Magnesium in PDB 5npu: Inferred Ancestral Pyruvate Decarboxylase

The structure of Inferred Ancestral Pyruvate Decarboxylase, PDB code: 5npu was solved by L.Buddrus, S.J.Crennell, D.J.Leak, M.J.Danson, E.S.V.Andrews, V.L.Arcus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.10 / 3.50
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.330, 108.330, 322.651, 90.00, 90.00, 120.00
R / Rfree (%)	24.6 / 31.9

The binding sites of Magnesium atom in the Inferred Ancestral Pyruvate Decarboxylase (pdb code 5npu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Inferred Ancestral Pyruvate Decarboxylase, PDB code: 5npu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Inferred Ancestral Pyruvate Decarboxylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Inferred Ancestral Pyruvate Decarboxylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:25.1 occ:1.00 HD21 A:ASN468 1.5 94.3 1.0 ND2 A:ASN468 2.0 78.6 1.0 OD1 A:ASN468 2.2 0.6 1.0 OD1 A:ASP441 2.2 44.3 1.0 O1B A:TPP602 2.2 0.4 1.0 CG A:ASN468 2.3 86.2 1.0 O2B A:TPP602 2.4 0.8 1.0 O1A A:TPP602 2.6 41.6 1.0 PB A:TPP602 2.7 52.6 1.0 HD22 A:ASN468 2.8 94.3 1.0 H A:ASP441 2.9 50.5 1.0 O A:ILE466 3.3 35.5 1.0 CG A:ASP441 3.4 43.3 1.0 O A:GLY470 3.4 47.6 1.0 HA3 A:GLY440 3.4 59.3 1.0 H A:ASN468 3.5 82.9 1.0 N A:ASP441 3.6 42.1 1.0 PA A:TPP602 3.7 31.9 1.0 O3A A:TPP602 3.7 0.3 1.0 HA2 A:GLY440 3.7 59.3 1.0 HG1 A:THR472 3.7 91.1 1.0 CB A:ASN468 3.8 76.2 1.0 OG1 A:THR472 3.9 75.9 1.0 H A:THR472 3.9 31.4 1.0 CA A:GLY440 4.0 49.5 1.0 N A:ASN468 4.0 69.1 1.0 O3B A:TPP602 4.0 99.0 1.0 H A:GLY442 4.0 46.7 1.0 HB3 A:ASN468 4.1 91.5 1.0 HG22 A:ILE466 4.1 36.9 1.0 OD2 A:ASP441 4.2 28.2 1.0 HB A:THR472 4.2 58.4 1.0 H A:GLY470 4.3 71.0 1.0 C A:GLY440 4.3 43.8 1.0 CB A:ASP441 4.3 57.6 1.0 HB2 A:ASN468 4.4 91.5 1.0 HB3 A:ASP441 4.4 69.1 1.0 CA A:ASN468 4.4 70.1 1.0 O2A A:TPP602 4.4 27.5 1.0 HB A:ILE466 4.5 47.4 1.0 C A:ILE466 4.5 35.9 1.0 CA A:ASP441 4.6 52.0 1.0 HA A:ASN467 4.6 30.3 1.0 HH22 A:ARG368 4.6 0.7 1.0 CB A:THR472 4.6 48.6 1.0 C A:GLY470 4.7 48.3 1.0 N A:THR472 4.7 26.2 1.0 N A:GLY442 4.8 38.9 1.0 C A:ASN467 4.8 37.1 1.0 C A:ASN468 4.9 70.6 1.0 H A:ARG469 4.9 54.9 1.0 CG2 A:ILE466 4.9 30.8 1.0 HA A:TYR471 5.0 46.0 1.0 O7 A:TPP602 5.0 67.0 1.0

Magnesium binding site 2 out of 4 in the Inferred Ancestral Pyruvate Decarboxylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Inferred Ancestral Pyruvate Decarboxylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:61.8 occ:1.00 O2B B:TPP602 1.7 73.6 1.0 OD1 B:ASP441 1.9 62.9 1.0 OD1 B:ASN468 2.1 97.4 1.0 O2A B:TPP602 2.4 97.8 1.0 O B:GLY470 2.5 92.2 1.0 HD21 B:ASN468 2.8 96.9 1.0 PB B:TPP602 2.9 74.1 1.0 CG B:ASN468 3.0 91.3 1.0 HG1 B:THR472 3.0 0.6 1.0 H B:ASP441 3.0 92.6 1.0 CG B:ASP441 3.1 65.5 1.0 ND2 B:ASN468 3.2 80.7 1.0 H B:THR472 3.3 96.3 1.0 H B:GLY442 3.4 0.5 1.0 PA B:TPP602 3.4 0.2 1.0 O3A B:TPP602 3.5 90.8 1.0 O1B B:TPP602 3.6 72.2 1.0 H B:GLY470 3.6 0.1 1.0 HA3 B:GLY440 3.6 79.7 1.0 N B:ASP441 3.7 77.1 1.0 OG1 B:THR472 3.7 0.5 1.0 H B:ASN468 3.7 97.3 1.0 C B:GLY470 3.7 0.6 1.0 OD2 B:ASP441 3.7 63.9 1.0 HD22 B:ASN468 4.0 96.9 1.0 HA B:TYR471 4.1 0.6 1.0 O B:ILE466 4.1 71.4 1.0 O3B B:TPP602 4.1 73.5 1.0 N B:THR472 4.1 80.2 1.0 HB B:THR472 4.1 0.9 1.0 HA2 B:GLY440 4.1 79.7 1.0 N B:GLY442 4.2 0.2 1.0 CA B:GLY440 4.2 66.4 1.0 CB B:ASP441 4.3 70.9 1.0 N B:GLY470 4.4 92.6 1.0 CB B:ASN468 4.4 93.3 1.0 C B:GLY440 4.4 73.6 1.0 N B:ASN468 4.4 81.1 1.0 CB B:THR472 4.4 0.4 1.0 CA B:ASP441 4.5 74.0 1.0 O7 B:TPP602 4.5 0.2 1.0 HB3 B:ASP441 4.5 85.1 1.0 O1A B:TPP602 4.5 93.7 1.0 N B:TYR471 4.6 91.6 1.0 CA B:GLY470 4.7 98.6 1.0 CA B:TYR471 4.7 89.7 1.0 H B:ARG469 4.8 0.2 1.0 CA B:ASN468 4.8 92.5 1.0 HB2 B:ASN468 4.8 0.9 1.0 C B:ASN468 4.9 93.4 1.0 C B:ASP441 4.9 80.8 1.0 HA3 B:GLY442 4.9 0.8 1.0 HA B:ASN467 4.9 92.4 1.0 HB3 B:ASN468 4.9 0.9 1.0 N B:ARG469 4.9 95.2 1.0 CA B:THR472 4.9 81.3 1.0 C B:TYR471 5.0 90.3 1.0 HD1 B:TYR471 5.0 87.9 1.0

