Sodium in PDB 8sfv: High Affinity Nanobodies to Gfp

The structure of High Affinity Nanobodies to Gfp, PDB code: 8sfv was solved by N.E.Ketaren, M.P.Rout, J.B.Bonanno, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.25 / 1.83
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	111.251, 111.251, 193.802, 90, 90, 90
R / Rfree (%)	18.3 / 20.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Sodium atom in the High Affinity Nanobodies to Gfp (pdb code 8sfv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the High Affinity Nanobodies to Gfp, PDB code: 8sfv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in the High Affinity Nanobodies to Gfp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Affinity Nanobodies to Gfp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:38.0 occ:1.00 H A:THR63 2.2 34.9 1.0 HG1 A:THR62 2.4 37.0 1.0 OG1 A:THR62 2.6 30.8 1.0 OG1 A:THR63 2.6 33.6 1.0 HA A:LEU60 2.6 34.4 1.0 O A:THR59 2.8 32.5 1.0 N A:THR63 2.9 29.0 1.0 H A:THR62 3.1 34.0 1.0 HG1 A:THR63 3.2 40.4 1.0 HD13 A:ILE98 3.2 41.4 1.0 HB A:THR63 3.2 39.0 1.0 CA A:LEU60 3.3 29.0 1.0 CB A:THR63 3.3 32.4 1.0 C A:LEU60 3.4 28.6 1.0 N A:THR62 3.5 28.3 1.0 HD11 A:ILE98 3.5 41.4 1.0 O A:LEU60 3.6 28.5 1.0 NA A:NA308 3.6 40.1 1.0 C A:THR59 3.7 30.4 1.0 CD1 A:ILE98 3.7 34.5 1.0 CA A:THR63 3.7 30.0 1.0 HD12 A:ILE98 3.7 41.4 1.0 C A:THR62 3.8 29.6 1.0 CB A:THR62 3.8 32.5 1.0 CA A:THR62 3.8 31.2 1.0 N A:VAL61 3.9 30.5 1.0 N A:LEU60 3.9 31.1 1.0 HD2 A:TYR106 4.0 42.4 1.0 O A:HOH491 4.1 32.4 1.0 HA A:THR63 4.1 36.1 1.0 H A:VAL61 4.1 36.7 1.0 HD23 A:LEU60 4.3 42.5 1.0 C A:VAL61 4.3 27.5 1.0 HE2 A:TYR106 4.3 40.4 1.0 HB A:THR62 4.4 39.1 1.0 O A:HOH438 4.4 33.5 1.0 NE2 A:HIS181 4.5 29.6 1.0 HD22 A:LEU60 4.5 42.5 1.0 HG23 A:THR62 4.6 38.2 1.0 CB A:LEU60 4.6 29.4 1.0 HB3 A:LEU60 4.7 34.8 1.0 H A:LEU60 4.7 37.5 1.0 CD2 A:TYR106 4.7 35.3 1.0 CA A:VAL61 4.7 28.8 1.0 CG2 A:THR63 4.7 34.0 1.0 CG2 A:THR62 4.8 31.8 1.0 HA A:THR62 4.8 37.6 1.0 CD2 A:LEU60 4.8 35.3 1.0 O A:THR62 4.8 31.3 1.0 CE2 A:TYR106 4.9 33.6 1.0 HG21 A:THR63 4.9 40.9 1.0 C A:THR63 5.0 34.1 1.0 HG21 A:ILE98 5.0 41.9 1.0 HH11 A:ARG96 5.0 37.1 1.0

