Sodium in PDB 4u9w: Crystal Structure of Natd Bound to H4/H2A Peptide and Coa

The structure of Crystal Structure of Natd Bound to H4/H2A Peptide and Coa, PDB code: 4u9w was solved by R.S.Magin, G.P.Liszczak, R.Marmorstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.24 / 2.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.901, 93.288, 100.329, 90.00, 96.69, 90.00
R / Rfree (%)	17.6 / 22.3

The binding sites of Sodium atom in the Crystal Structure of Natd Bound to H4/H2A Peptide and Coa (pdb code 4u9w). 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 Natd Bound to H4/H2A Peptide and Coa, PDB code: 4u9w:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Natd Bound to H4/H2A Peptide and Coa


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 Natd Bound to H4/H2A Peptide and Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:24.1 occ:1.00 C2P A:COA301 2.7 22.2 1.0 S1P A:COA301 2.8 30.0 1.0 N A:VAL140 3.0 12.8 1.0 NE2 A:GLN141 3.0 16.2 1.0 O A:VAL140 3.4 13.4 1.0 C3P A:COA301 3.4 19.2 1.0 OE2 A:GLU139 3.5 17.8 1.0 N4P A:COA301 3.5 21.2 1.0 CA A:GLU139 3.5 12.5 1.0 N F:SER1 3.6 16.3 1.0 C A:GLU139 3.7 14.5 1.0 CB F:SER1 3.7 22.1 1.0 CA F:SER1 3.8 19.5 1.0 C A:VAL140 3.9 13.4 1.0 CA A:VAL140 4.0 14.4 1.0 OG F:SER1 4.0 20.3 1.0 CD A:GLN141 4.1 15.9 1.0 CG1 A:VAL140 4.3 14.8 1.0 CB A:GLU139 4.3 14.9 1.0 CG A:GLN141 4.4 13.3 1.0 O A:TYR138 4.5 15.3 1.0 CD A:GLU139 4.5 16.3 1.0 N A:GLU139 4.6 13.1 1.0 C5P A:COA301 4.7 18.7 1.0 CB A:VAL140 4.8 14.3 1.0 O A:GLU139 4.9 16.5 1.0 N A:GLN141 5.0 12.5 1.0 C A:TYR138 5.0 12.2 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Natd Bound to H4/H2A Peptide and Coa


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 Natd Bound to H4/H2A Peptide and Coa within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:36.8 occ:1.00 C2P C:COA301 2.5 24.4 1.0 N C:VAL140 2.9 16.7 1.0 NE2 C:GLN141 3.1 28.2 1.0 N G:SER1 3.2 23.5 1.0 CA C:GLU139 3.2 22.7 1.0 CA G:SER1 3.3 23.2 1.0 OE2 C:GLU139 3.3 26.4 1.0 S1P C:COA301 3.5 37.0 1.0 C C:GLU139 3.5 22.3 1.0 O C:VAL140 3.7 28.4 1.0 CB G:SER1 3.7 25.9 1.0 C3P C:COA301 3.8 27.2 1.0 O C:TYR138 3.9 27.6 1.0 CD C:GLU139 3.9 28.3 1.0 N4P C:COA301 3.9 26.8 1.0 CG C:GLU139 3.9 31.4 1.0 CB C:GLU139 4.1 27.2 1.0 CA C:VAL140 4.1 19.8 1.0 N C:GLU139 4.1 23.5 1.0 OG G:SER1 4.2 23.9 1.0 C C:VAL140 4.2 23.2 1.0 CD C:GLN141 4.2 29.1 1.0 CG1 C:VAL140 4.3 21.7 1.0 C C:TYR138 4.4 25.9 1.0 CG C:GLN141 4.6 22.8 1.0 O C:GLU139 4.7 23.7 1.0 C G:SER1 4.8 25.0 1.0 CB C:VAL140 4.8 23.6 1.0 OE1 C:GLU139 4.9 24.7 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Natd Bound to H4/H2A Peptide and Coa


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 Natd Bound to H4/H2A Peptide and Coa within 5.0Å range: probe atom residue distance (Å) B Occ E:Na101 b:34.6 occ:1.00 C2P B:COA301 2.5 24.1 1.0 S1P B:COA301 2.7 38.4 1.0 N E:SER1 2.7 23.1 1.0 CA E:SER1 3.2 19.6 1.0 N B:VAL140 3.3 13.1 1.0 CA B:GLU139 3.6 16.2 1.0 C3P B:COA301 3.7 19.8 1.0 CB E:SER1 3.7 22.1 1.0 C B:GLU139 3.8 14.9 1.0 NE2 B:GLN141 4.0 17.3 1.0 OE2 B:GLU139 4.0 24.1 1.0 O B:TYR138 4.0 17.2 1.0 O B:VAL140 4.1 16.9 1.0 CG1 B:VAL140 4.2 12.6 1.0 N4P B:COA301 4.2 20.5 1.0 N B:GLU139 4.3 15.6 1.0 OG E:SER1 4.3 19.4 1.0 CA B:VAL140 4.4 12.3 1.0 C B:TYR138 4.5 13.8 1.0 O E:HOH201 4.6 12.8 1.0 CD B:GLU139 4.6 17.6 1.0 C E:SER1 4.6 21.4 1.0 C B:VAL140 4.6 14.6 1.0 CB B:GLU139 4.7 17.5 1.0 CG B:GLU139 4.7 20.6 1.0 O B:THR174 4.8 19.7 1.0 CB B:VAL140 4.9 14.2 1.0 O B:GLU139 5.0 12.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Natd Bound to H4/H2A Peptide and Coa


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 Natd Bound to H4/H2A Peptide and Coa within 5.0Å range: probe atom residue distance (Å) B Occ H:Na101 b:36.4 occ:1.00 N H:SER1 2.6 29.3 1.0 C2P D:COA301 2.6 28.2 1.0 S1P D:COA301 2.6 40.9 1.0 CA H:SER1 3.0 31.9 1.0 N D:VAL140 3.4 24.3 1.0 CB H:SER1 3.4 29.8 1.0 CA D:GLU139 3.6 26.7 1.0 C3P D:COA301 3.7 24.8 1.0 OE1 D:GLU139 3.8 36.7 1.0 O D:TYR138 3.9 29.3 1.0 C D:GLU139 3.9 25.5 1.0 NE2 D:GLN141 4.0 26.3 1.0 OG H:SER1 4.1 28.1 1.0 O D:VAL140 4.1 21.8 1.0 N4P D:COA301 4.3 27.2 1.0 CG1 D:VAL140 4.3 25.6 1.0 N D:GLU139 4.3 27.6 1.0 C D:TYR138 4.4 26.3 1.0 C H:SER1 4.5 31.6 1.0 O D:HOH414 4.5 23.8 1.0 CA D:VAL140 4.5 22.6 1.0 CB D:GLU139 4.6 24.4 1.0 CD D:GLU139 4.7 32.5 1.0 O D:THR174 4.7 25.7 1.0 C D:VAL140 4.7 24.5 1.0

R.S.Magin, G.P.Liszczak, R.Marmorstein. The Molecular Basis For Histone H4- and H2A-Specific Amino-Terminal Acetylation By Natd. Structure V. 23 332 2015.
ISSN: ISSN 0969-2126
PubMed: 25619998
DOI: 10.1016/J.STR.2014.10.025