Sodium in PDB 4j4s: Triple Mutant Sftavn

The structure of Triple Mutant Sftavn, PDB code: 4j4s was solved by L.Jiao, S.Ouyang, M.Liang, F.Niu, N.Shaw, W.Wu, W.Ding, C.Jin, Y.Zhu, F.Zhang, T.Wang, C.Li, X.Zuo, C.H.Luan, D.Li, Z.J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.81 / 2.44
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	95.489, 108.479, 221.408, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 26.7

The binding sites of Sodium atom in the Triple Mutant Sftavn (pdb code 4j4s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Triple Mutant Sftavn, PDB code: 4j4s:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Triple Mutant Sftavn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Triple Mutant Sftavn within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:53.1 occ:1.00 N A:ASP228 3.0 65.0 1.0 C A:GLY226 3.2 51.1 1.0 CA A:GLY226 3.2 44.4 1.0 N A:PRO227 3.5 58.5 1.0 CB A:ASP228 3.6 81.1 1.0 CA A:ASP228 3.6 67.3 1.0 O A:GLY226 3.6 46.1 1.0 O A:HOH430 3.6 52.0 1.0 N A:VAL230 3.7 52.4 1.0 CB A:VAL230 3.7 52.3 1.0 N A:GLY229 3.8 61.7 1.0 C A:ASP228 3.9 65.4 1.0 N A:GLY226 3.9 44.8 1.0 O A:VAL230 3.9 43.4 1.0 OD2 A:ASP228 3.9 88.6 1.0 CD A:PRO227 4.1 56.0 1.0 C A:PRO227 4.1 62.6 1.0 CA A:VAL230 4.2 48.2 1.0 CG A:ASP228 4.2 88.7 1.0 CA A:PRO227 4.4 55.8 1.0 C A:VAL230 4.5 49.3 1.0 CG2 A:VAL230 4.5 47.9 1.0 CG1 A:VAL230 4.6 37.2 1.0 C A:GLY229 4.7 46.3 1.0 O A:ASP228 4.7 59.2 1.0 CA A:GLY229 4.8 46.4 1.0 CB A:PRO227 4.9 64.8 1.0 O A:HOH444 5.0 59.8 1.0

Sodium binding site 2 out of 8 in the Triple Mutant Sftavn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Triple Mutant Sftavn within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:41.1 occ:1.00 O B:HOH401 2.9 42.5 1.0 N B:ASN17 3.1 51.2 1.0 NZ A:LYS55 3.3 49.5 1.0 CD2 B:LEU21 3.6 36.8 1.0 CG B:LEU21 3.8 43.0 1.0 CD A:LYS55 3.8 40.0 1.0 CD1 B:LEU21 3.8 38.7 1.0 CB B:ASN17 3.8 51.8 1.0 CE A:LYS55 3.9 43.9 1.0 CA B:LEU16 3.9 47.6 1.0 CA B:ASN17 4.0 55.3 1.0 C B:LEU16 4.0 53.6 1.0 CZ2 A:TRP114 4.1 36.6 1.0 NE1 A:TRP114 4.2 39.6 1.0 O B:ASN17 4.2 47.8 1.0 O B:GLN15 4.3 56.7 1.0 CD1 B:LEU16 4.4 48.8 1.0 C B:ASN17 4.5 47.7 1.0 CE2 A:TRP114 4.5 35.7 1.0 CG B:LEU16 4.6 42.9 1.0 OE1 B:GLU20 4.6 57.9 1.0 CB B:LEU16 4.6 41.4 1.0 CD B:GLU20 4.7 60.7 1.0 CG A:LYS55 5.0 40.2 1.0

Sodium binding site 3 out of 8 in the Triple Mutant Sftavn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Triple Mutant Sftavn within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:83.7 occ:1.00 OE2 A:GLU192 2.6 86.0 1.0 CD A:GLU192 3.5 68.8 1.0 CG A:GLU192 3.8 50.5 1.0 OE1 A:GLU192 4.6 65.4 1.0

Sodium binding site 4 out of 8 in the Triple Mutant Sftavn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Triple Mutant Sftavn within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:68.3 occ:1.00 N B:ASP228 2.9 60.0 1.0 CB B:ASP228 3.2 74.3 1.0 CA B:ASP228 3.3 68.8 1.0 C B:ASP228 3.5 81.6 1.0 C B:GLY226 3.6 57.5 1.0 CA B:GLY226 3.7 55.2 1.0 N B:PRO227 3.7 58.5 1.0 N B:GLY229 3.8 77.9 1.0 N B:VAL230 3.8 68.7 1.0 CB B:VAL230 3.9 69.5 1.0 CD B:PRO227 4.1 57.4 1.0 C B:PRO227 4.1 61.7 1.0 O B:ASP228 4.1 86.8 1.0 O B:GLY226 4.1 57.9 1.0 O B:VAL230 4.2 73.5 1.0 CG B:ASP228 4.3 77.6 1.0 CA B:VAL230 4.4 64.9 1.0 N B:GLY226 4.4 65.5 1.0 CA B:PRO227 4.5 61.4 1.0 OD2 B:ASP228 4.6 71.6 1.0 CG B:PRO227 4.6 56.3 1.0 CG2 B:VAL230 4.7 73.8 1.0 CG1 B:VAL230 4.7 65.9 1.0 C B:VAL230 4.7 70.5 1.0 C B:GLY229 4.8 71.3 1.0 CA B:GLY229 4.8 71.7 1.0

