Magnesium in PDB 5y5q: Crystal Structure of the Wssv Dutpase D88N/R158E Mutant in Complex with Dutp

The structure of Crystal Structure of the Wssv Dutpase D88N/R158E Mutant in Complex with Dutp, PDB code: 5y5q was solved by Q.Ma, K.Zang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.84 / 1.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.574, 75.527, 113.321, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 19.2

The binding sites of Magnesium atom in the Crystal Structure of the Wssv Dutpase D88N/R158E Mutant in Complex with Dutp (pdb code 5y5q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Wssv Dutpase D88N/R158E Mutant in Complex with Dutp, PDB code: 5y5q:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Wssv Dutpase D88N/R158E Mutant in Complex with Dutp


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 Wssv Dutpase D88N/R158E Mutant in Complex with Dutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:22.4 occ:1.00 O1B C:DUT202 2.0 24.0 1.0 O A:HOH604 2.0 21.6 1.0 O C:HOH385 2.1 24.1 1.0 O A:HOH618 2.1 23.1 1.0 O1A C:DUT202 2.1 19.6 1.0 O1G C:DUT202 2.2 28.9 1.0 PB C:DUT202 3.2 24.4 1.0 PA C:DUT202 3.3 20.1 1.0 PG C:DUT202 3.5 34.9 1.0 O3A C:DUT202 3.5 20.9 1.0 O3B C:DUT202 3.6 30.4 1.0 O A:HOH681 4.0 33.1 1.0 NE A:ARG71 4.1 27.7 1.0 OD1 A:ASP34 4.1 29.4 1.0 O A:HOH675 4.1 22.9 1.0 OE1 A:GLN118 4.1 20.6 1.0 NH2 A:ARG71 4.2 26.1 1.0 O2G C:DUT202 4.2 40.1 1.0 O C:HOH308 4.2 30.1 1.0 O C:HOH332 4.3 22.4 1.0 O2A C:DUT202 4.3 20.2 1.0 ND2 C:ASN88 4.3 31.3 1.0 OD2 A:ASP34 4.4 32.1 1.0 O5' C:DUT202 4.4 20.4 1.0 O2B C:DUT202 4.5 26.9 1.0 C5' C:DUT202 4.6 22.9 1.0 O3G C:DUT202 4.6 34.7 1.0 CZ A:ARG71 4.6 39.9 1.0 CG A:ASP34 4.7 28.1 1.0 CD A:GLN118 4.9 19.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Wssv Dutpase D88N/R158E Mutant in Complex with Dutp


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 Wssv Dutpase D88N/R158E Mutant in Complex with Dutp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:21.3 occ:1.00 O A:HOH712 2.0 20.5 1.0 O A:HOH601 2.1 23.2 1.0 O B:HOH306 2.1 19.1 1.0 O1B A:DUT501 2.1 22.2 1.0 O B:HOH369 2.1 20.5 1.0 O1A A:DUT501 2.1 19.5 1.0 PB A:DUT501 3.3 23.6 1.0 PA A:DUT501 3.3 20.4 1.0 O3A A:DUT501 3.6 21.4 1.0 O3B A:DUT501 3.9 28.1 1.0 O B:HOH379 4.0 29.9 1.0 O B:HOH378 4.1 21.8 1.0 NE B:ARG71 4.1 19.8 1.0 O A:HOH710 4.1 29.6 1.0 OD1 B:ASP34 4.1 22.3 1.0 O1G A:DUT501 4.2 34.8 1.0 OE1 B:GLN118 4.2 18.6 1.0 ND2 A:ASN88 4.2 30.8 1.0 O A:HOH612 4.2 19.8 1.0 NH2 B:ARG71 4.3 22.4 1.0 O2A A:DUT501 4.4 19.5 1.0 O5' A:DUT501 4.4 20.0 1.0 OD2 B:ASP34 4.5 23.5 1.0 C5' A:DUT501 4.5 22.4 1.0 O2B A:DUT501 4.5 26.0 1.0 PG A:DUT501 4.6 38.1 1.0 CZ B:ARG71 4.6 23.1 1.0 O3G A:DUT501 4.6 39.9 1.0 CG B:ASP34 4.7 20.2 1.0 CB B:ALA26 5.0 25.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Wssv Dutpase D88N/R158E Mutant in Complex with Dutp


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 Wssv Dutpase D88N/R158E Mutant in Complex with Dutp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:18.8 occ:1.00 O B:HOH304 2.0 26.4 1.0 O C:HOH344 2.0 19.4 1.0 O1B B:DUT202 2.0 21.4 1.0 O1A B:DUT202 2.1 17.2 1.0 O C:HOH305 2.1 18.5 1.0 O B:HOH411 2.1 20.9 1.0 PB B:DUT202 3.2 19.8 1.0 PA B:DUT202 3.3 18.4 1.0 O3A B:DUT202 3.5 19.1 1.0 O3B B:DUT202 3.8 28.8 1.0 O B:HOH320 4.1 27.8 1.0 O C:HOH367 4.1 29.0 1.0 NH2 C:ARG71 4.1 25.2 1.0 NE C:ARG71 4.1 30.4 1.0 OD1 C:ASP34 4.1 29.9 1.0 OE1 C:GLN118 4.2 17.6 1.0 O C:HOH366 4.2 19.9 1.0 O1G B:DUT202 4.3 32.1 1.0 ND2 B:ASN88 4.3 26.6 1.0 O2A B:DUT202 4.3 18.6 1.0 O2G B:DUT202 4.4 40.0 1.0 O B:HOH329 4.4 21.0 1.0 OD2 C:ASP34 4.4 29.1 1.0 O5' B:DUT202 4.4 17.6 1.0 PG B:DUT202 4.4 39.5 1.0 C5' B:DUT202 4.5 17.1 1.0 O2B B:DUT202 4.5 20.8 1.0 CZ C:ARG71 4.6 36.6 1.0 CG C:ASP34 4.7 26.7 1.0 CD C:GLN118 5.0 17.5 1.0

K.Zang, F.Li, Q.Ma. The Dutpase of White Spot Syndrome Virus Assembles Its Active Sites in A Noncanonical Manner. J. Biol. Chem. V. 293 1088 2018.
ISSN: ESSN 1083-351X
PubMed: 29187596
DOI: 10.1074/JBC.M117.815266