Sodium in PDB 1yy6: The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide

All present enzymatic activity of The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide:
3.1.2.15;

The structure of The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide, PDB code: 1yy6 was solved by V.Saridakis, Y.Sheng, F.Sarkari, M.Holowaty, K.Shire, T.Nguyen, R.Zhang, J.Liao, W.Lee, A.M.Edwards, C.H.Arrowsmith, L.Frappier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 1.70
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	70.050, 70.050, 45.930, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Sodium atom in the The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide (pdb code 1yy6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 21 binding sites of Sodium where determined in the The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide, PDB code: 1yy6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 21 in the The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1001 b:18.8 occ:1.00 OD2 A:ASP164 2.6 13.8 1.0 O A:HOH2076 2.6 17.5 1.0 OD1 A:ASN163 2.7 11.1 1.0 OE1 A:GLN120 3.0 12.4 1.0 CE A:MET100 3.4 15.6 1.0 CG A:ASP164 3.5 13.7 1.0 CB A:ASP164 3.7 12.2 1.0 CG A:ASN163 3.7 10.7 1.0 CD A:GLN120 3.8 10.1 1.0 CG A:GLN120 3.8 8.6 1.0 ND2 A:ASN163 4.2 9.3 1.0 O A:HOH2023 4.2 24.8 1.0 O A:HOH2157 4.3 32.7 1.0 OG B:SER447 4.4 13.3 1.0 O A:HOH2079 4.4 24.9 1.0 CB A:GLN120 4.4 8.0 1.0 SD A:MET100 4.6 26.7 1.0 CB A:ALA123 4.6 7.6 1.0 OD1 A:ASP164 4.6 14.2 1.0 N A:ASP164 4.7 11.1 1.0 C A:ASN163 4.8 10.9 1.0 CA A:ASP164 4.8 11.1 1.0 O A:ASN163 4.9 11.5 1.0 CB A:ASN163 5.0 10.3 1.0

Sodium binding site 2 out of 21 in the The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1002 b:15.4 occ:1.00 OG A:SER131 2.7 9.2 1.0 O A:SER129 2.9 10.9 1.0 CB A:SER131 3.3 8.5 1.0 CB A:HIS201 3.5 12.5 1.0 N A:SER131 3.5 8.1 1.0 O A:HIS201 3.5 11.8 1.0 C A:TRP130 3.7 8.8 1.0 C A:HIS201 3.7 12.9 1.0 C A:SER129 3.9 11.2 1.0 CA A:SER131 4.0 8.7 1.0 CA A:TRP130 4.1 8.8 1.0 N A:GLY202 4.1 14.0 1.0 O A:TRP130 4.1 10.0 1.0 CA A:HIS201 4.2 12.4 1.0 CA A:GLY202 4.4 15.1 1.0 N A:TRP130 4.5 9.9 1.0 CG A:HIS201 4.7 12.4 1.0 O A:SER131 4.7 9.2 1.0 C A:SER131 4.8 8.5 1.0 N A:HIS201 4.8 12.4 1.0

Sodium binding site 3 out of 21 in the The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1003 b:24.5 occ:1.00 N A:THR128 3.0 13.9 1.0 O A:HOH2033 3.3 40.2 1.0 OG1 A:THR128 3.4 16.4 1.0 CA A:SER127 3.6 14.9 1.0 OG A:SER127 3.7 15.0 1.0 N A:SER129 3.7 12.8 1.0 C A:SER127 3.8 14.0 1.0 CA A:THR128 4.0 13.3 1.0 OG A:SER129 4.0 12.7 1.0 CB A:SER127 4.1 15.6 1.0 O A:HOH2115 4.1 44.0 1.0 CB A:SER129 4.1 13.1 1.0 C A:THR128 4.2 13.8 1.0 CB A:THR128 4.2 14.1 1.0 CA A:SER129 4.6 12.4 1.0 O A:HOH2114 4.6 42.6 1.0 O A:ASP126 4.6 18.5 1.0 CG2 A:THR128 4.8 14.5 1.0 N A:SER127 4.9 16.1 1.0

