Sodium in PDB 3qxt: Structure of An Anti-Methotrexate CDR1-3 Graft Vhh Antibody in Complex with Methotrexate

The structure of Structure of An Anti-Methotrexate CDR1-3 Graft Vhh Antibody in Complex with Methotrexate, PDB code: 3qxt was solved by S.W.Fanning, J.R.Horn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.70
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	103.063, 103.063, 157.073, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 19.5

The binding sites of Sodium atom in the Structure of An Anti-Methotrexate CDR1-3 Graft Vhh Antibody in Complex with Methotrexate (pdb code 3qxt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of An Anti-Methotrexate CDR1-3 Graft Vhh Antibody in Complex with Methotrexate, PDB code: 3qxt:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of An Anti-Methotrexate CDR1-3 Graft Vhh Antibody in Complex with Methotrexate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of An Anti-Methotrexate CDR1-3 Graft Vhh Antibody in Complex with Methotrexate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na132 b:38.0 occ:1.00 O A:HOH1106 2.3 36.8 1.0 O A:ARG74 2.4 20.4 1.0 O A:HOH1120 2.4 33.3 1.0 O A:HOH1098 2.5 35.3 1.0 O A:HOH1026 2.5 27.1 1.0 O A:HOH1023 2.8 27.3 1.0 C A:ARG74 3.6 20.9 1.0 O A:HOH1000 3.6 17.8 1.0 O A:HOH1097 4.0 30.7 1.0 CA A:ASP75 4.1 24.4 1.0 N A:ASP75 4.3 20.7 1.0 OD2 A:ASP75 4.6 40.0 1.0 N A:ARG74 4.6 17.7 1.0 CA A:ARG74 4.7 17.4 1.0 CG A:ARG74 4.7 15.7 1.0 N A:LYS76 4.9 24.8 1.0 CB A:ASP75 4.9 23.7 1.0 O A:HOH1070 5.0 40.6 1.0

Sodium binding site 2 out of 5 in the Structure of An Anti-Methotrexate CDR1-3 Graft Vhh Antibody in Complex with Methotrexate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of An Anti-Methotrexate CDR1-3 Graft Vhh Antibody in Complex with Methotrexate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na133 b:32.6 occ:1.00 OD1 A:ASP101 2.2 19.5 1.0 O A:HOH1066 2.3 35.0 1.0 O A:HOH1018 2.3 24.0 1.0 OD1 A:ASP102 2.6 31.6 1.0 OD1 A:ASP119 2.6 29.6 1.0 O A:GLY112 2.9 21.4 1.0 CG A:ASP101 3.1 20.3 1.0 CG A:ASP119 3.5 34.9 1.0 OD2 A:ASP101 3.6 23.0 1.0 O A:HOH1108 3.7 31.5 1.0 OD2 A:ASP119 3.7 32.3 1.0 CG A:ASP102 3.7 29.2 1.0 N A:ASP102 3.8 19.1 1.0 C A:GLY112 3.9 21.9 1.0 O B:HOH1031 4.0 26.1 0.5 OG1 A:THR106 4.0 21.2 1.0 CA A:ASP101 4.3 17.3 1.0 CB A:ASP101 4.3 17.2 1.0 O B:HOH1031 4.3 14.3 0.5 N A:ASN103 4.4 17.1 1.0 OD2 A:ASP102 4.4 40.7 1.0 C A:ASP101 4.5 16.1 1.0 CA A:ASP102 4.7 20.6 1.0 CA A:PRO113 4.7 19.0 1.0 N A:ASP119 4.7 20.2 1.0 CA A:GLY112 4.7 23.1 1.0 CB A:ASN103 4.7 17.4 1.0 C A:PRO113 4.8 23.7 1.0 CB A:ASP102 4.8 22.8 1.0 N A:PRO113 4.8 19.8 1.0 CB A:ASP119 4.9 24.8 1.0 C A:ASP102 4.9 21.1 1.0

