Sodium in PDB 6zwk: Crystal Structure of the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody)

The structure of Crystal Structure of the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody), PDB code: 6zwk was solved by A.G.Mcewen, E.Moeglin, D.Desplancq, E.Weiss, A.Poterszman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.49 / 1.55
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	87.412, 87.412, 105.409, 90, 90, 120
R / Rfree (%)	14.9 / 18.4

The structure of Crystal Structure of the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody) (pdb code 6zwk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody), PDB code: 6zwk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Crystal Structure of the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody)


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 Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:33.9 occ:1.00 O A:HOH314 2.2 33.9 1.0 O A:GLU100G 2.3 31.0 1.0 OD1 A:ASP95 2.4 29.4 1.0 O A:HOH321 2.6 39.2 1.0 OE1 A:GLU101 2.6 36.6 1.0 OE2 A:GLU101 2.8 40.2 1.0 CD A:GLU101 3.0 38.2 1.0 HH22 A:ARG100 3.0 58.5 0.7 HH21 A:ARG100 3.3 58.5 0.7 H A:TYR96 3.3 28.7 1.0 NH2 A:ARG100 3.4 48.7 0.7 C A:GLU100G 3.4 29.6 1.0 HA A:ASP95 3.4 28.4 1.0 CG A:ASP95 3.5 26.6 1.0 HB3 A:GLU100G 3.6 40.2 1.0 N A:TYR96 3.8 23.9 1.0 HA A:GLU100G 4.0 37.0 1.0 HA A:TYR100H 4.1 32.0 1.0 CA A:ASP95 4.1 23.7 1.0 O A:TYR96 4.1 25.9 1.0 H A:GLU101 4.1 35.4 1.0 CA A:GLU100G 4.2 30.9 1.0 HB3 A:TYR96 4.2 30.2 1.0 CB A:ASP95 4.2 24.0 1.0 C A:ASP95 4.2 23.2 1.0 OH G:TYR142 4.3 30.2 1.0 CB A:GLU100G 4.3 33.5 1.0 HH G:TYR142 4.3 36.2 1.0 CG A:GLU101 4.3 36.1 1.0 OD2 A:ASP95 4.4 27.0 1.0 HB2 A:ASP95 4.4 28.8 1.0 HG3 A:GLU101 4.5 43.4 1.0 N A:TYR100H 4.5 28.2 1.0 OE1 A:GLU100G 4.6 41.8 1.0 N A:GLU101 4.6 29.5 1.0 HH22 A:ARG100 4.6 39.5 0.3 O A:HOH309 4.6 48.1 1.0 CZ A:ARG100 4.7 47.5 0.7 CA A:TYR100H 4.7 26.7 1.0 CA A:TYR96 4.7 24.5 1.0 HB2 A:GLU100G 4.7 40.2 1.0 C A:TYR96 4.8 24.6 1.0 CB A:TYR96 4.9 25.2 1.0 HB2 A:GLU101 4.9 40.1 1.0 HG2 A:GLU101 5.0 43.4 1.0 C A:TYR100H 5.0 27.8 1.0

Sodium binding site 2 out of 7 in the Crystal Structure of the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody)


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 Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:37.3 occ:1.00 O B:HOH405 2.0 30.0 0.5 O B:GLU100G 2.2 33.9 1.0 O B:HOH336 2.3 34.7 1.0 O B:HOH325 2.4 34.4 1.0 OE2 B:GLU101 2.4 38.8 0.5 OD1 B:ASP95 2.4 29.5 1.0 OE1 B:GLU101 2.4 41.3 0.5 OE2 B:GLU101 2.5 42.6 0.5 CD B:GLU101 2.8 41.6 0.5 CD B:GLU101 3.3 38.7 0.5 C B:GLU100G 3.4 31.9 1.0 OE1 B:GLU101 3.5 38.4 0.5 H B:TYR96 3.5 28.5 1.0 HB3 B:GLU100G 3.5 41.7 1.0 CG B:ASP95 3.5 25.1 1.0 HH21 B:ARG100 3.5 47.4 1.0 HH22 B:ARG100 3.6 47.4 1.0 HA B:ASP95 3.6 27.4 1.0 NH2 B:ARG100 3.9 39.5 1.0 HA B:GLU100G 4.0 39.7 1.0 N B:TYR96 4.0 23.8 1.0 HA B:TYR100H 4.1 35.8 1.0 CA B:GLU100G 4.1 33.0 1.0 OH H:TYR142 4.2 27.9 1.0 HH H:TYR142 4.2 33.4 1.0 O B:TYR96 4.3 26.0 1.0 CB B:GLU100G 4.3 34.7 1.0 CA B:ASP95 4.3 22.8 1.0 H B:GLU101 4.3 40.7 0.5 H B:GLU101 4.3 40.7 0.5 OE1 B:GLU100G 4.3 42.3 1.0 OD2 B:ASP95 4.3 25.2 1.0 CG B:GLU101 4.4 40.1 0.5 CB B:ASP95 4.4 22.7 1.0 N B:TYR100H 4.4 30.6 1.0 C B:ASP95 4.5 23.6 1.0 HB3 B:TYR96 4.5 30.9 1.0 HB2 B:ASP95 4.5 27.2 1.0 CG B:GLU101 4.6 37.7 0.5 CA B:TYR100H 4.7 29.9 1.0 HG2 B:GLU101 4.7 45.3 0.5 N B:GLU101 4.7 33.9 1.0 HG2 B:GLU101 4.7 48.1 0.5 HB2 B:GLU100G 4.7 41.7 1.0 HG3 B:GLU101 4.8 48.1 0.5 CA B:TYR96 4.9 24.3 1.0 HB3 B:GLU101 5.0 43.1 0.5 C B:TYR100H 5.0 33.4 1.0