Sodium binding site 4 out of 21 in the The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1004 b:20.3 occ:1.00 O A:SER87 2.8 10.3 1.0 NZ A:LYS98 2.8 7.9 1.0 CE A:LYS98 3.1 6.7 1.0 CD A:LYS98 3.5 7.6 1.0 NA A:NA1014 3.6 22.9 1.0 C A:SER87 3.7 9.7 1.0 CA A:PRO88 3.8 9.7 1.0 CD A:PRO89 4.1 9.7 1.0 N A:PRO88 4.2 10.0 1.0 C A:PRO88 4.3 9.2 1.0 CD2 A:LEU86 4.3 16.1 1.0 CG A:LEU86 4.3 16.0 1.0 N A:PRO89 4.4 10.4 1.0 CG A:LYS98 4.4 7.3 1.0 O A:LEU86 4.7 8.7 1.0 CB A:LEU86 4.8 13.0 1.0 C A:LEU86 4.8 9.7 1.0 CA A:SER87 4.9 9.0 1.0 N A:SER87 4.9 8.5 1.0

Sodium binding site 5 out of 21 in the The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1005 b:23.6 occ:1.00 NA A:NA1015 2.8 21.3 1.0 O A:HOH2116 2.9 42.3 1.0 O A:PRO88 3.0 8.6 1.0 O A:HOH2117 3.1 29.7 1.0 C A:PRO88 3.6 9.2 1.0 O A:PRO89 3.7 11.7 1.0 CD2 A:PHE71 3.8 8.7 1.0 C A:PRO89 3.8 11.4 1.0 CB A:PRO88 4.1 8.3 1.0 N A:CYS90 4.1 11.1 1.0 CB A:CYS90 4.2 11.0 1.0 N A:PRO89 4.3 10.4 1.0 CA A:PRO88 4.3 9.7 1.0 N A:PRO88 4.4 10.0 1.0 CA A:CYS90 4.4 11.3 1.0 CD A:PRO88 4.4 9.5 1.0 CA A:PRO89 4.4 10.2 1.0 CE2 A:PHE71 4.4 10.1 1.0 CG A:PHE71 4.5 10.3 1.0 OG A:SER87 4.5 8.7 1.0 CB A:PHE71 4.5 9.6 1.0 O A:GLN72 4.7 11.2 1.0 CG A:PRO88 4.8 9.1 1.0 CB A:SER87 4.9 9.2 1.0

Sodium binding site 6 out of 21 in the The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1006 b:17.6 occ:1.00 NZ A:LYS98 2.7 7.9 1.0 NE2 A:GLN120 2.7 7.0 1.0 O A:HOH2111 2.8 27.5 1.0 CE A:LYS98 3.4 6.7 1.0 NA A:NA1011 3.5 21.5 1.0 CD A:LYS98 3.5 7.6 1.0 CD2 A:LEU86 3.6 16.1 1.0 NA A:NA1014 3.7 22.9 1.0 NA A:NA1020 3.7 17.9 1.0 CD A:GLN120 3.7 10.1 1.0 O A:HOH2184 3.9 15.3 1.0 OE1 A:GLN120 4.0 12.4 1.0 CB A:ALA123 4.0 7.6 1.0 O A:HOH2186 4.2 14.6 1.0 O A:HOH2079 4.3 24.9 1.0 N A:GLU124 4.4 12.0 1.0 CG A:LEU86 4.6 16.0 1.0 OE2 A:GLU124 4.7 33.0 1.0 CB A:GLU124 4.7 16.9 1.0 CA A:ALA123 4.8 9.8 1.0 CG A:LYS98 4.8 7.3 1.0 C A:ALA123 4.8 11.2 1.0 N A:ALA123 4.9 8.8 1.0 CG A:GLN120 5.0 8.6 1.0 CD1 A:LEU86 5.0 15.0 1.0 CA A:GLU124 5.0 15.0 1.0

