 Fab in Complex with Hiv Proximal Mper Peptide


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 DH1317.8 Fab in Complex with Hiv Proximal Mper Peptide within 5.0Å range: probe atom residue distance (Å) B Occ L:Na301 b:68.4 occ:1.00 OH L:TYR36 2.6 66.1 1.0 HA H:TYR100D 2.6 93.3 1.0 HE1 L:TYR36 2.7 77.4 1.0 HB3 L:ALA34 2.9 80.0 1.0 O H:TYR100C 3.0 75.8 1.0 OE1 L:GLN89 3.1 71.9 1.0 CE1 L:TYR36 3.3 63.7 1.0 HB3 L:GLN89 3.4 81.2 1.0 CZ L:TYR36 3.4 64.7 1.0 HG23 L:THR91 3.5 94.5 1.0 CA H:TYR100D 3.5 76.9 1.0 CB L:ALA34 3.6 65.9 1.0 HB2 L:ALA34 3.6 80.0 1.0 HG2 L:GLN89 3.7 84.8 1.0 HE1 H:MET100E 3.7 82.0 1.0 HB1 L:ALA34 3.7 80.0 1.0 CD L:GLN89 3.8 72.5 1.0 HG21 L:THR91 3.8 94.5 1.0 HB3 H:TYR100D 3.8 89.6 1.0 C H:TYR100C 3.9 77.4 1.0 CG L:GLN89 4.0 69.8 1.0 CG2 L:THR91 4.0 78.0 1.0 H H:MET100E 4.1 88.9 1.0 SD H:MET100E 4.1 73.0 1.0 CB H:TYR100D 4.1 73.9 1.0 N H:TYR100D 4.1 78.8 1.0 CB L:GLN89 4.2 66.8 1.0 CE H:MET100E 4.2 67.6 1.0 HE2 H:MET100E 4.2 82.0 1.0 O L:GLN89 4.2 64.8 1.0 HB2 H:TYR100D 4.2 89.6 1.0 HG22 L:THR91 4.3 94.5 1.0 C H:TYR100D 4.5 74.9 1.0 N H:MET100E 4.5 73.3 1.0 CD1 L:TYR36 4.6 60.0 1.0 CE2 L:TYR36 4.7 61.9 1.0 NE2 L:GLN89 4.8 72.6 1.0 HB2 L:GLN89 4.8 81.2 1.0 C L:GLN89 4.8 64.2 1.0 CA L:ALA34 4.9 64.3 1.0 H H:TYR100D 4.9 95.6 1.0 H L:ALA34 4.9 75.4 1.0 HB2 H:TYR100C 5.0 96.6 1.0 HD1 L:TYR36 5.0 73.0 1.0 HG3 L:GLN89 5.0 84.8 1.0 HE22 L:GLN89 5.0 88.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of DH1317.8 Fab in Complex with Hiv Proximal Mper Peptide