Sodium binding site 3 out of 7 in the Crystal Structure of the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody)


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 Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:32.5 occ:1.00 O C:GLU100G 2.2 29.9 1.0 OE1 C:GLU101 2.3 42.5 0.6 O C:HOH357 2.3 34.0 1.0 O C:HOH312 2.4 31.9 1.0 OD1 C:ASP95 2.4 28.1 1.0 OE1 C:GLU101 2.4 31.7 0.4 OE2 C:GLU101 2.5 33.5 0.4 CD C:GLU101 2.8 32.9 0.4 CD C:GLU101 3.0 39.7 0.6 OE2 C:GLU101 3.0 37.6 0.6 HH21 C:ARG100 3.2 40.5 0.6 HH22 C:ARG100 3.2 40.5 0.6 C C:GLU100G 3.4 28.4 1.0 CG C:ASP95 3.5 25.5 1.0 HB3 C:GLU100G 3.5 36.5 1.0 NH2 C:ARG100 3.5 33.8 0.6 H C:TYR96 3.6 29.2 1.0 HA C:ASP95 3.6 27.9 1.0 O C:HOH302 3.6 31.9 0.6 HA C:GLU100G 3.9 34.5 1.0 HA C:TYR100H 4.0 31.3 1.0 OH I:TYR142 4.1 28.1 1.0 N C:TYR96 4.1 24.4 1.0 HH I:TYR142 4.1 33.7 1.0 CA C:GLU100G 4.1 28.8 1.0 O C:HOH342 4.2 34.2 0.4 CB C:GLU100G 4.2 30.4 1.0 CA C:ASP95 4.3 23.2 1.0 CB C:ASP95 4.3 23.8 1.0 CG C:GLU101 4.3 32.6 0.4 OD2 C:ASP95 4.3 26.1 1.0 O C:HOH426 4.3 54.1 1.0 OE1 C:GLU100G 4.3 38.7 1.0 O C:TYR96 4.4 26.9 1.0 O C:HOH323 4.4 47.0 1.0 N C:TYR100H 4.4 26.2 1.0 HB2 C:ASP95 4.4 28.6 1.0 CG C:GLU101 4.4 37.8 0.6 H C:GLU101 4.4 36.5 0.4 H C:GLU101 4.4 36.5 0.6 C C:ASP95 4.5 23.7 1.0 HB3 C:TYR96 4.5 32.9 1.0 HG2 C:GLU101 4.6 45.4 0.6 HG2 C:GLU101 4.6 39.1 0.4 CA C:TYR100H 4.6 26.1 1.0 HG3 C:GLU101 4.7 39.1 0.4 HB2 C:GLU100G 4.7 36.5 1.0 N C:GLU101 4.8 30.4 1.0 O C:HOH302 4.8 35.6 0.4 CZ C:ARG100 4.8 34.0 0.6 HG3 C:GLU101 5.0 45.4 0.6

Sodium binding site 4 out of 7 in the Crystal Structure of the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody)