Sodium binding site 7 out of 21 in the The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1007 b:21.0 occ:1.00 O A:TRP130 2.5 10.0 1.0 ND1 A:HIS160 2.9 25.0 1.0 N A:HIS160 2.9 12.1 1.0 O A:THR128 3.3 14.4 1.0 C A:THR128 3.3 13.8 1.0 CB A:HIS160 3.4 17.8 1.0 N A:TRP130 3.4 9.9 1.0 C A:TRP130 3.5 8.8 1.0 CG A:HIS160 3.5 22.7 1.0 CB A:PHE159 3.6 9.6 1.0 CD1 A:TRP130 3.6 10.1 1.0 CA A:HIS160 3.8 14.6 1.0 CA A:THR128 3.8 13.3 1.0 NE1 A:TRP130 3.8 8.6 1.0 N A:SER129 3.8 12.8 1.0 C A:PHE159 3.9 11.4 1.0 CG A:TRP130 3.9 9.3 1.0 CA A:TRP130 3.9 8.8 1.0 CA A:PHE159 3.9 9.8 1.0 C A:SER129 4.0 11.2 1.0 CE1 A:HIS160 4.0 25.8 1.0 CD2 A:PHE159 4.1 10.6 1.0 CE2 A:TRP130 4.2 9.3 1.0 CD2 A:TRP130 4.2 9.8 1.0 CA A:SER129 4.3 12.4 1.0 CG A:PHE159 4.4 10.8 1.0 O A:SER127 4.4 13.0 1.0 CB A:TRP130 4.5 9.4 1.0 N A:THR128 4.7 13.9 1.0 O A:SER129 4.7 10.9 1.0 N A:SER131 4.7 8.1 1.0 CD2 A:HIS160 4.8 24.6 1.0 CB A:THR128 4.8 14.1 1.0 C A:SER127 4.9 14.0 1.0 C A:HIS160 5.0 13.4 1.0 CZ2 A:TRP130 5.0 9.6 1.0 NE2 A:HIS160 5.0 25.6 1.0

Sodium binding site 8 out of 21 in the The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1008 b:22.3 occ:1.00 O A:ASN122 2.6 12.4 1.0 O A:HOH2080 2.7 16.2 1.0 O A:SER125 2.8 15.0 1.0 NE1 A:TRP130 3.1 8.6 1.0 CZ2 A:TRP130 3.6 9.6 1.0 CE2 A:TRP130 3.6 9.3 1.0 C A:SER125 3.7 15.9 1.0 O A:ALA123 3.8 12.1 1.0 C A:ASN122 3.8 11.6 1.0 C A:ALA123 4.0 11.2 1.0 O A:HOH2185 4.0 36.2 1.0 CB A:SER125 4.0 16.3 1.0 O A:SER127 4.0 13.0 1.0 CA A:ALA123 4.1 9.8 1.0 N A:SER125 4.1 14.9 1.0 CA A:SER125 4.1 15.8 1.0 CB A:HIS160 4.1 17.8 1.0 CD1 A:TRP130 4.2 10.1 1.0 CA A:HIS160 4.2 14.6 1.0 N A:ALA123 4.4 8.8 1.0 OG A:SER125 4.6 15.9 1.0 OD1 A:ASN122 4.7 15.8 1.0 O A:HOH2112 4.7 39.0 1.0 CG A:ASN122 4.7 13.6 1.0 N A:GLU124 4.7 12.0 1.0 C A:GLU124 4.8 15.3 1.0 O A:HOH2048 4.8 51.5 1.0 CB A:ASN122 4.8 11.9 1.0 N A:ASP126 4.9 17.0 1.0 CH2 A:TRP130 4.9 9.2 1.0 CD2 A:TRP130 4.9 9.8 1.0 N A:HIS160 4.9 12.1 1.0 ND2 A:ASN163 4.9 9.3 1.0 N A:SER127 5.0 16.1 1.0 CA A:ASN122 5.0 11.7 1.0