Sodium binding site 2 out of 11 in the High Affinity Nanobodies to Gfp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High Affinity Nanobodies to Gfp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:54.0 occ:1.00 OE2 A:GLU5 2.5 73.4 1.0 O A:HOH481 2.5 44.5 1.0 O A:LYS79 2.6 46.5 1.0 HG2 A:GLU5 2.6 80.9 1.0 O A:HOH420 2.7 42.1 1.0 HG3 A:GLU5 2.7 80.9 1.0 HB3 A:ASP82 2.8 44.6 1.0 HB2 A:LYS79 2.8 65.7 1.0 CG A:GLU5 2.9 67.3 1.0 CD A:GLU5 3.1 64.1 1.0 C A:LYS79 3.4 48.0 1.0 HA A:LYS79 3.5 61.4 1.0 CB A:LYS79 3.7 54.7 1.0 CB A:ASP82 3.7 37.1 1.0 CA A:LYS79 3.8 51.1 1.0 HB2 A:ASP82 3.8 44.6 1.0 HD12 A:LEU194 3.8 58.9 1.0 HD11 A:LEU194 3.8 58.9 1.0 O A:HOH409 4.0 60.0 1.0 HD13 A:LEU194 4.1 58.9 1.0 CD1 A:LEU194 4.1 49.0 1.0 H A:ASP82 4.2 47.2 1.0 HG3 A:LYS79 4.2 88.9 1.0 OD2 A:ASP82 4.2 36.3 1.0 HB3 A:LYS79 4.3 65.7 1.0 OE1 A:GLU5 4.3 69.0 1.0 HB2 A:LYS85 4.3 46.3 1.0 CG A:ASP82 4.4 38.0 1.0 HD2 A:LYS85 4.4 43.6 1.0 CB A:GLU5 4.4 58.7 1.0 CG A:LYS79 4.5 74.0 1.0 HA A:GLN80 4.5 58.2 1.0 N A:GLN80 4.6 48.8 1.0 O A:ASP82 4.6 39.1 1.0 HB3 A:SER2 4.8 96.0 1.0 CA A:ASP82 4.8 39.2 1.0 HB3 A:GLU5 4.8 70.6 1.0 N A:ASP82 4.8 39.3 1.0 HB2 A:SER2 4.9 96.0 1.0 HA A:GLU5 4.9 61.4 1.0 HB2 A:GLU5 4.9 70.6 1.0

Sodium binding site 3 out of 11 in the High Affinity Nanobodies to Gfp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High Affinity Nanobodies to Gfp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:57.9 occ:1.00 O A:PRO54 2.7 39.8 1.0 HE2 A:HIS139 2.9 56.2 1.0 HD22 A:LEU137 3.2 51.8 1.0 O A:HOH401 3.4 61.2 1.0 HA A:PRO54 3.5 47.7 1.0 O A:LEU137 3.5 46.0 1.0 HB2 A:PRO54 3.6 56.4 1.0 NE2 A:HIS139 3.6 46.8 1.0 C A:PRO54 3.6 42.6 1.0 HA A:LEU137 3.6 51.3 1.0 HD2 A:HIS139 3.7 61.5 1.0 HD23 A:LEU137 3.8 51.8 1.0 CA A:PRO54 3.9 39.7 1.0 HB3 A:LEU137 3.9 53.5 1.0 CD2 A:LEU137 4.0 43.1 1.0 CD2 A:HIS139 4.0 51.2 1.0 CB A:PRO54 4.1 46.9 1.0 CA A:LEU137 4.3 42.7 1.0 HB3 A:PRO54 4.3 56.4 1.0 C A:LEU137 4.3 42.1 1.0 CB A:LEU137 4.5 44.5 1.0 HE1 A:HIS25 4.6 105.2 1.0 HD21 A:LEU137 4.6 51.8 1.0 ND1 A:HIS25 4.8 91.6 1.0 HA A:VAL55 4.8 39.6 1.0 CE1 A:HIS139 4.8 46.2 1.0 CG A:LEU137 4.8 45.1 1.0 N A:VAL55 4.8 37.6 1.0 CE1 A:HIS25 4.9 87.6 1.0

Sodium binding site 4 out of 11 in the High Affinity Nanobodies to Gfp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of High Affinity Nanobodies to Gfp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:31.9 occ:0.50 HE A:ARG168 2.3 50.0 1.0 HH21 A:ARG168 2.5 46.8 1.0 O A:HOH421 3.1 40.8 1.0 NE A:ARG168 3.1 41.6 1.0 HB3 A:ASN146 3.1 40.0 1.0 NH2 A:ARG168 3.3 38.9 1.0 CG A:ASN146 3.5 34.3 1.0 CZ A:ARG168 3.6 48.7 1.0 CB A:ASN146 3.7 33.3 1.0 ND2 A:ASN146 3.7 28.5 1.0 OD1 A:ASN146 3.8 40.2 1.0 HD22 A:ASN146 3.9 34.3 1.0 HH22 A:ARG168 4.0 46.8 1.0 HD21 A:ASN146 4.0 34.3 1.0 HB2 A:ASN146 4.0 40.0 1.0 HD2 A:ARG168 4.1 49.5 1.0 CD A:ARG168 4.2 41.2 1.0 HB2 A:ARG168 4.4 47.0 1.0 HD21 A:ASN170 4.7 48.3 1.0 HB3 A:ARG168 4.7 47.0 1.0 HD3 A:ARG168 4.9 49.5 1.0 H A:SER147 4.9 36.1 1.0 OD1 A:ASN170 5.0 36.8 1.0 NH1 A:ARG168 5.0 46.5 1.0 CB A:ARG168 5.0 39.1 1.0

