Sodium in PDB 7jlk: Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv

The structure of Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv, PDB code: 7jlk was solved by C.Weidle, M.Pancera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.62 / 1.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.019, 85.244, 113.636, 90, 99.73, 90
R / Rfree (%)	17.9 / 23.5

The structure of Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv also contains other interesting chemical elements:

Chlorine

(Cl)

14 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv (pdb code 7jlk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 17 binding sites of Sodium where determined in the Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv, PDB code: 7jlk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 17 in the Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv


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 GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv within 5.0Å range: probe atom residue distance (Å) B Occ H:Na201 b:55.5 occ:1.00 OG H:SER100B 2.5 41.6 1.0 HB2 H:SER100B 2.9 42.1 1.0 HA H:SER100B 3.0 37.9 1.0 HE1 H:TYR97 3.1 37.2 1.0 CB H:SER100B 3.1 35.1 1.0 CL L:CL205 3.2 62.0 1.0 O H:HOH352 3.4 45.9 1.0 CA H:SER100B 3.6 31.6 1.0 H H:ALA100C 3.9 36.5 1.0 CE1 H:TYR97 4.0 31.0 1.0 HD1 L:TYR94 4.0 38.8 1.0 O B:HOH545 4.0 51.3 1.0 HB3 H:SER100B 4.0 42.1 1.0 O H:HOH363 4.3 47.3 1.0 OH H:TYR97 4.4 28.9 1.0 N H:ALA100C 4.5 30.4 1.0 H L:TYR94 4.6 34.5 1.0 CD1 L:TYR94 4.6 32.4 1.0 N H:SER100B 4.6 26.0 1.0 C H:SER100B 4.6 32.0 1.0 CZ H:TYR97 4.7 28.9 1.0 HE1 L:TYR94 4.8 31.9 1.0 HA L:ASN93 4.8 35.6 1.0 HD1 H:TYR97 4.8 39.0 1.0 H2 B:GLU1 4.9 80.2 1.0 HB2 L:TYR94 4.9 39.4 1.0 CD1 H:TYR97 4.9 32.5 1.0 CL H:CL205 4.9 55.1 1.0 H H:SER100B 5.0 31.2 1.0 CE1 L:TYR94 5.0 26.6 1.0

Sodium binding site 2 out of 17 in the Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv


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 GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv within 5.0Å range: probe atom residue distance (Å) B Occ H:Na202 b:59.8 occ:1.00 HE21 H:GLN39 2.4 40.9 1.0 O H:HOH337 2.5 47.1 1.0 HA2 H:GLY44 2.8 58.9 1.0 HG3 H:GLN39 3.1 41.4 1.0 HE2 L:PHE87 3.1 52.2 1.0 NE2 H:GLN39 3.2 34.1 1.0 HZ L:PHE87 3.2 57.1 1.0 O H:HOH350 3.5 47.4 1.0 CE2 L:PHE87 3.7 43.5 1.0 HE22 H:GLN39 3.7 40.9 1.0 CZ L:PHE87 3.7 47.6 1.0 CA H:GLY44 3.7 49.1 1.0 HG2 H:GLN39 3.7 41.4 1.0 CG H:GLN39 3.7 34.5 1.0 HG H:LEU45 3.8 39.3 1.0 O H:HOH359 3.9 43.9 1.0 CD H:GLN39 3.9 32.2 1.0 H H:GLY44 4.0 51.3 1.0 C H:GLY44 4.3 47.1 1.0 HA3 H:GLY44 4.3 58.9 1.0 H H:LEU45 4.3 55.7 1.0 N H:GLY44 4.3 42.8 1.0 N H:LEU45 4.5 46.4 1.0 O L:HOH304 4.5 44.6 1.0 O H:HOH306 4.7 55.1 1.0 CG H:LEU45 4.8 32.8 1.0 CD2 L:PHE87 4.9 54.9 1.0 CE1 L:PHE87 4.9 57.2 1.0 O L:GLY100 4.9 37.6 1.0 O H:GLY44 5.0 49.9 1.0 HD21 H:LEU45 5.0 36.4 1.0

Sodium binding site 3 out of 17 in the Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv


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 GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:50.1 occ:1.00 O A:HOH509 2.5 41.4 1.0 O A:GLY55 2.8 41.8 1.0 O A:HOH507 3.1 39.8 1.0 HA A:THR70 3.2 43.7 1.0 CL A:CL306 3.3 81.9 1.0 HG22 A:THR70 3.4 45.9 1.0 HD11 A:ILE51 3.4 41.0 1.0 O A:MET69 3.5 35.3 1.0 HG23 A:THR57 3.6 44.2 1.0 HA2 A:GLY55 3.6 48.2 1.0 HA3 A:GLY55 3.7 48.2 1.0 C A:GLY55 3.7 31.7 1.0 HD12 A:ILE51 3.8 41.0 1.0 CA A:GLY55 3.9 40.2 1.0 HG21 A:THR57 3.9 44.2 1.0 HH21 A:ARG71 4.0 62.3 1.0 CD1 A:ILE51 4.1 34.2 1.0 CA A:THR70 4.2 36.5 1.0 CG2 A:THR57 4.2 36.9 1.0 O A:HOH425 4.2 45.4 1.0 CG2 A:THR70 4.2 38.2 1.0 HG13 A:ILE51 4.5 45.3 1.0 C A:MET69 4.5 34.2 1.0 NH2 A:ARG71 4.5 51.9 1.0 HG22 A:THR57 4.5 44.2 1.0 H A:ARG71 4.6 44.1 1.0 HG23 A:THR70 4.6 45.9 1.0 HH22 A:ARG71 4.6 62.3 1.0 HB A:THR70 4.6 43.4 1.0 CB A:THR70 4.6 36.1 1.0 HD2 A:ARG71 4.6 51.0 1.0 HD13 A:ILE51 4.8 41.0 1.0 O A:HOH563 4.8 45.6 1.0 N A:THR70 4.8 35.1 1.0 CG1 A:ILE51 4.9 37.8 1.0 HG21 A:THR70 4.9 45.9 1.0 N A:GLY56 5.0 37.2 1.0

Sodium binding site 4 out of 17 in the Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv


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 GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:49.0 occ:1.00 O A:HOH458 2.6 49.8 1.0 O B:HOH539 2.6 42.5 1.0 H A:GLY162 3.0 52.2 1.0 O A:VAL163 3.0 37.3 1.0 HE1 A:HIS164 3.3 49.0 1.0 HA2 A:GLY162 3.4 53.1 1.0 CE1 A:HIS164 3.5 40.9 1.0 N A:GLY162 3.6 43.5 1.0 H A:VAL163 3.6 47.3 1.0 N A:VAL163 3.7 39.4 1.0 CA A:GLY162 3.7 44.2 1.0 C A:GLY162 3.7 42.8 1.0 OD1 B:ASP167 3.8 38.3 1.0 ND1 A:HIS164 3.9 41.5 1.0 O A:HOH487 3.9 45.8 1.0 C A:VAL163 3.9 39.3 1.0 NE2 A:HIS164 4.0 43.6 1.0 HE2 A:HIS164 4.2 52.3 1.0 O B:HOH452 4.2 43.0 1.0 O B:HOH462 4.3 45.2 1.0 O A:GLY162 4.4 35.8 1.0 CA A:VAL163 4.4 31.7 1.0 O B:HOH534 4.4 45.8 1.0 HA A:SER161 4.5 60.0 1.0 O A:THR160 4.6 49.6 1.0 CG A:HIS164 4.6 38.0 1.0 HA3 A:GLY162 4.7 53.1 1.0 C A:SER161 4.7 47.9 1.0 CD2 A:HIS164 4.7 36.5 1.0 HB A:VAL163 4.8 40.4 1.0 CG B:ASP167 4.9 40.0 1.0 O A:HOH576 4.9 39.7 1.0 HA A:HIS164 4.9 47.2 1.0 HD21 B:ASN138 5.0 63.0 1.0 N A:HIS164 5.0 34.9 1.0

