Magnesium in PDB 9kbi: The Structure of B19V NS1_2-570/Dsdna/Amppnp

The binding sites of Magnesium atom in the The Structure of B19V NS1_2-570/Dsdna/Amppnp (pdb code 9kbi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the The Structure of B19V NS1_2-570/Dsdna/Amppnp, PDB code: 9kbi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the The Structure of B19V NS1_2-570/Dsdna/Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of B19V NS1_2-570/Dsdna/Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:121.1 occ:1.00 O3G A:ANP601 2.1 141.2 1.0 OG1 A:THR335 2.1 116.2 1.0 O2G A:ANP601 3.0 141.2 1.0 PG A:ANP601 3.1 141.2 1.0 CB A:THR335 3.5 116.2 1.0 OD1 A:ASP372 3.7 98.3 1.0 N3B A:ANP601 3.9 141.2 1.0 NZ A:LYS334 4.0 121.5 1.0 OD2 A:ASP372 4.0 98.3 1.0 O2B A:ANP601 4.0 141.2 1.0 CG2 A:THR335 4.2 116.2 1.0 CG A:ASP372 4.2 98.3 1.0 O1G A:ANP601 4.3 141.2 1.0 CE A:LYS334 4.4 121.5 1.0 N A:THR335 4.4 116.2 1.0 CA A:THR335 4.5 116.2 1.0 OG1 A:THR413 4.5 89.9 1.0 OE1 A:GLU373 4.6 102.4 1.0 PB A:ANP601 4.7 141.2 1.0 CD A:GLU373 4.9 102.4 1.0

Magnesium binding site 2 out of 8 in the The Structure of B19V NS1_2-570/Dsdna/Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of B19V NS1_2-570/Dsdna/Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:131.4 occ:1.00 OG1 D:THR335 2.1 132.7 1.0 O2G D:ANP601 2.2 149.6 1.0 OE1 D:GLU373 2.6 111.2 1.0 OD1 D:ASP372 3.3 107.8 1.0 PG D:ANP601 3.3 149.6 1.0 CD D:GLU373 3.3 111.2 1.0 CB D:THR335 3.4 132.7 1.0 O1G D:ANP601 3.6 149.6 1.0 O2B D:ANP601 3.7 149.6 1.0 N3B D:ANP601 3.8 149.6 1.0 OE2 D:GLU373 3.9 111.2 1.0 CG2 D:THR335 4.1 132.7 1.0 CG D:ASP372 4.2 107.8 1.0 OD2 D:ASP372 4.2 107.8 1.0 CG D:GLU373 4.2 111.2 1.0 OG1 D:THR413 4.4 101.7 1.0 PB D:ANP601 4.5 149.6 1.0 CA D:THR335 4.5 132.7 1.0 N D:THR335 4.6 132.7 1.0 O3G D:ANP601 4.6 149.6 1.0 CB D:THR413 4.9 101.7 1.0 O1A D:ANP601 4.9 149.6 1.0

Magnesium binding site 3 out of 8 in the The Structure of B19V NS1_2-570/Dsdna/Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of B19V NS1_2-570/Dsdna/Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg602 b:111.1 occ:1.00 O3G F:ANP601 2.2 132.9 1.0 OG1 F:THR335 2.5 116.4 1.0 OE1 F:GLU373 2.9 107.7 1.0 OD2 F:ASP372 3.3 103.6 1.0 CB F:THR335 3.3 116.4 1.0 PG F:ANP601 3.6 132.9 1.0 CG2 F:THR335 3.7 116.4 1.0 CD F:GLU373 4.0 107.7 1.0 N3B F:ANP601 4.0 132.9 1.0 O2B F:ANP601 4.1 132.9 1.0 CG F:ASP372 4.2 103.6 1.0 O2G F:ANP601 4.2 132.9 1.0 OD1 F:ASP372 4.3 103.6 1.0 CG F:GLU373 4.3 107.7 1.0 O2A F:ANP601 4.5 132.9 1.0 O1G F:ANP601 4.7 132.9 1.0 CA F:THR335 4.7 116.4 1.0 PB F:ANP601 4.8 132.9 1.0

Magnesium binding site 4 out of 8 in the The Structure of B19V NS1_2-570/Dsdna/Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of B19V NS1_2-570/Dsdna/Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg602 b:133.4 occ:1.00 N3B G:ANP601 2.1 137.3 1.0 O3G G:ANP601 2.1 137.3 1.0 O2B G:ANP601 2.1 137.3 1.0 OG1 G:THR335 2.4 116.5 1.0 PB G:ANP601 2.5 137.3 1.0 PG G:ANP601 2.6 137.3 1.0 CB G:THR335 2.8 116.5 1.0 O2A G:ANP601 3.0 137.3 1.0 O3A G:ANP601 3.0 137.3 1.0 PA G:ANP601 3.2 137.3 1.0 O1A G:ANP601 3.2 137.3 1.0 N G:THR335 3.6 116.5 1.0 O2G G:ANP601 3.6 137.3 1.0 O1G G:ANP601 3.8 137.3 1.0 CA G:THR335 3.8 116.5 1.0 O1B G:ANP601 3.9 137.3 1.0 CG2 G:THR335 4.0 116.5 1.0 NZ G:LYS334 4.3 121.5 1.0 O5' G:ANP601 4.7 137.3 1.0 C G:THR335 4.8 116.5 1.0 C G:LYS334 4.8 121.5 1.0 N G:ASN336 4.9 113.5 1.0 N G:LYS334 4.9 121.5 1.0 OE2 G:GLU373 5.0 102.6 1.0

