Sodium in PDB 5zmj: Crystal Structure of the Fab Region of A Neutralizing Fully Human Antibody Against Gm-Csf

The structure of Crystal Structure of the Fab Region of A Neutralizing Fully Human Antibody Against Gm-Csf, PDB code: 5zmj was solved by C.Angkawidjaja, T.Torashima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.37 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.120, 66.690, 129.040, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.1

The binding sites of Sodium atom in the Crystal Structure of the Fab Region of A Neutralizing Fully Human Antibody Against Gm-Csf (pdb code 5zmj). 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 the Fab Region of A Neutralizing Fully Human Antibody Against Gm-Csf, PDB code: 5zmj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Fab Region of A Neutralizing Fully Human Antibody Against Gm-Csf


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 the Fab Region of A Neutralizing Fully Human Antibody Against Gm-Csf within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:10.1 occ:1.00 O H:HOH523 3.2 12.3 1.0 NE L:ARG99 3.2 19.4 1.0 NE1 H:TRP47 3.2 14.5 1.0 NE H:ARG99 3.2 17.0 1.0 NH2 L:ARG99 3.3 19.0 1.0 NH2 H:ARG99 3.7 16.4 1.0 CZ L:ARG99 3.7 17.1 1.0 CB H:ARG99 3.7 15.8 1.0 CZ2 H:TRP47 3.8 14.3 1.0 CE2 H:TRP47 3.8 12.4 1.0 CZ H:ARG99 3.9 19.0 1.0 CB L:ARG99 4.0 15.6 1.0 CD H:LYS35 4.1 12.2 1.0 CB H:LYS35 4.1 14.8 1.0 CG H:ARG99 4.1 19.7 1.0 CD H:ARG99 4.3 20.5 1.0 CD1 H:TRP47 4.3 14.6 1.0 CG L:ARG99 4.3 16.6 1.0 CD L:ARG99 4.3 19.3 1.0 CZ3 L:TRP92 4.5 19.1 1.0 CG H:LYS35 4.6 12.7 1.0 O H:PRO100 4.8 16.8 1.0 CB H:TRP50 4.8 14.4 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Fab Region of A Neutralizing Fully Human Antibody Against Gm-Csf


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 the Fab Region of A Neutralizing Fully Human Antibody Against Gm-Csf within 5.0Å range: probe atom residue distance (Å) B Occ H:Na303 b:10.1 occ:1.00 O H:HOH499 3.1 22.7 1.0 N H:THR74 3.2 12.0 1.0 OG1 H:THR74 3.3 22.2 1.0 CG2 H:THR74 3.6 17.5 1.0 CB H:THR74 3.9 16.3 1.0 O H:LEU72 3.9 12.9 1.0 CA H:ASP73 3.9 14.0 1.0 C H:ASP73 4.1 13.1 1.0 CA H:THR74 4.1 14.2 1.0 C H:LEU72 4.3 13.4 1.0 N H:ASP73 4.4 12.9 1.0 CB H:LEU72 4.6 20.7 1.0 OD1 H:ASP73 4.8 14.7 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Fab Region of A Neutralizing Fully Human Antibody Against Gm-Csf


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 the Fab Region of A Neutralizing Fully Human Antibody Against Gm-Csf within 5.0Å range: probe atom residue distance (Å) B Occ L:Na306 b:10.8 occ:1.00 O H:HOH591 2.9 25.0 1.0 O H:HOH536 3.0 13.5 1.0 O H:HOH512 3.1 10.3 1.0 N L:THR167 3.3 9.3 1.0 O H:HOH479 3.4 29.9 1.0 CA L:THR166 3.6 7.6 1.0 OG1 L:THR167 3.6 11.8 1.0 CG2 L:THR167 3.7 12.2 1.0 CB L:THR166 3.8 8.1 1.0 C L:THR166 4.0 7.8 1.0 CB L:THR167 4.1 10.1 1.0 CA L:THR167 4.3 10.5 1.0 CG2 L:THR166 4.5 8.9 1.0 O L:HOH480 4.5 13.7 1.0 O H:ALA182 4.6 11.1 1.0 O L:HOH470 4.7 18.3 1.0 O L:THR165 4.8 11.7 1.0 N L:THR166 4.9 7.6 1.0 O L:THR167 5.0 10.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Fab Region of A Neutralizing Fully Human Antibody Against Gm-Csf


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 the Fab Region of A Neutralizing Fully Human Antibody Against Gm-Csf within 5.0Å range: probe atom residue distance (Å) B Occ L:Na307 b:15.0 occ:1.00 O L:HOH484 3.1 20.0 1.0 O L:HOH446 3.2 20.1 1.0 N L:TYR33 3.5 19.2 1.0 N H:PHE103 3.6 18.7 1.0 CA H:ARG102 3.8 21.9 1.0 CD2 L:TYR33 3.8 22.4 1.0 CB L:TYR33 3.9 20.0 1.0 O H:PHE103 4.1 23.3 1.0 CB L:SER32 4.1 22.3 1.0 CB H:ARG102 4.1 25.4 1.0 O H:HOH416 4.2 37.5 1.0 C H:ARG102 4.2 21.7 1.0 CA L:TYR33 4.3 17.2 1.0 CG H:ARG102 4.3 24.5 1.0 CA L:SER32 4.3 19.0 1.0 CG L:TYR33 4.3 20.8 1.0 C L:SER32 4.4 19.4 1.0 OG L:SER32 4.5 18.6 1.0 NH1 L:ARG99 4.5 17.8 1.0 CA H:PHE103 4.6 22.7 1.0 O L:TYR33 4.6 17.3 1.0 CD2 H:PHE103 4.8 19.1 1.0 C H:PHE103 4.8 27.8 1.0 CE2 L:TYR33 4.9 24.8 1.0 CB H:PHE103 4.9 20.5 1.0 O H:PRO101 4.9 19.0 1.0 CB L:TRP92 4.9 17.7 1.0 C L:TYR33 4.9 19.5 1.0 N H:ARG102 5.0 22.2 1.0 OH L:TYR35 5.0 19.4 1.0

C.Angkawidjaja, T.Torashima. Crystal Structure of the Fab Region of A Neutralizing Antibody Against Granulocyte-Macrophage Colony-Stimulating Factor. Acta Crystallogr.,Sect.F V. 75 634 2019.
ISSN: ESSN 2053-230X
PubMed: 31584011
DOI: 10.1107/S2053230X1901238X