Sodium binding site 5 out of 17 in the Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:60.8 occ:1.00 O B:HOH482 2.4 38.5 1.0 O A:HOH488 2.5 36.7 1.0 HB B:THR164 2.9 49.6 1.0 O A:THR165 2.9 37.9 1.0 O A:HOH506 3.2 43.8 1.0 HG22 B:THR164 3.2 50.2 1.0 O A:HOH552 3.3 51.0 1.0 H A:THR165 3.4 46.2 1.0 HG21 B:THR164 3.4 50.2 1.0 CG2 B:THR164 3.6 41.8 1.0 CB B:THR164 3.7 41.4 1.0 O B:HOH559 3.7 50.2 1.0 C A:THR165 3.8 41.0 1.0 N A:THR165 3.9 38.5 1.0 H B:GLU165 4.0 40.7 1.0 HA B:THR164 4.0 44.4 1.0 HA A:HIS164 4.1 47.2 1.0 HD3 A:PRO167 4.2 38.9 1.0 HA A:PHE166 4.2 44.4 1.0 HB A:THR165 4.4 52.1 1.0 CA B:THR164 4.4 37.0 1.0 CA A:THR165 4.5 37.4 1.0 HG23 B:THR164 4.5 50.2 1.0 N B:GLU165 4.7 33.9 1.0 HB3 A:HIS164 4.7 40.2 1.0 O B:HOH555 4.7 39.9 1.0 N A:PHE166 4.7 35.5 1.0 O B:HOH452 4.8 43.0 1.0 C A:HIS164 4.8 37.7 1.0 OG1 B:THR164 4.8 33.8 1.0 CA A:HIS164 4.8 39.3 1.0 CA A:PHE166 4.9 37.0 1.0 CB A:THR165 5.0 43.4 1.0 HB2 B:GLU165 5.0 49.7 1.0

Sodium binding site 6 out of 17 in the Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:69.0 occ:1.00 O A:HOH437 2.7 60.7 1.0 HG B:CYS214 3.1 115.5 1.0 O A:THR219 3.2 79.2 1.0 C A:THR219 3.7 86.2 1.0 SG B:CYS214 4.1 96.3 1.0 O A:LYS218 4.1 99.7 1.0 HA A:THR219 4.1 117.8 1.0 CA A:THR219 4.5 98.2 1.0 C A:LYS218 4.7 106.6 1.0 N A:THR219 4.9 106.4 1.0

Sodium binding site 7 out of 17 in the Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:56.1 occ:1.00 H B:VAL146 2.3 68.5 1.0 OE2 B:GLU161 2.6 67.8 1.0 N B:VAL146 3.1 57.0 1.0 HA B:LYS145 3.1 87.6 1.0 HB B:VAL146 3.4 63.9 1.0 O B:VAL146 3.4 52.0 1.0 CD B:GLU161 3.6 64.0 1.0 HD2 B:LYS145 3.6 90.1 1.0 O B:ALA144 3.9 44.1 1.0 OE1 B:GLU161 3.9 53.4 1.0 O B:HOH409 3.9 44.6 1.0 CA B:VAL146 3.9 60.3 1.0 CA B:LYS145 4.0 73.0 1.0 C B:LYS145 4.0 62.9 1.0 C B:VAL146 4.0 58.9 1.0 CB B:VAL146 4.1 53.2 1.0 HG23 B:VAL146 4.1 50.3 1.0 HG3 B:LYS145 4.1 88.4 1.0 HE3 B:LYS145 4.4 103.4 1.0 CD B:LYS145 4.4 75.1 1.0 CG2 B:VAL146 4.6 41.9 1.0 CG B:LYS145 4.7 73.6 1.0 C B:ALA144 4.7 50.7 1.0 HZ2 B:LYS145 4.8 111.8 1.0 HA B:VAL146 4.8 72.3 1.0 N B:LYS145 4.8 61.5 1.0 CE B:LYS145 4.9 86.2 1.0 CG B:GLU161 4.9 52.6 1.0 CB B:LYS145 4.9 77.8 1.0 HG3 B:GLU161 5.0 63.1 1.0

