Magnesium in PDB 5y5p: Crystal Structure of the Dutpase of White Spot Syndrome Virus in Complex with Du,Ppi and MG2+

The structure of Crystal Structure of the Dutpase of White Spot Syndrome Virus in Complex with Du,Ppi and MG2+, PDB code: 5y5p 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)	40.60 / 2.03
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	88.129, 57.266, 110.795, 90.00, 95.67, 90.00
R / Rfree (%)	19.4 / 21.9

The binding sites of Magnesium atom in the Crystal Structure of the Dutpase of White Spot Syndrome Virus in Complex with Du,Ppi and MG2+ (pdb code 5y5p). 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 Dutpase of White Spot Syndrome Virus in Complex with Du,Ppi and MG2+, PDB code: 5y5p:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Dutpase of White Spot Syndrome Virus in Complex with Du,Ppi and MG2+


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 Dutpase of White Spot Syndrome Virus in Complex with Du,Ppi and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:22.9 occ:1.00 O A:HOH664 2.0 18.1 1.0 O A:HOH677 2.0 24.7 1.0 O4 A:POP502 2.0 20.6 1.0 O2 A:POP502 2.0 28.7 1.0 O A:HOH688 2.0 24.9 1.0 O B:HOH310 2.1 22.6 1.0 P2 A:POP502 3.2 22.4 1.0 P1 A:POP502 3.3 25.3 1.0 O A:POP502 3.4 23.4 1.0 O6 A:POP502 3.8 24.1 1.0 O1 A:POP502 3.9 21.1 1.0 NH2 A:ARG161 3.9 25.4 1.0 O A:HOH604 3.9 21.6 1.0 NE B:ARG71 4.0 22.8 1.0 OD1 B:ASP34 4.0 27.0 1.0 OE1 B:GLN118 4.1 29.2 1.0 O B:HOH303 4.3 20.5 1.0 NH2 B:ARG71 4.4 18.4 1.0 O5 A:POP502 4.4 23.0 1.0 OG1 A:THR169 4.4 28.3 1.0 OD2 A:ASP88 4.5 30.5 1.0 O3 A:POP502 4.5 24.8 1.0 O B:HOH336 4.6 22.3 1.0 CZ B:ARG71 4.7 26.6 1.0 OD2 B:ASP34 4.7 25.2 1.0 O5' A:DUR501 4.7 24.8 1.0 CG B:ASP34 4.8 24.1 1.0 CB B:ALA26 4.8 22.9 1.0 C5' A:DUR501 4.8 23.3 1.0 CD B:GLN118 4.8 30.3 1.0 CZ A:ARG161 4.8 38.0 1.0 CD B:ARG71 5.0 22.5 1.0 NH1 A:ARG161 5.0 23.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Dutpase of White Spot Syndrome Virus in Complex with Du,Ppi and MG2+


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 Dutpase of White Spot Syndrome Virus in Complex with Du,Ppi and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:66.5 occ:1.00 O4 B:POP203 2.1 68.1 1.0 O1 B:POP203 2.1 69.6 1.0 O C:HOH350 2.3 42.6 1.0 O B:HOH319 2.6 39.1 1.0 P2 B:POP203 3.3 69.0 1.0 P1 B:POP203 3.3 69.2 1.0 O B:POP203 3.5 72.4 1.0 OE1 C:GLN118 3.7 45.3 1.0 O6 B:POP203 3.8 67.7 1.0 O2 B:POP203 3.8 68.5 1.0 NH2 B:ARG161 4.0 56.5 1.0 O B:HOH330 4.0 30.1 1.0 NE C:ARG71 4.2 42.8 1.0 NH2 C:ARG71 4.2 42.6 1.0 OD1 C:ASP34 4.2 44.5 1.0 OG1 B:THR169 4.4 56.4 1.0 O C:HOH326 4.4 30.9 1.0 O5 B:POP203 4.5 66.7 1.0 O3 B:POP203 4.5 62.1 1.0 OD2 B:ASP88 4.5 51.0 1.0 CD C:GLN118 4.6 53.0 1.0 CZ C:ARG71 4.6 57.1 1.0 O5' B:DUR202 4.7 57.1 1.0 NE2 C:GLN118 4.9 41.3 1.0 CZ B:ARG161 4.9 77.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Dutpase of White Spot Syndrome Virus in Complex with Du,Ppi and MG2+