Sodium binding site 5 out of 11 in the High Affinity Nanobodies to Gfp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of High Affinity Nanobodies to Gfp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:40.1 occ:1.00 HH A:TYR145 2.1 38.7 1.0 H A:THR62 2.3 34.0 1.0 HG1 A:THR62 2.5 37.0 1.0 HG23 A:THR62 2.7 38.2 1.0 O A:HOH491 2.7 32.4 1.0 OH A:TYR145 2.8 32.2 1.0 HB A:VAL61 2.9 31.6 1.0 O A:PRO58 2.9 30.8 1.0 H A:VAL61 3.0 36.7 1.0 N A:THR62 3.1 28.3 1.0 HE1 A:HIS169 3.1 36.2 1.0 HE1 A:TYR145 3.2 33.8 1.0 OG1 A:THR62 3.3 30.8 1.0 N A:VAL61 3.4 30.5 1.0 O A:THR59 3.4 32.5 1.0 HA A:THR59 3.5 34.5 1.0 CG2 A:THR62 3.5 31.8 1.0 C A:THR59 3.6 30.4 1.0 NA A:NA304 3.6 38.0 1.0 CZ A:TYR145 3.7 28.5 1.0 CB A:VAL61 3.7 26.7 1.0 CE1 A:TYR145 3.8 28.1 1.0 CB A:THR62 3.8 32.5 1.0 CA A:VAL61 3.9 28.8 1.0 HG21 A:ILE167 3.9 39.6 1.0 CE1 A:HIS169 3.9 30.1 1.0 C A:VAL61 4.0 27.5 1.0 HG21 A:THR62 4.0 38.2 1.0 CA A:THR59 4.0 28.9 1.0 HG13 A:ILE167 4.0 38.1 1.0 N A:LEU60 4.0 31.1 1.0 C A:PRO58 4.0 29.6 1.0 CA A:THR62 4.1 31.2 1.0 C A:LEU60 4.1 28.6 1.0 HG22 A:THR62 4.2 38.2 1.0 NE2 A:HIS169 4.3 32.5 1.0 HG12 A:VAL61 4.3 37.3 1.0 HE1 A:HIS181 4.4 40.6 1.0 H A:LEU60 4.5 37.5 1.0 H A:THR63 4.5 34.9 1.0 CA A:LEU60 4.5 29.0 1.0 HA A:LEU60 4.5 34.4 1.0 HG23 A:VAL61 4.5 36.0 1.0 N A:THR59 4.6 29.5 1.0 NE2 A:HIS181 4.6 29.6 1.0 CG1 A:VAL61 4.6 31.0 1.0 HA A:THR62 4.6 37.6 1.0 CG2 A:VAL61 4.7 29.9 1.0 HB A:THR62 4.7 39.1 1.0 CE1 A:HIS181 4.8 33.8 1.0 HA A:VAL61 4.8 34.7 1.0 CG2 A:ILE167 4.8 32.9 1.0 CG1 A:ILE167 4.9 31.6 1.0 O A:LEU60 4.9 28.5 1.0 HG21 A:VAL61 5.0 36.0 1.0