Sodium binding site 5 out of 8 in the Triple Mutant Sftavn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Triple Mutant Sftavn within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:86.6 occ:1.00 CD B:ARG26 3.0 42.2 1.0 NH1 B:ARG26 3.5 45.6 1.0 CD C:PRO227 3.6 40.9 1.0 CB B:ARG26 3.9 36.3 1.0 CA C:GLY223 3.9 61.5 1.0 NE B:ARG26 4.0 45.0 1.0 CG B:ARG26 4.0 40.3 1.0 CA C:GLY226 4.1 43.6 1.0 CZ B:ARG26 4.2 47.6 1.0 O C:LEU225 4.2 49.4 1.0 N C:PRO227 4.4 47.8 1.0 O C:LYS220 4.5 56.8 1.0 CG C:PRO227 4.6 37.2 1.0 C C:GLY226 4.6 51.9 1.0 O C:GLY223 4.7 56.9 1.0 C C:GLY223 4.8 54.4 1.0 CA B:ARG26 4.9 45.4 1.0 N C:GLY223 4.9 58.9 1.0 C C:LEU225 5.0 48.3 1.0 N C:GLY226 5.0 42.6 1.0

Sodium binding site 6 out of 8 in the Triple Mutant Sftavn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Triple Mutant Sftavn within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:79.2 occ:1.00 O B:HOH414 2.7 64.0 1.0 CG2 B:THR180 3.1 50.3 1.0 O B:ALA176 3.8 59.9 1.0 O B:HOH405 4.0 61.8 1.0 CG1 B:VAL132 4.4 69.4 1.0 C B:ALA176 4.6 51.8 1.0 CB B:THR180 4.6 59.4 1.0 CB B:ALA176 4.7 45.7 1.0 CG2 B:VAL132 4.8 57.1 1.0 CA B:ALA176 4.9 48.2 1.0

Sodium binding site 7 out of 8 in the Triple Mutant Sftavn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Triple Mutant Sftavn within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:44.3 occ:1.00 N C:ASP228 3.1 60.4 1.0 CG2 C:VAL230 3.3 57.9 1.0 CA C:GLY226 3.5 43.6 1.0 C C:GLY226 3.6 51.9 1.0 CB C:ASP228 3.6 45.6 1.0 CA C:ASP228 3.6 51.5 1.0 N C:GLY229 3.6 61.5 1.0 C C:ASP228 3.7 60.2 1.0 N C:PRO227 3.7 47.8 1.0 N C:VAL230 3.8 57.7 1.0 CD C:PRO227 4.0 40.9 1.0 O C:VAL230 4.1 50.3 1.0 O C:GLY226 4.2 42.6 1.0 N C:GLY226 4.2 42.6 1.0 C C:PRO227 4.3 63.9 1.0 O C:ASP228 4.3 67.5 1.0 CB C:VAL230 4.5 59.5 1.0 CA C:VAL230 4.5 52.9 1.0 CG C:PRO227 4.5 37.2 1.0 CA C:PRO227 4.6 53.5 1.0 CG C:ASP228 4.6 56.5 1.0 CA C:GLY229 4.7 52.2 1.0 C C:GLY229 4.8 59.9 1.0 C C:VAL230 4.8 54.6 1.0 OD2 C:ASP228 4.8 43.9 1.0

Sodium binding site 8 out of 8 in the Triple Mutant Sftavn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Triple Mutant Sftavn within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:80.7 occ:1.00 CG2 D:VAL230 2.6 95.4 1.0 N D:ASP228 3.4 0.0 1.0 CD D:PRO227 3.4 0.9 1.0 CA D:GLY226 3.5 0.4 1.0 N D:PRO227 3.6 0.9 1.0 C D:GLY226 3.7 0.1 1.0 CG D:PRO227 3.8 0.4 1.0 CB D:ASP228 3.9 0.3 1.0 CB D:VAL230 4.0 99.4 1.0 CA D:ASP228 4.0 0.9 1.0 OD2 D:ASP228 4.1 0.2 1.0 N D:VAL230 4.3 0.9 1.0 N D:GLY226 4.4 0.8 1.0 C D:ASP228 4.4 0.1 1.0 C D:PRO227 4.4 0.5 1.0 CA D:PRO227 4.5 0.3 1.0 O D:GLY226 4.5 98.1 1.0 CG D:ASP228 4.5 0.8 1.0 O D:VAL230 4.5 95.9 1.0 N D:GLY229 4.5 0.6 1.0 CA D:VAL230 4.7 0.4 1.0 CB D:PRO227 4.7 0.6 1.0

L.Jiao, S.Ouyang, M.Liang, F.Niu, N.Shaw, W.Wu, W.Ding, C.Jin, Y.Peng, Y.Zhu, F.Zhang, T.Wang, C.Li, X.Zuo, C.H.Luan, D.Li, Z.J.Liu. Structure of Severe Fever with Thrombocytopenia Syndrome Virus Nucleocapsid Protein in Complex with Suramin Reveals Therapeutic Potential J.Virol. V. 87 6829 2013.
ISSN: ISSN 0022-538X
PubMed: 23576501
DOI: 10.1128/JVI.00672-13