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 Dutpase of White Spot Syndrome Virus in Complex with Du,Ppi and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:41.9 occ:1.00 O D:HOH607 1.9 34.6 1.0 O F:HOH649 2.0 33.7 1.0 O1 F:POP502 2.1 46.5 1.0 O5 F:POP502 2.1 46.9 1.0 O F:HOH638 2.2 42.6 1.0 O F:HOH607 2.4 41.3 1.0 P2 F:POP502 3.3 49.7 1.0 P1 F:POP502 3.4 47.7 1.0 O F:POP502 3.5 46.3 1.0 O4 F:POP502 3.8 50.3 1.0 O2 F:POP502 3.9 52.8 1.0 OE1 D:GLN118 3.9 39.6 1.0 OD1 D:ASP34 3.9 32.6 1.0 NH1 F:ARG161 4.0 51.2 1.0 NE D:ARG71 4.1 37.0 1.0 NH1 D:ARG71 4.2 40.6 1.0 O F:HOH603 4.2 42.2 1.0 O D:HOH609 4.3 30.6 1.0 OG1 F:THR169 4.3 43.2 1.0 O6 F:POP502 4.5 52.7 1.0 O3 F:POP502 4.6 39.8 1.0 OD2 F:ASP88 4.6 50.8 1.0 CD D:GLN118 4.6 46.4 1.0 CZ D:ARG71 4.7 49.8 1.0 O D:HOH657 4.7 37.6 1.0 O5' F:DUR501 4.8 44.3 1.0 CG D:ASP34 4.8 36.1 1.0 NE2 D:GLN118 4.9 34.6 1.0 CB D:ALA26 4.9 41.1 1.0 OD2 D:ASP34 4.9 43.4 1.0 CZ F:ARG161 4.9 63.9 1.0 C5' F:DUR501 5.0 45.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Dutpase of White Spot Syndrome Virus in Complex with Du,Ppi and MG2+


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 Dutpase of White Spot Syndrome Virus in Complex with Du,Ppi and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:17.9 occ:1.00 O E:HOH338 1.9 20.6 1.0 O5 D:POP502 2.0 21.5 1.0 O D:HOH673 2.0 15.9 1.0 O2 D:POP502 2.1 21.9 1.0 O D:HOH650 2.2 26.7 1.0 O E:HOH301 2.2 24.4 1.0 P2 D:POP502 3.2 21.1 1.0 P1 D:POP502 3.3 21.4 1.0 O D:POP502 3.4 23.2 1.0 O6 D:POP502 3.7 20.4 1.0 NH2 D:ARG161 3.9 21.0 1.0 O3 D:POP502 3.9 18.3 1.0 NE E:ARG71 4.0 26.3 1.0 O D:HOH617 4.0 23.7 1.0 OD1 E:ASP34 4.1 27.0 1.0 NH2 E:ARG71 4.2 19.7 1.0 OE1 E:GLN118 4.2 25.5 1.0 O E:HOH307 4.3 18.5 1.0 OG1 D:THR169 4.3 20.2 1.0 O4 D:POP502 4.4 27.6 1.0 O1 D:POP502 4.5 17.9 1.0 OD2 E:ASP34 4.5 27.9 1.0 OD2 D:ASP88 4.5 32.3 1.0 CZ E:ARG71 4.6 23.3 1.0 O E:HOH332 4.7 25.8 1.0 CG E:ASP34 4.7 27.0 1.0 CB E:ALA26 4.7 21.1 1.0 CZ D:ARG161 4.8 27.7 1.0 O5' D:DUR501 4.8 24.5 1.0 C5' D:DUR501 4.8 23.5 1.0 CD E:GLN118 4.9 31.5 1.0 NH1 D:ARG161 5.0 22.1 1.0 CD E:ARG71 5.0 26.2 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