Magnesium in PDB 4wrk: The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion

The structure of The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion, PDB code: 4wrk was solved by A.A.Bendes, I.Leveles, B.G.Vertessy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.57 / 2.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	108.420, 108.420, 167.050, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.8

The binding sites of Magnesium atom in the The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion (pdb code 4wrk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion, PDB code: 4wrk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:50.4 occ:1.00 O1B A:DUP201 2.1 54.9 1.0 O2G A:DUP201 2.2 58.6 1.0 O1A A:DUP201 2.3 53.7 1.0 PB A:DUP201 3.3 54.8 1.0 PG A:DUP201 3.5 65.2 1.0 PA A:DUP201 3.6 57.1 1.0 O3B A:DUP201 3.7 64.2 1.0 OD1 A:ASP28 3.8 49.6 1.0 N3A A:DUP201 3.8 60.5 1.0 NE A:ARG64 4.1 51.5 1.0 O3G A:DUP201 4.5 70.4 1.0 O2A A:DUP201 4.5 46.2 1.0 O1G A:DUP201 4.5 58.9 1.0 O2B A:DUP201 4.5 50.0 1.0 O5' A:DUP201 4.6 50.9 1.0 CG A:ARG64 4.7 41.0 1.0 CG A:ASP28 4.7 50.4 1.0 OD2 A:ASP28 4.8 51.8 1.0 NH2 A:ARG64 4.8 48.4 1.0 OE1 A:GLN136 4.9 38.5 1.0 CD A:ARG64 4.9 43.9 1.0 CZ A:ARG64 5.0 49.6 1.0

Magnesium binding site 2 out of 6 in the The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:58.4 occ:0.99 O2A B:DUP201 1.8 58.8 1.0 O B:HOH310 1.9 33.8 0.6 O1B B:DUP201 2.6 71.4 1.0 PA B:DUP201 3.2 58.8 1.0 O2G B:DUP201 3.5 63.4 1.0 PB B:DUP201 3.7 69.4 1.0 N3A B:DUP201 3.7 51.7 1.0 OD1 B:ASP28 3.8 42.6 1.0 NE B:ARG64 4.1 48.8 1.0 O5' B:DUP201 4.1 50.9 1.0 OE1 B:GLN136 4.2 40.8 1.0 O1A B:DUP201 4.3 50.4 1.0 O3B B:DUP201 4.3 76.4 1.0 CD B:GLN136 4.4 42.6 1.0 NE2 B:GLN136 4.5 39.8 1.0 PG B:DUP201 4.5 71.9 1.0 CG B:ARG64 4.5 40.3 1.0 NH2 B:ARG64 4.8 52.6 1.0 CD B:ARG64 4.8 39.9 1.0 CZ B:ARG64 4.8 52.2 1.0 O2B B:DUP201 4.9 58.5 1.0 CG B:ASP28 4.9 44.2 1.0 CB B:ARG64 5.0 40.3 1.0

Magnesium binding site 3 out of 6 in the The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:33.7 occ:1.00 O1A C:DUP201 2.0 40.1 1.0 O3G C:DUP201 2.3 40.5 1.0 O1B C:DUP201 2.4 39.2 1.0 PA C:DUP201 3.4 36.4 1.0 PB C:DUP201 3.5 42.0 1.0 PG C:DUP201 3.6 39.1 1.0 OD1 C:ASP28 3.6 39.0 1.0 N3A C:DUP201 3.8 35.1 1.0 O3B C:DUP201 3.9 43.1 1.0 OE1 C:GLN136 3.9 41.0 1.0 O2A C:DUP201 4.1 35.1 1.0 NE C:ARG64 4.2 38.2 1.0 O1G C:DUP201 4.3 39.8 1.0 CD C:GLN136 4.4 35.8 1.0 NE2 C:GLN136 4.5 30.8 1.0 OD2 C:ASP28 4.5 43.1 1.0 CG C:ASP28 4.5 37.9 1.0 O5' C:DUP201 4.5 34.1 1.0 O2G C:DUP201 4.7 36.7 1.0 O2B C:DUP201 4.8 39.3 1.0 CG C:ARG64 4.8 34.8 1.0 NH2 C:ARG64 4.8 40.2 1.0 C5' C:DUP201 4.9 33.9 1.0 CD C:ARG64 5.0 35.3 1.0 CZ C:ARG64 5.0 41.4 1.0

