Sodium in PDB 4pp4: Minute Virus of Mice Non-Structural Protein-1N-Terminal Nuclease Domain Reveals A Unique ZN2+ Coordination in the Active Site Pocket and Shows A Novel Mode of Dna Recognition at the Origin of Replication

The structure of Minute Virus of Mice Non-Structural Protein-1N-Terminal Nuclease Domain Reveals A Unique ZN2+ Coordination in the Active Site Pocket and Shows A Novel Mode of Dna Recognition at the Origin of Replication, PDB code: 4pp4 was solved by S.K.Tewary, H.Zhao, L.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.71 / 1.45
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.940, 121.650, 41.820, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 18.5

The binding sites of Sodium atom in the Minute Virus of Mice Non-Structural Protein-1N-Terminal Nuclease Domain Reveals A Unique ZN2+ Coordination in the Active Site Pocket and Shows A Novel Mode of Dna Recognition at the Origin of Replication (pdb code 4pp4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Minute Virus of Mice Non-Structural Protein-1N-Terminal Nuclease Domain Reveals A Unique ZN2+ Coordination in the Active Site Pocket and Shows A Novel Mode of Dna Recognition at the Origin of Replication, PDB code: 4pp4:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Minute Virus of Mice Non-Structural Protein-1N-Terminal Nuclease Domain Reveals A Unique ZN2+ Coordination in the Active Site Pocket and Shows A Novel Mode of Dna Recognition at the Origin of Replication


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Minute Virus of Mice Non-Structural Protein-1N-Terminal Nuclease Domain Reveals A Unique ZN2+ Coordination in the Active Site Pocket and Shows A Novel Mode of Dna Recognition at the Origin of Replication within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:22.2 occ:1.00 OG A:SER231 2.7 15.2 1.0 OD1 A:ASP91 2.7 13.1 1.0 O A:HOH409 3.0 16.6 1.0 HG A:LEU229 3.0 23.8 1.0 HG12 A:VAL116 3.0 22.9 1.0 HB3 A:SER231 3.1 16.9 1.0 HD2 A:HIS118 3.2 13.2 1.0 HZ1 A:LYS95 3.3 19.4 1.0 HG A:SER231 3.3 18.2 1.0 HA A:SER230 3.3 15.9 1.0 C A:SER230 3.4 15.4 1.0 N A:SER231 3.4 12.8 1.0 CB A:SER231 3.4 14.1 1.0 HG11 A:VAL116 3.4 22.9 1.0 CG A:ASP91 3.5 12.2 1.0 H A:SER231 3.5 15.4 1.0 HB A:VAL116 3.5 20.7 1.0 HD23 A:LEU229 3.5 26.7 1.0 CG1 A:VAL116 3.6 19.1 1.0 OD2 A:ASP91 3.7 15.0 1.0 CA A:SER230 3.7 13.2 1.0 O A:SER230 3.8 14.9 1.0 CG A:LEU229 3.8 19.8 1.0 HZ2 A:LYS95 3.8 19.4 1.0 HD21 A:LEU229 3.8 26.7 1.0 CD2 A:HIS118 3.8 11.0 1.0 NZ A:LYS95 3.9 16.2 1.0 HE3 A:LYS95 3.9 18.8 1.0 CD2 A:LEU229 3.9 22.3 1.0 CA A:SER231 4.0 12.0 1.0 N A:SER230 4.0 14.5 1.0 O A:VAL116 4.0 17.0 1.0 NE2 A:HIS118 4.0 12.7 1.0 CB A:VAL116 4.1 17.3 1.0 C A:LEU229 4.2 14.8 1.0 O A:LEU229 4.2 15.5 1.0 HB2 A:SER231 4.2 16.9 1.0 HB3 A:LEU229 4.3 22.2 1.0 CE A:LYS95 4.4 15.6 1.0 H A:SER230 4.4 17.4 1.0 HG13 A:VAL116 4.5 22.9 1.0 C A:VAL116 4.5 13.6 1.0 HG21 A:THR66 4.5 18.7 1.0 CB A:LEU229 4.6 18.5 1.0 HB2 A:ASP91 4.6 13.8 1.0 HZ3 A:LYS95 4.6 19.4 1.0 HA A:GLN117 4.7 13.1 1.0 HA A:SER231 4.7 14.4 1.0 CB A:ASP91 4.7 11.5 1.0 HE2 A:LYS95 4.8 18.8 1.0 HD11 A:LEU229 4.8 29.4 1.0 H A:HIS118 4.8 13.4 1.0 HD22 A:LEU229 4.9 26.7 1.0 CD1 A:LEU229 4.9 24.5 1.0 CA A:VAL116 4.9 11.8 1.0 C A:SER231 5.0 13.7 1.0

Sodium binding site 2 out of 3 in the Minute Virus of Mice Non-Structural Protein-1N-Terminal Nuclease Domain Reveals A Unique ZN2+ Coordination in the Active Site Pocket and Shows A Novel Mode of Dna Recognition at the Origin of Replication


