Magnesium in PDB 4dpv: Parvovirus/Dna Complex

The structure of Parvovirus/Dna Complex, PDB code: 4dpv was solved by M.S.Chapman, M.G.Rossmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.90
Space group	P 1 21 1 1
Cell size a, b, c (Å), α, β, γ (°)	263.210, 349.010, 267.320, 90.00, 90.82, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Parvovirus/Dna Complex (pdb code 4dpv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Parvovirus/Dna Complex, PDB code: 4dpv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Parvovirus/Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Parvovirus/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg12 b:1.0 occ:1.00 OP1 N:DC4 2.0 24.6 1.0 OD1 Z:ASN180 2.1 13.6 1.0 OP2 N:DT9 2.2 38.3 1.0 OP1 N:DT6 2.3 26.2 1.0 OP2 N:DC7 2.4 18.8 1.0 CG Z:ASN180 3.3 14.3 1.0 P N:DC4 3.3 24.6 1.0 P N:DT9 3.6 39.2 1.0 P N:DT6 3.6 27.3 1.0 P N:DC7 3.8 21.3 1.0 OP2 N:DC4 3.9 26.7 1.0 ND2 Z:ASN180 4.0 16.7 1.0 O5' N:DT9 4.1 42.7 1.0 O5' N:DC4 4.2 28.3 1.0 OP2 N:DT6 4.2 28.4 1.0 CB Z:ASN180 4.3 11.7 1.0 OP1 N:DC7 4.4 21.9 1.0 O3' N:DT8 4.4 36.7 1.0 C2' N:DT8 4.5 34.3 1.0 O3' N:DT6 4.5 20.9 1.0 O3' N:DA3 4.5 23.0 1.0 O5' N:DT6 4.6 25.0 1.0 O3' N:DC5 4.6 28.9 1.0 C3' N:DT6 4.6 23.8 1.0 C5' N:DC4 4.7 30.6 1.0 OP1 N:DT9 4.7 37.8 1.0 C3' N:DT8 4.8 35.3 1.0 C3' N:DA3 4.9 21.4 1.0 O5' N:DC7 5.0 21.3 1.0

Magnesium binding site 2 out of 4 in the Parvovirus/Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Parvovirus/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg13 b:7.1 occ:1.00 OP1 N:DT9 2.2 37.8 1.0 OP1 N:DA3 2.6 21.4 1.0 P N:DT9 3.6 39.2 1.0 P N:DA3 3.8 22.5 1.0 OP1 N:DC7 3.8 21.9 1.0 O5' N:DA3 3.9 19.7 1.0 O3' N:DT8 4.2 36.7 1.0 OP2 N:DT9 4.2 38.3 1.0 OG Z:SER179 4.2 19.5 1.0 OP1 N:DT2 4.3 57.2 1.0 OP2 N:DA3 4.4 22.0 1.0 C3' N:DT8 4.6 35.3 1.0 O5' N:DT9 4.8 42.7 1.0 OP2 N:DT2 4.9 57.6 1.0 C5' N:DT8 4.9 35.6 1.0 P N:DT2 4.9 55.8 1.0 ND2 Z:ASN180 4.9 16.7 1.0

Magnesium binding site 3 out of 4 in the Parvovirus/Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Parvovirus/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg585 b:1.0 occ:1.00 OD2 Z:ASP240 1.6 10.3 1.0 OD2 Z:ASP237 2.1 14.0 1.0 CG Z:ASP240 2.6 11.9 1.0 OD1 Z:ASP240 3.1 14.4 1.0 CG Z:ASP237 3.3 13.6 1.0 CB Z:ASP237 3.7 12.4 1.0 CB Z:ASP240 4.1 9.8 1.0 OD1 Z:ASP237 4.4 12.6 1.0 MG Z:MG586 4.8 6.4 1.0 NE2 Z:GLN213 4.9 18.2 1.0

Magnesium binding site 4 out of 4 in the Parvovirus/Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Parvovirus/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg586 b:6.4 occ:1.00 OD2 Z:ASP239 1.8 29.7 1.0 OD1 Z:ASP237 2.4 12.6 1.0 CG Z:ASP237 3.0 13.6 1.0 OD2 Z:ASP237 3.0 14.0 1.0 CG Z:ASP239 3.1 28.4 1.0 CB Z:ASP239 3.9 22.0 1.0 OD1 Z:ASP239 4.0 30.7 1.0 CB Z:ASP237 4.4 12.4 1.0 CD Z:PRO238 4.8 11.1 1.0 MG Z:MG585 4.8 1.0 1.0 N Z:ASP239 5.0 13.7 1.0

Q.Xie, M.S.Chapman. Canine Parvovirus Capsid Structure, Analyzed at 2.9 A Resolution. J.Mol.Biol. V. 264 497 1996.
ISSN: ISSN 0022-2836
PubMed: 8969301
DOI: 10.1006/JMBI.1996.0657