Sodium binding site 6 out of 11 in the High Affinity Nanobodies to Gfp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of High Affinity Nanobodies to Gfp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:41.1 occ:1.00 O3 A:CR266 2.7 37.9 1.0 HB3 A:ALA110 2.8 43.2 1.0 OD1 A:ASN121 2.8 35.0 1.0 O A:HOH473 2.8 34.1 1.0 HD21 A:ASN121 3.0 38.1 1.0 HB1 A:ALA110 3.1 43.2 1.0 HA31 A:CR266 3.1 38.6 1.0 HB3 A:GLN94 3.1 43.4 1.0 HG21 A:VAL112 3.1 44.4 1.0 HG22 A:VAL112 3.1 44.4 1.0 HG23 A:VAL112 3.2 44.4 1.0 CB A:ALA110 3.2 35.9 1.0 CG2 A:VAL112 3.3 37.0 1.0 CG A:ASN121 3.3 31.9 1.0 ND2 A:ASN121 3.4 31.6 1.0 HB2 A:ALA110 3.4 43.2 1.0 HE21 A:GLN94 3.4 41.5 1.0 NE2 A:GLN94 3.5 34.5 1.0 C3 A:CR266 3.6 34.1 1.0 HE22 A:GLN94 3.7 41.5 1.0 CD A:GLN94 3.8 36.8 1.0 CA3 A:CR266 3.8 32.1 1.0 CB A:GLN94 3.8 36.1 1.0 HB2 A:GLN94 4.0 43.4 1.0 HG2 A:GLN94 4.0 40.0 1.0 HA32 A:CR266 4.0 38.6 1.0 O A:THR63 4.1 30.9 1.0 HD22 A:ASN121 4.1 38.1 1.0 CG A:GLN94 4.1 33.2 1.0 HG12 A:ILE123 4.1 41.9 1.0 O A:HOH415 4.3 36.8 1.0 OE1 A:GLN94 4.4 35.2 1.0 HE1 A:TYR92 4.5 42.6 1.0 O A:HOH452 4.5 39.4 1.0 HG13 A:ILE123 4.6 41.9 1.0 CB A:ASN121 4.6 34.3 1.0 HB2 A:ASN121 4.6 41.3 1.0 CA A:ALA110 4.7 40.0 1.0 HD11 A:ILE123 4.8 39.3 1.0 CG1 A:ILE123 4.8 34.8 1.0 HG13 A:VAL68 4.8 36.4 1.0 CB A:VAL112 4.8 34.7 1.0 HA A:VAL68 4.9 36.1 1.0 HA A:ASN121 4.9 40.5 1.0 HG12 A:VAL68 4.9 36.4 1.0

Sodium binding site 7 out of 11 in the High Affinity Nanobodies to Gfp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of High Affinity Nanobodies to Gfp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:46.2 occ:1.00 HD22 A:ASN144 2.1 45.4 1.0 ND2 A:ASN144 3.0 37.8 1.0 HB3 A:ASN144 3.0 36.7 1.0 HD21 A:ASN144 3.5 45.4 1.0 HB2 A:ASN144 3.5 36.7 1.0 CB A:ASN144 3.6 30.5 1.0 CG A:ASN144 3.8 27.8 1.0 O A:HOH423 4.5 45.4 1.0 OE1 A:GLU142 4.8 50.7 1.0 OD1 A:ASN144 5.0 33.8 1.0

Sodium binding site 8 out of 11 in the High Affinity Nanobodies to Gfp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of High Affinity Nanobodies to Gfp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na206 b:55.0 occ:1.00 HG B:SER53 2.3 45.0 1.0 HG B:SER55 2.4 54.6 1.0 O B:HOH330 2.5 39.7 1.0 O B:HOH346 2.7 43.9 1.0 OG B:SER55 2.9 45.4 1.0 HB2 B:SER53 2.9 48.5 1.0 OG B:SER53 3.0 37.4 1.0 OG1 B:THR57 3.1 51.7 1.0 HG1 B:THR57 3.2 62.1 1.0 CB B:SER53 3.3 40.3 1.0 HB3 B:SER53 3.5 48.5 1.0 H B:SER55 3.7 53.5 1.0 HB3 B:ASP58 3.8 41.3 1.0 HB2 B:ASP58 3.8 41.3 1.0 O B:HOH349 3.8 35.9 1.0 HB3 B:SER55 3.8 56.1 1.0 H B:THR57 4.0 52.6 1.0 CB B:SER55 4.0 46.7 1.0 H B:ASP58 4.2 49.8 1.0 CB B:ASP58 4.2 34.7 1.0 N B:ASP58 4.4 41.4 1.0 N B:SER55 4.4 44.5 1.0 CB B:THR57 4.5 54.4 1.0 N B:THR57 4.6 43.8 1.0 H B:GLY56 4.6 50.3 1.0 O B:HOH313 4.7 35.3 1.0 HB2 B:SER55 4.7 56.1 1.0 CA B:SER55 4.8 48.7 1.0 CA B:SER53 4.8 35.5 1.0 C B:THR57 4.8 50.8 1.0 CA B:THR57 4.9 43.5 1.0 H B:ARG54 4.9 42.6 1.0 HB B:THR57 4.9 65.3 1.0 CA B:ASP58 5.0 40.2 1.0

