Magnesium in PDB 8dpd: Superfolder Gfp TYR74PCNPHE Mutant

The structure of Superfolder Gfp TYR74PCNPHE Mutant, PDB code: 8dpd was solved by C.M.Phillips-Piro, B.Papoutsis, J.Piacentini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.90 / 1.51
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	47.222, 47.222, 346.153, 90, 90, 120
R / Rfree (%)	20.8 / 25.2

The binding sites of Magnesium atom in the Superfolder Gfp TYR74PCNPHE Mutant (pdb code 8dpd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Superfolder Gfp TYR74PCNPHE Mutant, PDB code: 8dpd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Superfolder Gfp TYR74PCNPHE Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Superfolder Gfp TYR74PCNPHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg307 b:25.1 occ:1.00 H A:TRP57 2.3 24.5 1.0 H12 A:EDO305 2.5 57.6 1.0 O A:HOH512 3.0 32.7 1.0 HB2 A:TRP57 3.0 24.1 1.0 O A:HOH470 3.0 28.2 1.0 HA A:PRO56 3.0 25.2 1.0 HD3 A:PRO58 3.1 24.7 1.0 O A:HOH446 3.1 30.7 1.0 HD1 A:TRP57 3.1 28.4 1.0 N A:TRP57 3.1 20.4 1.0 HD1 A:TYR143 3.2 27.9 1.0 HD2 A:PRO58 3.4 24.7 1.0 HB3 A:PRO56 3.4 28.4 1.0 C1 A:EDO305 3.6 48.0 1.0 CD A:PRO58 3.7 20.6 1.0 CA A:PRO56 3.7 21.0 1.0 CB A:TRP57 3.8 20.1 1.0 H22 A:EDO305 3.8 56.6 1.0 CD1 A:TRP57 3.8 23.7 1.0 C A:PRO56 3.9 18.2 1.0 CD1 A:TYR143 4.0 23.2 1.0 CA A:TRP57 4.0 22.4 1.0 CB A:PRO56 4.0 23.6 1.0 C2 A:EDO305 4.2 47.2 1.0 CG A:TRP57 4.2 20.9 1.0 H11 A:EDO305 4.2 57.6 1.0 HE1 A:TYR143 4.2 29.8 1.0 O1 A:EDO305 4.2 50.8 1.0 HO1 A:EDO305 4.4 60.9 1.0 H21 A:EDO305 4.4 56.6 1.0 HB2 A:TYR143 4.5 29.6 1.0 HB2 A:PRO56 4.5 28.4 1.0 CE1 A:TYR143 4.5 24.8 1.0 HB3 A:TRP57 4.6 24.1 1.0 HZ3 A:LYS209 4.6 28.9 1.0 O A:HOH448 4.7 26.0 1.0 N A:PRO58 4.7 16.0 1.0 HA A:TRP57 4.7 26.9 1.0 HG2 A:PRO58 4.8 22.2 1.0 CG A:PRO58 4.8 18.5 1.0 O A:HOH617 4.8 46.9 1.0 C A:TRP57 4.9 17.4 1.0 HA A:TYR143 4.9 26.0 1.0 CG A:TYR143 5.0 28.3 1.0

Magnesium binding site 2 out of 4 in the Superfolder Gfp TYR74PCNPHE Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Superfolder Gfp TYR74PCNPHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg308 b:23.9 occ:1.00 H A:LEU207 2.5 22.1 1.0 HA A:VAL206 2.7 22.8 1.0 HA A:ASN144 2.8 28.1 1.0 H A:PHE145 2.8 22.5 1.0 N A:LEU207 3.3 18.4 1.0 HB2 A:ASN144 3.3 25.8 1.0 HG A:LEU207 3.4 22.7 1.0 N A:PHE145 3.4 18.8 1.0 O A:HOH433 3.4 32.8 1.0 CA A:ASN144 3.5 23.4 1.0 HG13 A:VAL206 3.5 28.1 1.0 CA A:VAL206 3.6 19.0 1.0 CB A:ASN144 3.7 21.5 1.0 HB3 A:ASN144 3.7 25.8 1.0 HB2 A:LEU207 3.9 22.7 1.0 C A:ASN144 3.9 17.8 1.0 O A:SER205 4.0 33.4 1.0 C A:VAL206 4.0 19.5 1.0 HG22 A:VAL206 4.2 25.7 1.0 HB2 A:PHE145 4.2 22.2 1.0 CG A:LEU207 4.2 18.9 1.0 O A:PHE145 4.2 21.3 1.0 O A:HOH551 4.3 36.0 1.0 CA A:LEU207 4.3 19.6 1.0 CB A:LEU207 4.3 18.9 1.0 O A:LEU207 4.3 25.8 1.0 HB3 A:PHE145 4.3 22.2 1.0 CG1 A:VAL206 4.4 23.4 1.0 CA A:PHE145 4.4 17.1 1.0 CB A:VAL206 4.5 19.0 1.0 N A:VAL206 4.5 24.4 1.0 CB A:PHE145 4.5 18.5 1.0 C A:SER205 4.6 36.4 1.0 HG12 A:VAL206 4.7 28.1 1.0 O A:TYR143 4.7 22.1 1.0 N A:ASN144 4.8 20.3 1.0 C A:PHE145 4.8 22.3 1.0 C A:LEU207 4.8 22.9 1.0 CG2 A:VAL206 4.8 21.4 1.0 HD23 A:LEU207 4.8 21.7 1.0 HD12 A:LEU207 4.9 23.7 1.0 O A:ASN144 5.0 17.6 1.0

