Magnesium in PDB 8wwo: Crystal Structure of the Afsv Topoisomerase Atpase Domain in Complex with Amppnp

The structure of Crystal Structure of the Afsv Topoisomerase Atpase Domain in Complex with Amppnp, PDB code: 8wwo was solved by W.Kuang, Z.Deng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.96 / 2.20
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	85.658, 85.658, 212.071, 90, 90, 120
R / Rfree (%)	17.6 / 22.1

The binding sites of Magnesium atom in the Crystal Structure of the Afsv Topoisomerase Atpase Domain in Complex with Amppnp (pdb code 8wwo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Afsv Topoisomerase Atpase Domain in Complex with Amppnp, PDB code: 8wwo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Afsv Topoisomerase Atpase Domain in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Afsv Topoisomerase Atpase Domain in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:22.0 occ:1.00 O2B A:ANP501 1.9 17.8 1.0 OD1 A:ASN64 2.0 17.1 1.0 O3G A:ANP501 2.0 17.9 1.0 O2A A:ANP501 2.2 17.5 1.0 O A:HOH618 2.4 16.2 1.0 O A:HOH737 2.4 17.5 1.0 PB A:ANP501 3.0 20.2 1.0 CG A:ASN64 3.1 17.5 1.0 PA A:ANP501 3.3 19.2 1.0 PG A:ANP501 3.3 18.8 1.0 O3A A:ANP501 3.4 19.0 1.0 ND2 A:ASN64 3.5 16.5 1.0 N3B A:ANP501 3.6 18.8 1.0 O A:HOH650 3.7 21.0 1.0 O A:HOH693 4.0 16.4 1.0 O5' A:ANP501 4.2 17.8 1.0 CA A:GLY142 4.2 19.8 1.0 OE1 A:GLU60 4.3 19.6 1.0 O1G A:ANP501 4.3 18.1 1.0 O1B A:ANP501 4.3 18.4 1.0 O A:GLU60 4.3 20.7 1.0 O2G A:ANP501 4.3 20.7 1.0 CB A:ASN64 4.4 22.0 1.0 O1A A:ANP501 4.5 18.9 1.0 OD2 A:ASP67 4.6 21.7 1.0 CA A:ASN64 4.6 20.0 1.0 CA A:GLY147 4.7 16.1 1.0 N A:ASN64 4.7 19.8 1.0 N A:GLY147 4.8 16.9 1.0 N A:LEU148 4.9 19.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Afsv Topoisomerase Atpase Domain in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Afsv Topoisomerase Atpase Domain in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:21.9 occ:1.00 O2B B:ANP501 1.8 15.7 1.0 OD1 B:ASN64 2.0 18.5 1.0 O3G B:ANP501 2.1 19.1 1.0 O2A B:ANP501 2.2 18.2 1.0 O B:HOH756 2.3 17.8 1.0 O B:HOH622 2.4 20.6 1.0 PB B:ANP501 3.0 17.2 1.0 CG B:ASN64 3.0 17.2 1.0 PG B:ANP501 3.3 19.8 1.0 PA B:ANP501 3.4 17.6 1.0 O3A B:ANP501 3.5 17.9 1.0 ND2 B:ASN64 3.5 17.1 1.0 O B:HOH632 3.6 21.5 1.0 N3B B:ANP501 3.6 17.4 1.0 O B:HOH662 4.1 15.2 1.0 CA B:GLY142 4.2 19.3 1.0 O5' B:ANP501 4.2 18.2 1.0 OE1 B:GLU60 4.3 20.5 1.0 O1B B:ANP501 4.3 18.1 1.0 CB B:ASN64 4.3 19.9 1.0 O1G B:ANP501 4.3 21.6 1.0 O B:GLU60 4.4 20.3 1.0 O2G B:ANP501 4.4 15.6 1.0 CA B:ASN64 4.5 19.6 1.0 OD2 B:ASP67 4.5 22.9 1.0 O1A B:ANP501 4.6 18.1 1.0 N B:ASN64 4.6 19.8 1.0 CA B:GLY147 4.8 17.0 1.0 N B:GLY147 4.9 16.7 1.0 N B:LEU148 5.0 19.1 1.0 N B:GLY142 5.0 20.