Sodium binding site 9 out of 21 in the The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1009 b:19.0 occ:1.00 ND2 A:ASN122 2.5 11.2 1.0 O A:HOH2081 2.9 21.9 1.0 NA A:NA1011 2.9 21.5 1.0 N A:SER125 3.0 14.9 1.0 N A:GLU124 3.3 12.0 1.0 C A:ASN122 3.4 11.6 1.0 CA A:ASN122 3.4 11.7 1.0 CG A:PRO96 3.5 9.4 1.0 CG A:ASN122 3.5 13.6 1.0 O A:ASN122 3.6 12.4 1.0 CB A:SER125 3.7 16.3 1.0 CB A:GLU124 3.7 16.9 1.0 CA A:GLU124 3.7 15.0 1.0 C A:GLU124 3.8 15.3 1.0 N A:ALA123 3.8 8.8 1.0 CA A:SER125 3.8 15.8 1.0 O A:HOH2045 4.0 19.9 1.0 CB A:ASN122 4.1 11.9 1.0 C A:ALA123 4.2 11.2 1.0 CD A:PRO96 4.3 10.3 1.0 OD1 A:ASN122 4.5 15.8 1.0 N A:ASN122 4.6 11.5 1.0 CA A:ALA123 4.6 9.8 1.0 O A:HOH2154 4.6 43.9 1.0 O A:HOH2186 4.8 14.6 1.0 CB A:PRO96 4.8 10.2 1.0 CG A:GLU124 4.9 25.1 1.0 O A:GLU124 4.9 16.0 1.0 OG A:SER125 5.0 15.9 1.0

Sodium binding site 10 out of 21 in the The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Crystal Structure of the N-Terminal Domain of Hausp/USP7 Complexed with An EBNA1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1010 b:22.1 occ:1.00 O A:HOH2121 2.6 34.3 1.0 O A:ASP186 2.8 15.8 1.0 O A:HOH2104 2.8 21.9 1.0 N A:ARG77 3.0 12.3 1.0 O A:ASP187 3.4 12.4 1.0 CB A:ASP187 3.7 14.2 1.0 CG A:LYS188 3.7 12.1 1.0 C A:ASP187 3.8 12.7 1.0 CA A:ARG77 3.8 13.4 1.0 CB A:GLU76 3.9 12.7 1.0 C A:ASP186 3.9 15.3 1.0 C A:GLU76 4.0 12.7 1.0 CA A:GLU76 4.0 12.3 1.0 CA A:ASP187 4.2 13.6 1.0 CG A:ARG77 4.2 21.0 1.0 CE A:LYS188 4.3 20.3 1.0 O A:HOH2052 4.3 40.4 1.0 N A:LYS188 4.4 11.1 1.0 O A:HOH2122 4.5 40.3 1.0 N A:ASP187 4.5 14.2 1.0 CG A:GLU76 4.6 15.7 1.0 CB A:ARG77 4.6 15.8 1.0 CD A:LYS188 4.6 15.0 1.0 CG A:ASP187 4.7 15.9 1.0 CG A:ASP186 4.7 22.1 1.0 OD2 A:ASP186 4.7 23.8 1.0 OE1 A:GLU76 4.8 19.1 1.0 CA A:LYS188 4.8 10.5 1.0 CB A:LYS188 4.8 11.3 1.0 OD1 A:ASP186 4.9 24.9 1.0 O A:HOH2034 4.9 25.1 1.0 OD1 A:ASP187 4.9 16.1 1.0

V.Saridakis, Y.Sheng, F.Sarkari, M.N.Holowaty, K.Shire, T.Nguyen, R.G.Zhang, J.Liao, W.Lee, A.M.Edwards, C.H.Arrowsmith, L.Frappier. Structure of the P53 Binding Domain of Hausp/USP7 Bound to Epstein-Barr Nuclear Antigen 1 Implications For Ebv-Mediated Immortalization. Mol.Cell V. 18 25 2005.
ISSN: ISSN 1097-2765
PubMed: 15808506
DOI: 10.1016/J.MOLCEL.2005.02.029