Magnesium binding site 3 out of 4 in the Superfolder Gfp TYR74PCNPHE Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Superfolder Gfp TYR74PCNPHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg309 b:33.5 occ:1.00 OG A:SER28 3.0 24.3 1.0 HG21 A:THR50 3.1 29.1 1.0 HG22 A:THR50 3.1 29.1 1.0 HG23 A:THR50 3.1 29.1 1.0 CG2 A:THR50 3.3 24.2 1.0 HB2 A:SER28 3.3 27.5 1.0 HG A:SER28 3.6 29.2 1.0 CB A:SER28 3.7 22.9 1.0 O A:HOH484 3.8 38.4 1.0 HB3 A:SER28 4.1 27.5 1.0 HG1 A:THR49 4.5 33.2 1.0 OG1 A:THR49 4.7 27.7 1.0 CB A:THR50 4.8 26.7 1.0 H11 A:EDO302 4.8 56.6 1.0 OD1 A:ASP19 4.9 37.0 1.0 CA A:SER28 5.0 20.4 1.0

Magnesium binding site 4 out of 4 in the Superfolder Gfp TYR74PCNPHE Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Superfolder Gfp TYR74PCNPHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg310 b:44.4 occ:1.00 HG23 A:THR186 2.3 46.7 1.0 HG21 A:THR186 2.9 46.7 1.0 CG2 A:THR186 3.0 38.9 1.0 HG12 A:VAL93 3.2 31.4 1.0 O A:GLN184 3.2 27.8 1.0 OE1 A:GLU95 3.2 43.5 1.0 HB2 A:GLN184 3.2 43.3 1.0 HA A:ASN185 3.3 34.8 1.0 H A:THR186 3.3 35.0 1.0 HG3 A:GLU95 3.4 30.4 1.0 O A:VAL93 3.4 27.4 1.0 HB A:VAL93 3.5 32.2 1.0 N A:THR186 3.5 29.2 1.0 HE2 A:LYS158 3.6 80.5 1.0 OG1 A:THR186 3.6 49.0 1.0 C A:GLN184 3.6 34.0 1.0 HG1 A:THR186 3.6 58.9 1.0 HG22 A:THR186 3.7 46.7 1.0 CB A:THR186 3.8 35.8 1.0 HB2 A:GLU95 3.8 29.2 1.0 C A:ASN185 3.8 30.4 1.0 CA A:ASN185 3.8 28.9 1.0 H A:GLU95 3.9 24.6 1.0 N A:ASN185 3.9 26.1 1.0 CD A:GLU95 4.0 41.7 1.0 CG1 A:VAL93 4.0 26.2 1.0 CB A:GLN184 4.0 36.1 1.0 CG A:GLU95 4.0 25.3 1.0 HB3 A:GLN184 4.1 43.3 1.0 C A:VAL93 4.1 21.7 1.0 CB A:VAL93 4.2 26.8 1.0 CA A:THR186 4.2 34.8 1.0 HG11 A:VAL93 4.3 31.4 1.0 HA A:GLN94 4.3 24.7 1.0 CB A:GLU95 4.4 24.3 1.0 N A:GLU95 4.4 20.5 1.0 CE A:LYS158 4.4 67.0 1.0 HE3 A:LYS158 4.5 80.5 1.0 CA A:GLN184 4.5 30.1 1.0 H A:ASN185 4.6 31.4 1.0 O A:ASN185 4.6 31.2 1.0 HB A:THR186 4.6 43.0 1.0 HG13 A:VAL93 4.7 31.4 1.0 N A:GLN94 4.7 24.1 1.0 CA A:VAL93 4.8 29.1 1.0 HA A:THR186 4.9 41.8 1.0 CA A:GLN94 4.9 20.6 1.0 HG2 A:GLU95 4.9 30.4 1.0 C A:GLN94 5.0 19.3 1.0 HZ2 A:LYS158 5.0 55.2 1.0

C.M.Phillips-Piro, B.Papoutsis, J.Piacentini. Superfolder Gfp TYR74PCNPHE Mutant To Be Published.