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 Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:33.6 occ:1.00 O D:GLU100G 2.2 33.0 1.0 O D:HOH328 2.3 33.2 1.0 OD1 D:ASP95 2.4 28.4 1.0 OE1 D:GLU101 2.4 32.1 0.3 OE2 D:GLU101 2.5 31.8 0.3 O D:HOH420 2.5 43.1 0.7 O D:HOH314 2.6 39.4 1.0 OE2 D:GLU101 2.7 33.2 0.7 CD D:GLU101 2.8 31.0 0.3 OE1 D:GLU101 2.9 34.3 0.7 HH22 D:ARG100 2.9 45.1 0.6 CD D:GLU101 3.0 33.3 0.7 HH21 D:ARG100 3.0 45.1 0.6 H D:TYR96 3.3 27.4 1.0 NH2 D:ARG100 3.3 37.6 0.6 C D:GLU100G 3.4 31.2 1.0 HA D:ASP95 3.4 27.6 1.0 CG D:ASP95 3.5 26.0 1.0 HB3 D:GLU100G 3.6 42.9 1.0 N D:TYR96 3.8 22.9 1.0 HA D:GLU100G 3.9 40.0 1.0 HA D:TYR100H 4.1 32.6 1.0 CA D:ASP95 4.1 23.0 1.0 O D:TYR96 4.1 24.2 1.0 CA D:GLU100G 4.1 33.4 1.0 H D:GLU101 4.2 33.1 0.3 H D:GLU101 4.2 33.1 0.7 HB3 D:TYR96 4.2 28.5 1.0 CB D:ASP95 4.2 24.3 1.0 C D:ASP95 4.2 22.7 1.0 OH J:TYR142 4.2 31.5 1.0 HG3 D:GLU101 4.3 38.7 0.7 CG D:GLU101 4.3 30.3 0.3 CG D:GLU101 4.3 32.2 0.7 HH J:TYR142 4.3 37.8 1.0 O D:HOH310 4.3 54.3 1.0 CB D:GLU100G 4.3 35.7 1.0 OD2 D:ASP95 4.4 25.9 1.0 HB2 D:ASP95 4.4 29.2 1.0 N D:TYR100H 4.5 28.9 1.0 CZ D:ARG100 4.6 36.6 0.6 N D:GLU101 4.6 27.6 1.0 HG2 D:GLU101 4.6 36.4 0.3 CA D:TYR100H 4.7 27.2 1.0 OE1 D:GLU100G 4.7 43.1 1.0 HG3 D:GLU101 4.7 36.4 0.3 CA D:TYR96 4.7 23.1 1.0 HB2 D:GLU100G 4.8 42.9 1.0 C D:TYR96 4.8 24.0 1.0 HH22 D:ARG100 4.9 47.8 0.4 HG2 D:GLU101 4.9 38.7 0.7 CB D:TYR96 4.9 23.7 1.0 C D:TYR100H 5.0 28.2 1.0 HB2 D:GLU101 5.0 36.1 0.7

Sodium binding site 5 out of 7 in the Crystal Structure of the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody)


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 the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody) within 5.0Å range: probe atom residue distance (Å) B Occ E:Na201 b:45.1 occ:1.00 O E:HOH320 2.0 44.3 1.0 O E:GLU100G 2.2 36.9 1.0 OE1 E:GLU101 2.2 46.0 0.5 O E:HOH318 2.4 35.6 1.0 OD1 E:ASP95 2.4 34.4 1.0 OE1 E:GLU101 2.5 46.0 0.5 O E:HOH424 2.5 55.8 0.5 OE2 E:GLU101 2.6 48.6 0.5 O E:HOH416 2.6 36.7 0.3 CD E:GLU101 2.8 46.7 0.5 CD E:GLU101 3.1 46.7 0.5 C E:GLU100G 3.4 32.6 1.0 OE2 E:GLU101 3.4 49.0 0.5 HH22 E:ARG100 3.4 45.0 0.7 HB3 E:GLU100G 3.5 40.0 1.0 HH21 E:ARG100 3.5 45.0 0.7 CG E:ASP95 3.6 29.5 1.0 H E:TYR96 3.6 32.8 1.0 NH2 E:ARG100 3.7 37.5 0.7 HA E:ASP95 3.7 30.6 1.0 HA E:GLU100G 3.9 39.6 1.0 HA E:TYR100H 4.0 33.6 1.0 OH K:TYR142 4.0 29.6 1.0 CA E:GLU100G 4.1 33.0 1.0 HH K:TYR142 4.1 35.5 1.0 O E:HOH441 4.2 53.6 1.0 N E:TYR96 4.2 27.3 1.0 CB E:GLU100G 4.2 33.3 1.0 OE1 E:GLU100G 4.2 39.2 1.0 CG E:GLU101 4.3 43.5 0.5 OD2 E:ASP95 4.4 29.7 1.0 N E:TYR100H 4.4 29.2 1.0 CA E:ASP95 4.4 25.5 1.0 O E:TYR96 4.4 32.2 1.0 CB E:ASP95 4.4 25.9 1.0 CG E:GLU101 4.5 43.5 0.5 O E:HOH452 4.5 56.4 1.0 HG2 E:GLU101 4.5 52.3 0.5 H E:GLU101 4.5 40.1 1.0 HG2 E:GLU101 4.6 52.2 0.5 CA E:TYR100H 4.6 28.0 1.0 HB3 E:TYR96 4.6 37.0 1.0 HB2 E:ASP95 4.6 31.0 1.0 C E:ASP95 4.6 25.9 1.0 O E:HOH418 4.6 49.3 1.0 HB2 E:GLU100G 4.7 40.0 1.0 HG3 E:GLU101 4.7 52.2 0.5 N E:GLU101 4.8 33.4 1.0 CZ E:ARG100 4.8 35.9 0.7 C E:TYR100H 4.9 31.4 1.0