Sodium binding site 8 out of 17 in the Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:47.9 occ:1.00 H B:GLU81 2.3 39.8 1.0 HG2 B:GLU81 2.3 50.4 1.0 HB3 B:GLU81 2.6 43.1 1.0 HD2 B:PRO80 2.8 41.3 1.0 HB3 B:GLU79 2.9 36.8 1.0 CG B:GLU81 3.0 42.0 1.0 N B:GLU81 3.0 33.1 1.0 CB B:GLU81 3.2 35.9 1.0 HB2 B:PRO80 3.3 41.5 1.0 CD B:GLU81 3.4 54.3 1.0 CD B:PRO80 3.6 34.4 1.0 O B:HOH523 3.6 43.4 1.0 CA B:GLU81 3.7 35.5 1.0 N B:PRO80 3.7 30.9 1.0 CB B:GLU79 3.8 30.7 1.0 HG3 B:GLU81 3.8 50.4 1.0 HB2 B:GLU79 3.8 36.8 1.0 OE2 B:GLU81 3.9 54.9 1.0 OE1 B:GLU81 3.9 72.4 1.0 C B:PRO80 3.9 29.8 1.0 CB B:PRO80 4.0 34.6 1.0 HB2 B:GLU81 4.0 43.1 1.0 HG2 B:PRO80 4.1 34.6 1.0 CA B:PRO80 4.1 32.4 1.0 CG B:PRO80 4.1 28.9 1.0 HA B:GLU81 4.2 42.6 1.0 C B:GLU79 4.2 27.2 1.0 O B:HOH472 4.4 42.0 1.0 HD3 B:PRO80 4.4 41.3 1.0 CA B:GLU79 4.6 29.3 1.0 OE2 B:GLU79 4.7 27.0 1.0 HG3 B:GLU79 4.8 40.0 1.0 CG B:GLU79 4.8 33.3 1.0 HA B:GLU79 4.8 35.1 1.0 HB3 B:PRO80 4.8 41.5 1.0 C B:GLU81 4.9 33.0 1.0 O B:GLU79 4.9 31.7 1.0 H B:ASP82 4.9 32.0 1.0

Sodium binding site 9 out of 17 in the Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:52.7 occ:1.00 O B:HOH427 2.6 30.7 1.0 O B:HOH558 2.8 42.7 1.0 HE1 B:PHE97 3.4 51.9 1.0 HD1 B:PHE97 3.7 40.7 1.0 O A:HOH415 3.8 44.0 1.0 O A:HOH513 4.1 44.3 1.0 CE1 B:PHE97 4.1 43.2 1.0 O A:HOH420 4.2 32.0 1.0 CD1 B:PHE97 4.2 34.0 1.0 OE2 B:GLU1 4.3 68.0 1.0 HG3 B:GLU1 4.6 65.8 1.0 OE1 B:GLU96 4.7 36.4 1.0 O B:HOH529 4.7 37.4 1.0 HG3 B:GLU96 4.8 34.1 1.0 O B:HOH471 5.0 42.6 1.0

Sodium binding site 10 out of 17 in the Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of GLVRC01 Fab in Complex with Anti-Idiotype IV1 Scfv within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:62.7 occ:1.00 HH11 B:ARG18 2.4 69.1 1.0 HH12 B:ARG18 2.7 69.1 1.0 NH1 B:ARG18 2.7 57.5 1.0 O B:HOH420 2.9 45.3 1.0 HG21 B:THR74 3.0 45.1 1.0 HD2 B:ARG18 3.5 68.5 1.0 CZ B:ARG18 3.8 59.3 1.0 CG2 B:THR74 3.9 37.5 1.0 OG1 B:THR74 4.0 30.1 1.0 HG23 B:THR74 4.2 45.1 1.0 CD B:ARG18 4.3 57.1 1.0 NE B:ARG18 4.4 58.9 1.0 O B:HOH544 4.4 35.5 1.0 CB B:THR74 4.6 35.4 1.0 HD3 B:ARG18 4.6 68.5 1.0 HG22 B:THR74 4.6 45.1 1.0 HH22 B:ARG18 4.7 83.5 1.0 HG1 B:THR74 4.7 36.1 1.0 NH2 B:ARG18 4.7 69.6 1.0 HB B:THR74 4.8 42.4 1.0

E.Seydoux, Y.H.Wan, J.Feng, A.Wall, S.Aljedani, L.J.Homad, A.J.Maccamy, C.Weidle, M.D.Gray, L.Brumage, J.J.Taylor, M.Pancera, L.Stamatatos, A.T.Mcguire. Development of A Novel VRC01-Class Germline Targeting Immunogen Derived From Anti-Idiotypic Antibodies To Be Published.