Sodium binding site 3 out of 5 in the Structure of An Anti-Methotrexate CDR1-3 Graft Vhh Antibody in Complex with Methotrexate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of An Anti-Methotrexate CDR1-3 Graft Vhh Antibody in Complex with Methotrexate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na132 b:30.9 occ:1.00 OD1 B:ASP101 2.3 27.0 1.0 OD1 B:ASP102 2.3 34.8 1.0 OD1 B:ASP119 2.4 32.9 1.0 O B:HOH1044 2.4 22.6 1.0 O B:GLY112 2.5 26.6 1.0 O B:HOH1087 2.6 23.8 1.0 CG B:ASP101 3.2 22.9 1.0 CG B:ASP119 3.3 37.5 1.0 CG B:ASP102 3.3 36.3 1.0 OD2 B:ASP119 3.6 34.2 1.0 C B:GLY112 3.6 26.7 1.0 N B:ASP102 3.6 26.4 1.0 NA B:NA133 3.7 33.2 1.0 OD2 B:ASP101 3.8 25.3 1.0 OD2 B:ASP102 4.0 41.7 1.0 OG1 B:THR106 4.0 25.7 1.0 N B:ASN103 4.2 28.8 1.0 CA B:PRO113 4.3 23.0 1.0 CB B:ASP102 4.4 28.5 1.0 CA B:ASP101 4.4 24.4 1.0 CB B:ASP101 4.4 24.1 1.0 C B:PRO113 4.4 24.8 1.0 CA B:ASP102 4.4 29.5 1.0 N B:ASP119 4.5 26.4 1.0 C B:ASP101 4.5 25.3 1.0 N B:PRO113 4.5 23.2 1.0 CA B:GLY112 4.5 24.9 1.0 O B:HOH1055 4.5 26.3 1.0 CB B:ASP119 4.7 30.5 1.0 CB B:ASN103 4.7 28.8 1.0 C B:ASP102 4.8 30.7 1.0 O B:HOH1083 4.8 26.8 1.0

Sodium binding site 4 out of 5 in the Structure of An Anti-Methotrexate CDR1-3 Graft Vhh Antibody in Complex with Methotrexate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of An Anti-Methotrexate CDR1-3 Graft Vhh Antibody in Complex with Methotrexate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na133 b:33.2 occ:1.00 O B:HOH1044 2.3 22.6 1.0 O B:HOH1083 2.3 26.8 1.0 O B:SER111 2.4 28.6 1.0 O B:GLY112 2.5 26.6 1.0 O B:HOH1055 2.7 26.3 1.0 O B:HOH1017 3.1 22.0 1.0 C B:GLY112 3.1 26.7 1.0 CA B:GLY112 3.4 24.9 1.0 C B:SER111 3.5 27.0 1.0 NA B:NA132 3.7 30.9 1.0 O B:HOH1087 3.9 23.8 1.0 N B:GLY112 3.9 27.0 1.0 O B:PRO113 4.1 26.3 1.0 N B:PRO113 4.2 23.2 1.0 C B:PRO113 4.5 24.8 1.0 OD2 B:ASP119 4.5 34.2 1.0 CA B:SER111 4.8 29.3 1.0 CA B:PRO113 4.8 23.0 1.0 OD1 B:ASP119 5.0 32.9 1.0 O B:HOH1025 5.0 22.0 1.0

Sodium binding site 5 out of 5 in the Structure of An Anti-Methotrexate CDR1-3 Graft Vhh Antibody in Complex with Methotrexate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of An Anti-Methotrexate CDR1-3 Graft Vhh Antibody in Complex with Methotrexate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na134 b:45.1 occ:1.00 O B:HOH1018 2.4 40.5 1.0 O B:ARG74 2.5 26.5 1.0 O B:HOH1075 2.6 37.4 1.0 O B:HOH1048 2.6 32.2 1.0 O B:HOH1034 2.7 25.6 1.0 C B:ARG74 3.7 26.5 1.0 O B:HOH1021 3.8 22.7 1.0 CA B:ASP75 4.0 30.1 1.0 N B:ASP75 4.3 25.7 1.0 OD2 B:ASP75 4.4 44.2 1.0 O B:HOH1093 4.6 43.2 1.0 N B:LYS76 4.7 31.8 1.0 CB B:ASP75 4.8 30.8 1.0 N B:ARG74 4.8 22.2 1.0 CA B:ARG74 4.8 23.4 1.0 O B:HOH1053 4.9 38.3 1.0 CG B:ARG74 4.9 22.9 1.0 C B:ASP75 4.9 31.5 1.0

S.W.Fanning, J.R.Horn. An Anti-Hapten Camelid Antibody Reveals A Cryptic Binding Site with Significant Energetic Contributions From A Nonhypervariable Loop. Protein Sci. V. 20 1196 2011.
ISSN: ISSN 0961-8368
PubMed: 21557375
DOI: 10.1002/PRO.648