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 DH1317.8 Fab in Complex with Hiv Proximal Mper Peptide within 5.0Å range: probe atom residue distance (Å) B Occ L:Na302 b:58.2 occ:1.00 HE2 H:HIS164 2.6 63.8 1.0 HB2 L:ASP167 2.9 65.4 1.0 HG1 L:THR164 3.1 66.8 1.0 NE2 H:HIS164 3.1 52.3 1.0 O L:THR172 3.2 49.8 1.0 HA L:TYR173 3.2 65.5 1.0 OG L:SER174 3.4 51.6 1.0 C L:TYR173 3.4 51.3 1.0 C L:THR172 3.5 48.9 1.0 HG L:SER174 3.5 62.9 1.0 OG1 L:THR172 3.5 58.9 1.0 CA L:TYR173 3.6 53.8 1.0 N L:SER174 3.6 49.0 1.0 HG1 L:THR172 3.7 71.6 1.0 H L:SER174 3.7 59.7 1.0 OD1 L:ASN138 3.7 61.3 1.0 N L:TYR173 3.7 51.8 1.0 OG1 L:THR164 3.7 54.8 1.0 O L:TYR173 3.8 52.6 1.0 HB2 L:SER174 3.8 62.2 1.0 CD2 H:HIS164 3.8 49.0 1.0 HA L:ASN138 3.9 65.5 1.0 CB L:ASP167 3.9 53.7 1.0 HD2 H:HIS164 3.9 59.8 1.0 H L:ASP167 3.9 65.0 1.0 CE1 H:HIS164 3.9 52.1 1.0 CB L:SER174 4.0 51.0 1.0 HE1 H:HIS164 4.1 63.5 1.0 H L:ASN138 4.2 69.2 1.0 HB3 L:ASP167 4.2 65.4 1.0 H L:TYR173 4.3 63.1 1.0 CA L:SER174 4.4 49.8 1.0 CB L:THR172 4.4 53.9 1.0 N L:ASP167 4.5 53.4 1.0 HB L:THR172 4.5 65.6 1.0 CA L:THR172 4.5 49.9 1.0 O L:GLU165 4.6 57.4 1.0 OD1 L:ASP167 4.6 67.3 1.0 H L:THR172 4.6 64.2 1.0 CG L:ASP167 4.7 59.4 1.0 CA L:ASP167 4.7 53.3 1.0 CA L:ASN138 4.7 53.8 1.0 HA L:SER174 4.8 60.7 1.0 CG L:ASN138 4.8 59.5 1.0 N L:ASN138 4.8 56.8 1.0 HA L:ASP167 4.8 64.9 1.0 CG H:HIS164 4.8 52.6 1.0 HB L:THR164 4.8 64.6 1.0 OD1 L:ASP170 4.8 57.5 1.0 ND1 H:HIS164 4.9 52.7 1.0 CB L:THR164 4.9 53.0 1.0 HB3 L:SER174 4.9 62.2 1.0 HG21 L:THR164 5.0 61.8 1.0 N L:THR172 5.0 52.7 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of DH1317.8 Fab in Complex with Hiv Proximal Mper Peptide


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 DH1317.8 Fab in Complex with Hiv Proximal Mper Peptide within 5.0Å range: probe atom residue distance (Å) B Occ L:Na303 b:63.3 occ:1.00 OG L:SER171 2.6 53.3 1.0 HD12 L:ILE106 2.6 74.2 1.0 HA L:SER171 2.7 67.0 1.0 O L:ASP167 2.7 52.9 1.0 O L:PRO80 2.8 55.7 1.0 HG11 L:VAL83 3.0 70.9 1.0 HB3 L:PRO80 3.1 73.0 1.0 HA L:PRO80 3.2 71.1 1.0 HG13 L:VAL83 3.2 70.9 1.0 HA L:SER168 3.3 71.2 1.0 HG21 L:VAL83 3.3 70.8 1.0 CA L:SER171 3.3 55.0 1.0 CB L:SER171 3.3 51.7 1.0 H L:SER171 3.5 62.0 1.0 C L:PRO80 3.5 59.7 1.0 CD1 L:ILE106 3.5 61.1 1.0 CG1 L:VAL83 3.5 58.3 1.0 HB3 L:SER171 3.5 63.0 1.0 CA L:PRO80 3.6 58.4 1.0 HG2 L:GLN166 3.6 71.2 1.0 CB L:PRO80 3.7 60.1 1.0 N L:SER171 3.8 51.2 1.0 C L:ASP167 3.8 55.2 1.0 HD11 L:ILE106 3.8 74.2 1.0 HB L:ILE106 3.9 67.4 1.0 HD13 L:ILE106 4.0 74.2 1.0 HG22 L:VAL83 4.0 70.8 1.0 HB2 L:PRO80 4.0 73.0 1.0 CG2 L:VAL83 4.0 58.2 1.0 CA L:SER168 4.0 58.6 1.0 C L:SER168 4.2 59.2 1.0 HB3 L:GLN166 4.2 68.9 1.0 HB2 L:SER171 4.2 63.0 1.0 HG12 L:VAL83 4.3 70.9 1.0 CG L:GLN166 4.4 58.5 1.0 N L:SER168 4.4 56.6 1.0 HG21 L:ILE106 4.4 63.9 1.0 CB L:VAL83 4.4 56.8 1.0 CD L:GLN166 4.4 55.5 1.0 CG1 L:ILE106 4.4 57.5 1.0 O L:SER168 4.5 61.3 1.0 CB L:ILE106 4.5 55.4 1.0 HG13 L:ILE106 4.6 70.0 1.0 C L:SER171 4.7 52.2 1.0 H L:VAL83 4.7 67.1 1.0 N L:LYS169 4.7 58.0 1.0 OE1 L:GLN166 4.7 56.8 1.0 N L:GLU81 4.7 58.1 1.0 NE2 L:GLN166 4.8 54.1 1.0 CB L:GLN166 4.8 56.6 1.0 H L:LYS169 4.8 68.9 1.0 HG23 L:VAL83 4.9 70.8 1.0 HA L:GLU81 4.9 69.6 1.0 CG2 L:ILE106 4.9 52.4 1.0 O L:GLN166 4.9 57.2 1.0 HE21 L:GLN166 4.9 66.0 1.0 C L:GLN166 4.9 55.5 1.0 C L:ASP170 4.9 52.7 1.0 N L:ASP167 4.9 53.4 1.0 HB L:VAL83 4.9 69.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of DH1317.8 Fab in Complex with Hiv Proximal Mper Peptide