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Minute Virus of Mice Non-Structural Protein-1N-Terminal Nuclease Domain Reveals A Unique ZN2+ Coordination in the Active Site Pocket and Shows A Novel Mode of Dna Recognition at the Origin of Replication within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:30.9 occ:1.00 H A:LEU51 2.0 23.7 1.0 HA A:GLU50 2.6 24.2 1.0 O A:LYS49 2.8 19.8 1.0 O A:HOH401 2.8 14.4 1.0 HG A:LEU51 2.8 22.4 1.0 N A:LEU51 2.9 19.8 1.0 HG23 A:ILE89 3.1 16.7 1.0 HB2 A:LEU51 3.1 22.0 1.0 HD12 A:LEU51 3.4 26.6 1.0 CA A:GLU50 3.5 20.2 1.0 CG A:LEU51 3.5 18.7 1.0 HD22 A:LEU93 3.6 19.0 1.0 CB A:LEU51 3.6 18.3 1.0 C A:GLU50 3.7 18.6 1.0 HG A:LEU56 3.7 50.5 1.0 HD21 A:LEU56 3.7 29.2 1.0 HD23 A:LEU56 3.8 29.2 1.0 C A:LYS49 3.8 17.3 1.0 CA A:LEU51 3.8 22.2 1.0 HG12 A:ILE89 3.9 17.5 1.0 O A:HOH407 3.9 20.4 1.0 CD1 A:LEU51 3.9 22.2 1.0 CG2 A:ILE89 3.9 13.9 1.0 HG21 A:ILE89 4.0 16.7 1.0 N A:GLU50 4.1 22.0 1.0 CD2 A:LEU56 4.1 24.3 1.0 HB2 A:ALA160 4.2 21.5 1.0 HD11 A:LEU51 4.3 26.6 1.0 CG A:LEU56 4.4 42.1 1.0 CD2 A:LEU93 4.4 15.8 1.0 HD13 A:ILE89 4.4 21.3 1.0 HB1 A:ALA160 4.5 21.5 1.0 O A:LEU51 4.5 23.0 1.0 HD11 A:LEU93 4.5 20.0 1.0 HG A:LEU93 4.5 17.4 1.0 HB3 A:LEU51 4.5 22.0 1.0 HA A:LEU51 4.5 26.6 1.0 HG22 A:ILE89 4.5 16.7 1.0 HG2 A:GLU50 4.6 26.6 1.0 HD21 A:LEU93 4.6 19.0 1.0 CG1 A:ILE89 4.6 14.6 1.0 C A:LEU51 4.7 24.4 1.0 CB A:GLU50 4.7 23.9 1.0 OE1 A:GLN60 4.7 19.4 1.0 OG A:SER92 4.7 15.2 1.0 HD13 A:LEU51 4.8 26.6 1.0 HB3 A:GLU50 4.8 28.7 1.0 CB A:ALA160 4.8 17.9 1.0 HG A:SER92 4.8 18.3 1.0 CB A:ILE89 4.9 13.4 1.0 CD2 A:LEU51 4.9 23.5 1.0 O A:GLU50 4.9 24.0 1.0 HA A:ILE89 4.9 15.5 1.0 H A:GLU50 4.9 26.4 1.0 CG A:LEU93 5.0 14.5 1.0 HD23 A:LEU51 5.0 28.2 1.0 HB2 A:LYS49 5.0 20.8 1.0 CD1 A:ILE89 5.0 17.8 1.0

Sodium binding site 3 out of 3 in the Minute Virus of Mice Non-Structural Protein-1N-Terminal Nuclease Domain Reveals A Unique ZN2+ Coordination in the Active Site Pocket and Shows A Novel Mode of Dna Recognition at the Origin of Replication


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Minute Virus of Mice Non-Structural Protein-1N-Terminal Nuclease Domain Reveals A Unique ZN2+ Coordination in the Active Site Pocket and Shows A Novel Mode of Dna Recognition at the Origin of Replication within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:48.8 occ:1.00 OG A:SER220 2.6 41.8 1.0 HG A:SER220 2.6 50.2 1.0 OG1 A:THR83 2.7 23.7 1.0 HD3 A:PRO222 2.8 38.0 1.0 HB3 A:SER220 2.9 45.5 1.0 HG1 A:THR83 3.0 28.5 1.0 CB A:SER220 3.2 38.0 1.0 HG21 A:THR83 3.3 22.2 1.0 HB2 A:ASP80 3.4 46.1 1.0 HA A:SER220 3.5 46.5 1.0 HA A:PRO221 3.6 45.4 1.0 HG3 A:PRO222 3.6 59.9 1.0 CB A:THR83 3.7 20.6 1.0 CD A:PRO222 3.7 31.7 1.0 HB A:THR83 3.7 24.7 1.0 OD2 A:ASP80 3.8 48.0 1.0 CG2 A:THR83 3.9 18.5 1.0 CA A:SER220 3.9 38.8 1.0 CG A:PRO222 4.1 49.9 1.0 H A:ASP80 4.1 34.8 1.0 HB2 A:SER220 4.1 45.5 1.0 HG23 A:THR83 4.1 22.2 1.0 CB A:ASP80 4.2 38.5 1.0 HD2 A:PRO222 4.3 38.0 1.0 HG2 A:PRO222 4.3 59.9 1.0 CG A:ASP80 4.3 63.9 1.0 O A:HOH482 4.3 26.9 1.0 HZ2 A:TRP44 4.4 18.4 1.0 O A:HOH557 4.4 34.3 1.0 HG13 A:VAL79 4.4 28.8 1.0 CA A:PRO221 4.5 37.8 1.0 O A:HOH637 4.5 44.0 1.0 N A:PRO222 4.6 34.6 1.0 HG22 A:THR83 4.7 22.2 1.0 HB3 A:ASP80 4.8 46.1 1.0 N A:ASP80 4.8 29.0 1.0 C A:SER220 4.9 46.6 1.0 O A:THR219 4.9 35.6 1.0 C A:PRO221 5.0 30.4 1.0

S.K.Tewary, L.Liang, Z.Lin, A.Lynn, S.F.Cotmore, P.Tattersall, H.Zhao, L.Tang. Structures of Minute Virus of Mice Replication Initiator Protein N-Terminal Domain: Insights Into Dna Nicking and Origin Binding. Virology V.476C 61 2014.
ISSN: ISSN 0042-6822
PubMed: 25528417
DOI: 10.1016/J.VIROL.2014.11.022