Sodium binding site 6 out of 7 in the Crystal Structure of the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody)


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 the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody) within 5.0Å range: probe atom residue distance (Å) B Occ F:Na201 b:32.7 occ:1.00 O F:GLU100G 2.2 30.7 1.0 OD1 F:ASP95 2.3 28.3 1.0 OE2 F:GLU101 2.4 37.2 0.5 O F:HOH308 2.4 33.1 1.0 OE1 F:GLU101 2.4 34.5 0.5 O F:HOH303 2.4 34.1 1.0 OE1 F:GLU101 2.6 32.3 0.5 CD F:GLU101 2.7 35.5 0.5 OE2 F:GLU101 2.8 33.4 0.5 CD F:GLU101 3.0 32.5 0.5 H F:TYR96 3.2 26.5 1.0 HH21 F:ARG100 3.2 44.6 0.6 HH22 F:ARG100 3.3 44.6 0.6 HA F:ASP95 3.3 26.3 1.0 C F:GLU100G 3.4 28.7 1.0 CG F:ASP95 3.5 25.8 1.0 NH2 F:ARG100 3.5 37.1 0.6 O F:HOH423 3.5 25.4 0.4 HB3 F:GLU100G 3.5 36.1 1.0 N F:TYR96 3.7 22.1 1.0 O F:TYR96 3.9 24.2 1.0 HA F:GLU100G 4.0 35.0 1.0 CA F:ASP95 4.0 21.9 1.0 HA F:TYR100H 4.0 31.5 1.0 HB3 F:TYR96 4.0 28.8 1.0 C F:ASP95 4.1 21.9 1.0 CA F:GLU100G 4.1 29.1 1.0 H F:GLU101 4.2 33.0 0.5 H F:GLU101 4.2 33.0 0.5 CB F:ASP95 4.2 23.4 1.0 CG F:GLU101 4.2 33.5 0.5 OH L:TYR142 4.2 26.8 1.0 HH L:TYR142 4.3 32.1 1.0 CB F:GLU100G 4.3 30.1 1.0 CG F:GLU101 4.4 31.6 0.5 OD2 F:ASP95 4.4 26.4 1.0 HB2 F:ASP95 4.4 28.0 1.0 O F:HOH435 4.4 35.9 0.8 OE1 F:GLU100G 4.4 34.2 1.0 N F:TYR100H 4.4 26.7 1.0 O F:HOH340 4.5 48.5 1.0 HG3 F:GLU101 4.5 38.0 0.5 HG2 F:GLU101 4.5 40.3 0.5 CA F:TYR96 4.6 22.9 1.0 N F:GLU101 4.6 27.5 1.0 HG3 F:GLU101 4.6 40.3 0.5 C F:TYR96 4.6 22.8 1.0 CA F:TYR100H 4.6 26.2 1.0 CB F:TYR96 4.8 24.0 1.0 HB2 F:GLU100G 4.8 36.1 1.0 CZ F:ARG100 4.8 37.0 0.6 HB2 F:GLU101 4.9 35.9 0.5 C F:TYR100H 4.9 27.9 1.0 HG2 F:GLU101 5.0 38.0 0.5

Sodium binding site 7 out of 7 in the Crystal Structure of the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody)


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 the Phosphorylated C-Terminal Tail of Histone H2AX in Complex with A Specific Nanobody (C6 Gammaxbody) within 5.0Å range: probe atom residue distance (Å) B Occ F:Na202 b:27.0 occ:0.45 O F:HOH400 2.3 25.2 1.0 O F:HOH350 2.4 25.6 1.0 O F:HOH439 3.6 53.4 1.0 O F:HOH394 4.0 44.1 1.0 H F:THR57 4.2 24.2 1.0 O F:THR57 4.2 22.5 1.0 O F:HOH343 4.2 41.2 1.0 O F:HOH366 4.3 23.8 1.0 OG1 F:THR57 4.3 20.8 1.0 O F:HOH426 4.4 50.9 1.0 HG1 F:THR57 4.6 24.9 1.0 HG23 F:THR56 5.0 29.9 1.0

E.Moeglin, D.Desplancq, A.Stoessel, C.Massute, J.Ranniger, A.G.Mcewen, G.Zeder-Lutz, M.Oulad-Abdelghani, M.Chiper, P.Lafaye, P.Didier, A.Poterszman, E.Weiss. A Novel Nanobody Precisely Visualizes Phosphorylated Histone H2AX in Living Cancer Cells Under Drug-Induced Replication Stress Cancers (Basel) V. 13 2021.
ISSN: ESSN 2072-6694
DOI: 10.3390/CANCERS13133317