Sodium in PDB 3wrn: 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: 3wrn 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)	32.33 / 1.52
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	56.790, 121.430, 41.560, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 19.9

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 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

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 3wrn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 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: 3wrn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 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:Na301 b:31.6 occ:0.89 OG A:SER231 2.7 20.9 1.0 OD1 A:ASP91 2.8 18.1 1.0 O A:HOH411 3.0 25.4 1.0 CB A:SER231 3.3 18.4 1.0 C A:SER230 3.4 18.0 1.0 N A:SER231 3.4 17.3 1.0 CG A:ASP91 3.5 17.8 1.0 CG1 A:VAL116 3.5 24.3 1.0 OD2 A:ASP91 3.7 20.8 1.0 O A:SER230 3.8 19.0 1.0 CA A:SER230 3.8 16.9 1.0 CD2 A:LEU229 3.8 33.5 1.0 CD2 A:HIS118 3.9 14.4 1.0 CG A:LEU229 3.9 30.6 1.0 NZ A:LYS95 3.9 24.9 1.0 O A:VAL116 4.0 21.4 1.0 CA A:SER231 4.0 17.1 1.0 CB A:VAL116 4.1 20.5 1.0 N A:SER230 4.1 20.3 1.0 NE2 A:HIS118 4.1 17.0 1.0 O A:LEU229 4.2 20.7 1.0 C A:LEU229 4.2 21.2 1.0 CE A:LYS95 4.3 20.5 1.0 C A:VAL116 4.5 17.3 1.0 CB A:LEU229 4.6 31.1 1.0 CB A:ASP91 4.8 16.6 1.0 CA A:VAL116 4.9 18.3 1.0 C A:SER231 5.0 17.8 1.0

Sodium binding site 2 out of 2 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:Na302 b:28.2 occ:0.82 O A:LYS49 2.8 30.1 1.0 N A:LEU51 2.8 24.8 1.0 O A:HOH401 2.9 21.6 1.0 CG A:LEU51 3.4 25.2 1.0 CA A:GLU50 3.5 27.3 1.0 C A:GLU50 3.6 31.3 1.0 CB A:LEU51 3.6 27.1 1.0 C A:LYS49 3.8 37.9 1.0 CA A:LEU51 3.8 27.0 1.0 CD1 A:LEU51 3.9 26.9 1.0 CG2 A:ILE89 3.9 19.6 1.0 O A:HOH426 3.9 27.5 1.0 CD2 A:LEU56 4.0 32.2 1.0 N A:GLU50 4.1 35.6 1.0 CG A:LEU56 4.4 60.1 1.0 CD2 A:LEU93 4.4 19.0 1.0 O A:LEU51 4.5 27.6 1.0 CB A:GLU50 4.6 30.7 1.0 C A:LEU51 4.7 25.5 1.0 CD2 A:LEU51 4.7 27.3 1.0 CB A:ALA160 4.7 20.7 1.0 OE1 A:GLN60 4.8 24.5 1.0 CG1 A:ILE89 4.8 19.8 1.0 OG A:SER92 4.8 19.9 1.0 O A:GLU50 4.8 31.5 1.0 CB A:ILE89 4.9 17.0 1.0 CG A:LEU93 5.0 17.0 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