Magnesium binding site 4 out of 6 in the The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg203 b:44.0 occ:1.00 O1B D:DUP201 2.2 54.3 1.0 O1G D:DUP201 2.2 53.5 1.0 O1A D:DUP201 2.7 53.8 1.0 OE1 D:GLN136 3.3 45.6 1.0 PG D:DUP201 3.4 64.0 1.0 PB D:DUP201 3.4 52.9 1.0 OD1 D:ASP28 3.6 41.7 1.0 O3G D:DUP201 3.8 55.9 1.0 O3B D:DUP201 3.8 65.4 1.0 PA D:DUP201 3.9 49.2 1.0 N3A D:DUP201 4.2 47.4 1.0 NE D:ARG64 4.2 44.2 1.0 OD2 D:ASP28 4.3 49.3 1.0 CG D:ASP28 4.4 46.4 1.0 CD D:GLN136 4.5 39.4 1.0 O2B D:DUP201 4.6 48.9 1.0 O2G D:DUP201 4.7 55.6 1.0 O2A D:DUP201 4.7 42.9 1.0 NH2 D:ARG64 4.8 43.8 1.0 CG D:ARG64 4.9 36.1 1.0 CZ D:ARG64 5.0 43.6 1.0 CD D:ARG64 5.0 38.7 1.0

Magnesium binding site 5 out of 6 in the The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:32.4 occ:1.00 O1B F:DUP201 2.4 39.1 1.0 O1A F:DUP201 2.5 41.0 1.0 O3G F:DUP201 2.6 42.9 1.0 O2G F:DUP201 3.4 43.9 1.0 PG F:DUP201 3.5 43.8 1.0 PB F:DUP201 3.6 37.6 1.0 PA F:DUP201 3.8 35.2 1.0 OD1 E:ASP28 3.9 46.4 1.0 O3B F:DUP201 4.0 35.4 1.0 N3A F:DUP201 4.1 36.8 1.0 OE1 E:GLN136 4.3 41.3 1.0 NE E:ARG64 4.3 42.9 1.0 NE2 E:GLN136 4.5 42.4 1.0 CD E:GLN136 4.6 46.0 1.0 O2A F:DUP201 4.7 38.1 1.0 O2B F:DUP201 4.8 35.3 1.0 O1G F:DUP201 4.9 31.7 1.0 CG E:ASP28 4.9 51.6 1.0 NH2 E:ARG64 4.9 37.1 1.0 O5' F:DUP201 4.9 36.0 1.0

Magnesium binding site 6 out of 6 in the The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:43.4 occ:1.00 O F:HOH314 2.3 33.8 1.0 O2G D:DUP202 2.4 46.3 1.0 O2A D:DUP202 2.5 53.5 1.0 O1B D:DUP202 2.5 51.4 1.0 PG D:DUP202 3.6 56.4 1.0 PB D:DUP202 3.8 50.8 1.0 PA D:DUP202 3.9 48.0 1.0 OD1 F:ASP28 3.9 39.1 1.0 O3G D:DUP202 4.1 45.2 1.0 O3B D:DUP202 4.1 55.3 1.0 N3A D:DUP202 4.3 46.6 1.0 NE2 F:GLN136 4.5 34.5 1.0 OD2 F:ASP28 4.5 47.0 1.0 OE1 F:GLN136 4.6 45.5 1.0 CG F:ASP28 4.7 45.1 1.0 O1A D:DUP202 4.7 42.9 1.0 NE F:ARG64 4.7 47.4 1.0 CD F:GLN136 4.8 36.4 1.0 O1G D:DUP202 4.9 50.8 1.0 O5' D:DUP202 4.9 47.1 1.0 O2B D:DUP202 5.0 45.4 1.0

A.A.Bendes, I.Leveles, B.G.Vertessy. The 3D Structure of D95N Mutant Dutpase From Phage PHI11 of S. Aureus Reveals the Molecular Details For the Coordination of A Structural Mg(II) Ion To Be Published.