Sodium binding site 9 out of 11 in the High Affinity Nanobodies to Gfp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of High Affinity Nanobodies to Gfp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na207 b:67.5 occ:1.00 HH22 B:ARG54 2.2 72.2 1.0 HB3 B:PRO31 2.6 69.3 1.0 O B:ASN75 2.8 56.1 1.0 HH12 B:ARG54 2.8 62.1 1.0 OD1 B:ASN78 2.8 49.5 1.0 NH2 B:ARG54 3.0 60.1 1.0 HG3 B:PRO31 3.1 68.9 1.0 HB3 B:ASN75 3.3 61.2 1.0 CB B:PRO31 3.4 57.7 1.0 HA B:PRO31 3.4 62.7 1.0 NH1 B:ARG54 3.5 51.7 1.0 HH21 B:ARG54 3.6 72.2 1.0 CZ B:ARG54 3.7 60.1 1.0 CG B:PRO31 3.7 57.4 1.0 C B:ASN75 3.8 56.8 1.0 HA B:ASN75 3.8 64.0 1.0 CA B:PRO31 4.0 52.2 1.0 CG B:ASN78 4.0 54.5 1.0 CB B:ASN75 4.1 50.9 1.0 CA B:ASN75 4.1 53.3 1.0 HD21 B:ASN78 4.2 66.0 1.0 HB2 B:PRO31 4.2 69.3 1.0 HG2 B:PRO31 4.2 68.9 1.0 HH11 B:ARG54 4.3 62.1 1.0 ND2 B:ASN78 4.5 54.9 1.0 H B:THR32 4.7 58.5 1.0 HA B:ASN78 4.7 58.6 1.0 HB2 B:ASN75 4.7 61.2 1.0 N B:PRO31 4.8 52.3 1.0 CG B:ASN75 4.9 48.1 1.0 CD B:PRO31 4.9 56.6 1.0 H B:ASN78 4.9 62.8 1.0 HE1 B:MET3 4.9 56.6 1.0 HA B:ALA76 4.9 70.2 1.0 N B:ALA76 5.0 60.5 1.0

Sodium binding site 10 out of 11 in the High Affinity Nanobodies to Gfp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of High Affinity Nanobodies to Gfp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na208 b:61.2 occ:1.00 O B:HOH338 2.4 60.2 1.0 HB3 B:TYR81 2.5 53.0 1.0 HG B:SER25 2.8 60.0 1.0 O B:HOH337 2.9 46.1 1.0 OG B:SER25 3.1 49.9 1.0 HD2 B:TYR81 3.2 56.9 1.0 HG1 B:THR79 3.4 50.2 1.0 HB B:THR79 3.4 54.1 1.0 CB B:TYR81 3.5 44.1 1.0 CD2 B:TYR81 3.9 47.4 1.0 OG1 B:THR79 3.9 41.8 1.0 O B:VAL80 3.9 38.5 1.0 HB2 B:TYR81 3.9 53.0 1.0 HB2 B:SER25 4.1 50.5 1.0 C B:VAL80 4.1 35.7 1.0 CB B:THR79 4.1 45.0 1.0 CB B:SER25 4.1 42.0 1.0 CG B:TYR81 4.2 47.6 1.0 HH21 B:ARG23 4.2 84.2 1.0 HE B:ARG23 4.3 64.7 1.0 N B:TYR81 4.3 34.6 1.0 O B:HOH307 4.3 56.0 1.0 CA B:TYR81 4.4 40.2 1.0 HA B:TYR81 4.5 48.3 1.0 HA B:SER25 4.5 48.7 1.0 H B:VAL80 4.5 47.5 1.0 HG21 B:THR79 4.5 58.0 1.0 H B:CYS26 4.6 45.8 1.0 N B:VAL80 4.6 39.5 1.0 H B:TYR81 4.8 41.6 1.0 HB3 B:SER25 4.9 50.5 1.0 CA B:VAL80 4.9 36.7 1.0 O B:HOH348 4.9 57.4 1.0 HA B:VAL80 4.9 44.1 1.0 CA B:SER25 4.9 40.5 1.0 CG2 B:THR79 4.9 48.3 1.0 NH2 B:ARG23 5.0 70.1 1.0

N.E.Ketaren, M.P.Rout, S.Almo. High Affinity Nanobodies to Gfp To Be Published.