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

Protein crystallography data

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

Other elements in 6zwk:

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

Sodium Binding Sites:

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 6zwk

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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 6zwk

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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 6zwk

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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 6zwk

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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 6zwk

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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 6zwk

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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 6zwk

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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

Reference:

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
Page generated: Sat Aug 21 17:19:28 2021

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