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 DH1317.8 Fab in Complex with Hiv Proximal Mper Peptide within 5.0Å range: probe atom residue distance (Å) B Occ L:Na304 b:54.8 occ:1.00 HG1 L:THR180 2.4 72.0 1.0 OG1 L:THR180 2.7 59.2 1.0 HB2 L:GLN160 3.0 64.9 1.0 HG3 L:GLN160 3.2 63.9 1.0 OE1 L:GLN160 3.2 67.4 1.0 O L:THR178 3.2 52.1 1.0 HB L:THR178 3.4 66.4 1.0 HG22 L:THR178 3.6 63.8 1.0 CG L:GLN160 3.7 52.4 1.0 HB L:THR180 3.8 67.0 1.0 CB L:GLN160 3.8 53.3 1.0 H L:GLN160 3.8 59.7 1.0 CB L:THR180 3.8 55.1 1.0 CD L:GLN160 3.8 58.7 1.0 HA L:SER159 4.0 62.1 1.0 N L:GLN160 4.1 49.0 1.0 CB L:THR178 4.1 54.6 1.0 CG2 L:THR178 4.1 52.3 1.0 C L:THR178 4.1 53.5 1.0 HG21 L:THR178 4.2 63.8 1.0 H L:THR180 4.2 67.1 1.0 HG2 H:GLN171 4.3 79.2 1.0 N L:THR180 4.5 55.1 1.0 HB3 L:GLN160 4.5 64.9 1.0 C L:SER159 4.5 50.4 1.0 CA L:GLN160 4.6 51.4 1.0 OE1 H:GLN171 4.6 70.5 1.0 HG21 L:THR180 4.6 71.0 1.0 O L:ASN158 4.7 52.7 1.0 HG2 L:GLN160 4.7 63.9 1.0 CA L:SER159 4.7 50.9 1.0 CA L:THR180 4.7 55.0 1.0 CA L:THR178 4.7 53.5 1.0 CG2 L:THR180 4.8 58.4 1.0 HG21 H:VAL169 4.9 73.2 1.0 HA L:LEU179 4.9 63.8 1.0 C L:LEU179 5.0 54.0 1.0

B.M.Janus, A.Astavans, G.Ofek. Vaccine Induction of Heterologous Hiv-1 Neutralizing Antibody B Cell Lineages in Humans Cell(Cambridge,Mass.) 2024.
ISSN: ISSN 0092-8674