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Afsv Topoisomerase Atpase Domain in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Afsv Topoisomerase Atpase Domain in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:22.8 occ:1.00 O3G C:ANP501 2.0 19.5 1.0 O2B C:ANP501 2.0 20.5 1.0 O2A C:ANP501 2.1 20.4 1.0 OD1 C:ASN64 2.2 18.6 1.0 O C:HOH646 2.2 20.1 1.0 O C:HOH755 2.4 19.2 1.0 PB C:ANP501 3.0 18.3 1.0 CG C:ASN64 3.2 17.2 1.0 PG C:ANP501 3.2 19.7 1.0 PA C:ANP501 3.3 17.6 1.0 O3A C:ANP501 3.4 20.4 1.0 N3B C:ANP501 3.5 19.2 1.0 ND2 C:ASN64 3.6 17.9 1.0 O C:HOH640 3.9 20.4 1.0 O C:HOH642 3.9 19.5 1.0 O1G C:ANP501 4.1 22.4 1.0 O5' C:ANP501 4.2 20.1 1.0 CA C:GLY142 4.2 17.4 1.0 OE1 C:GLU60 4.2 18.6 1.0 O1B C:ANP501 4.3 19.2 1.0 O2G C:ANP501 4.3 18.4 1.0 O C:GLU60 4.4 18.8 1.0 O1A C:ANP501 4.5 19.6 1.0 CB C:ASN64 4.5 19.1 1.0 CA C:GLY147 4.7 16.4 1.0 OD2 C:ASP67 4.7 21.0 1.0 CA C:ASN64 4.7 20.5 1.0 N C:GLY147 4.8 16.0 1.0 N C:ASN64 4.9 20.0 1.0 N C:LEU148 4.9 18.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Afsv Topoisomerase Atpase Domain in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Afsv Topoisomerase Atpase Domain in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:22.9 occ:1.00 O2B D:ANP501 2.0 20.8 1.0 O3G D:ANP501 2.0 20.2 1.0 O2A D:ANP501 2.1 20.1 1.0 O D:HOH723 2.1 18.4 1.0 OD1 D:ASN64 2.1 18.7 1.0 O D:HOH619 2.3 20.9 1.0 PB D:ANP501 3.0 18.6 1.0 CG D:ASN64 3.1 17.9 1.0 PG D:ANP501 3.2 19.4 1.0 PA D:ANP501 3.3 18.6 1.0 O3A D:ANP501 3.4 21.4 1.0 N3B D:ANP501 3.5 17.8 1.0 ND2 D:ASN64 3.6 17.4 1.0 O D:HOH665 3.9 21.1 1.0 O D:HOH765 4.1 14.7 1.0 O1G D:ANP501 4.1 21.9 1.0 O5' D:ANP501 4.2 21.5 1.0 CA D:GLY142 4.3 20.2 1.0 OE1 D:GLU60 4.3 19.7 1.0 O D:GLU60 4.3 20.0 1.0 O1B D:ANP501 4.3 20.6 1.0 O2G D:ANP501 4.4 17.0 1.0 CB D:ASN64 4.5 20.6 1.0 O1A D:ANP501 4.5 20.1 1.0 CA D:GLY147 4.6 19.4 1.0 N D:GLY147 4.7 18.2 1.0 CA D:ASN64 4.7 20.7 1.0 OD2 D:ASP67 4.8 22.5 1.0 N D:LEU148 4.8 20.2 1.0 N D:ASN64 4.8 20.3 1.0

Z.Deng, W.Kuang, Z.Deng. N/A N/A.