Magnesium binding site 5 out of 8 in the The Structure of B19V NS1_2-570/Dsdna/Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of B19V NS1_2-570/Dsdna/Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg602 b:108.0 occ:1.00 OG1 H:THR335 2.1 114.9 1.0 O2G H:ANP601 2.1 132.3 1.0 CB H:THR335 3.3 114.9 1.0 PG H:ANP601 3.6 132.3 1.0 CG2 H:THR335 3.7 114.9 1.0 OE1 H:GLU373 3.8 106.5 1.0 OG1 H:THR413 4.2 92.3 1.0 O2B H:ANP601 4.2 132.3 1.0 CG H:ASP372 4.2 102.4 1.0 N3B H:ANP601 4.3 132.3 1.0 OD1 H:ASP372 4.4 102.4 1.0 OD2 H:ASP372 4.4 102.4 1.0 O3G H:ANP601 4.4 132.3 1.0 O1G H:ANP601 4.5 132.3 1.0 CA H:THR335 4.5 114.9 1.0 CB H:ASP372 4.6 102.4 1.0 CD H:GLU373 4.8 106.5 1.0 N H:THR335 4.8 114.9 1.0 PB H:ANP601 5.0 132.3 1.0

Magnesium binding site 6 out of 8 in the The Structure of B19V NS1_2-570/Dsdna/Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of B19V NS1_2-570/Dsdna/Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg602 b:145.3 occ:1.00 O2G I:ANP601 2.0 141.4 1.0 O1B I:ANP601 2.2 141.4 1.0 N3B I:ANP601 2.2 141.4 1.0 OG1 I:THR335 2.4 125.9 1.0 PB I:ANP601 2.4 141.4 1.0 PG I:ANP601 2.6 141.4 1.0 O2A I:ANP601 2.6 141.4 1.0 O3A I:ANP601 2.8 141.4 1.0 CB I:THR335 3.0 125.9 1.0 PA I:ANP601 3.1 141.4 1.0 O1G I:ANP601 3.3 141.4 1.0 O1A I:ANP601 3.4 141.4 1.0 O3G I:ANP601 3.9 141.4 1.0 N I:THR335 3.9 125.9 1.0 O2B I:ANP601 3.9 141.4 1.0 CA I:THR335 4.1 125.9 1.0 CG2 I:THR335 4.1 125.9 1.0 O5' I:ANP601 4.5 141.4 1.0

Magnesium binding site 7 out of 8 in the The Structure of B19V NS1_2-570/Dsdna/Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structure of B19V NS1_2-570/Dsdna/Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg602 b:145.3 occ:1.00 O2G J:ANP601 2.1 159.4 1.0 OG1 J:THR335 2.6 138.4 1.0 OE1 J:GLU373 2.7 121.6 1.0 O2B J:ANP601 2.8 159.4 1.0 PG J:ANP601 3.2 159.4 1.0 O1G J:ANP601 3.4 159.4 1.0 CD J:GLU373 3.7 121.6 1.0 CB J:THR335 3.7 138.4 1.0 N3B J:ANP601 3.8 159.4 1.0 PB J:ANP601 3.9 159.4 1.0 CG J:GLU373 4.0 121.6 1.0 OD1 J:ASP372 4.0 118.5 1.0 O1A J:ANP601 4.2 159.4 1.0 OD2 J:ASP372 4.4 118.5 1.0 NZ J:LYS334 4.5 141.6 1.0 O3G J:ANP601 4.5 159.4 1.0 N J:THR335 4.5 138.4 1.0 OG1 J:THR413 4.6 115.3 1.0 CG2 J:THR335 4.6 138.4 1.0 CG J:ASP372 4.7 118.5 1.0 O3A J:ANP601 4.7 159.4 1.0 CA J:THR335 4.7 138.4 1.0 OE2 J:GLU373 4.8 121.6 1.0 PA J:ANP601 4.8 159.4 1.0 CE J:LYS334 4.9 141.6 1.0 O2A J:ANP601 5.0 159.4 1.0

Magnesium binding site 8 out of 8 in the The Structure of B19V NS1_2-570/Dsdna/Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Structure of B19V NS1_2-570/Dsdna/Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg602 b:113.8 occ:1.00 OG1 L:THR335 2.1 106.3 1.0 O3G L:ANP601 2.1 122.4 1.0 CB L:THR335 2.6 106.3 1.0 CG2 L:THR335 2.9 106.3 1.0 PG L:ANP601 3.5 122.4 1.0 N3B L:ANP601 3.7 122.4 1.0 O2B L:ANP601 3.9 122.4 1.0 CA L:THR335 4.0 106.3 1.0 OD2 L:ASP372 4.1 103.2 1.0 O1A L:ANP601 4.2 122.4 1.0 OD1 L:ASP372 4.3 103.2 1.0 O2G L:ANP601 4.4 122.4 1.0 OE1 L:GLU373 4.5 102.6 1.0 PB L:ANP601 4.5 122.4 1.0 N L:THR335 4.5 106.3 1.0 O1G L:ANP601 4.5 122.4 1.0 O2A L:ANP601 4.6 122.4 1.0 CG L:ASP372 4.7 103.2 1.0 PA L:ANP601 4.8 122.4 1.0 C L:THR335 5.0 106.3 1.0 O3A L:ANP601 5.0 122.4 1.0

Y.Zhang, B.Fan, Y.Gao, J.Yang, W.Zhang, S.Su, L.Li, H.Li, Z.Luo, G.Tang, C.Wang, X.Zhang, H.Liu, J.Gan. Structural and Functional Studies of the Main Replication Protein NS1 of Human Parvovirus B19. Nucleic Acids Res. V. 53 2025.
ISSN: ESSN 1362-4962
PubMed: 40568941
DOI: 10.1093/NAR/GKAF562