Magnesium binding site 3 out of 4 in the Inferred Ancestral Pyruvate Decarboxylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Inferred Ancestral Pyruvate Decarboxylase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:0.5 occ:1.00 O1B C:TPP602 1.9 0.9 1.0 OD1 C:ASP441 2.1 0.6 1.0 OD1 C:ASN468 2.1 0.7 1.0 O1A C:TPP602 2.2 99.5 1.0 O C:GLY470 2.4 0.8 1.0 HG1 C:THR472 2.8 0.2 1.0 HD21 C:ASN468 2.9 0.8 1.0 PB C:TPP602 3.0 0.2 1.0 CG C:ASN468 3.0 0.5 1.0 H C:THR472 3.1 0.1 1.0 CG C:ASP441 3.3 1.0 1.0 H C:ASP441 3.3 0.5 1.0 H C:GLY442 3.3 0.2 1.0 O2B C:TPP602 3.3 0.2 1.0 ND2 C:ASN468 3.3 0.5 1.0 PA C:TPP602 3.3 0.2 1.0 O3A C:TPP602 3.5 99.7 1.0 OG1 C:THR472 3.6 0.7 1.0 C C:GLY470 3.6 0.8 1.0 H C:GLY470 3.7 0.9 1.0 HA3 C:GLY440 3.7 0.6 1.0 HA C:TYR471 3.8 0.8 1.0 N C:ASP441 3.8 0.3 1.0 OD2 C:ASP441 3.8 0.7 1.0 N C:THR472 3.9 0.1 1.0 H C:ASN468 3.9 0.5 1.0 HB C:THR472 4.0 0.2 1.0 N C:GLY442 4.1 96.0 1.0 HD22 C:ASN468 4.2 0.8 1.0 O3B C:TPP602 4.3 0.7 1.0 O7 C:TPP602 4.3 0.9 1.0 CB C:THR472 4.3 1.0 1.0 HA2 C:GLY440 4.4 0.6 1.0 N C:GLY470 4.4 0.1 1.0 CA C:GLY440 4.4 0.5 1.0 O C:ILE466 4.4 1.0 1.0 CB C:ASP441 4.4 0.7 1.0 O2A C:TPP602 4.4 94.9 1.0 CB C:ASN468 4.5 0.4 1.0 N C:TYR471 4.5 1.0 1.0 CA C:TYR471 4.5 0.8 1.0 C C:GLY440 4.5 97.4 1.0 CA C:ASP441 4.6 0.8 1.0 N C:ASN468 4.6 0.3 1.0 CA C:GLY470 4.6 0.9 1.0 HA3 C:GLY442 4.7 0.6 1.0 HB3 C:ASP441 4.7 0.1 1.0 HD1 C:TYR471 4.7 0.8 1.0 C C:TYR471 4.7 0.4 1.0 CA C:THR472 4.8 0.6 1.0 HB2 C:ASN468 4.8 0.0 1.0 CA C:ASN468 4.9 0.3 1.0 C C:ASP441 4.9 99.3 1.0 C C:ASN468 4.9 0.4 1.0

Magnesium binding site 4 out of 4 in the Inferred Ancestral Pyruvate Decarboxylase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Inferred Ancestral Pyruvate Decarboxylase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:75.6 occ:1.00 O2A D:TPP602 1.9 82.6 1.0 O D:GLY470 2.1 81.5 1.0 OD1 D:ASN468 2.1 0.7 1.0 OD1 D:ASP441 2.2 89.0 1.0 O2B D:TPP602 2.3 85.3 1.0 HG1 D:THR472 2.7 0.6 1.0 HD21 D:ASN468 2.8 0.5 1.0 H D:THR472 2.9 0.5 1.0 CG D:ASN468 3.0 99.9 1.0 PB D:TPP602 3.2 83.6 1.0 PA D:TPP602 3.3 84.4 1.0 O3B D:TPP602 3.3 82.2 1.0 ND2 D:ASN468 3.3 0.2 1.0 C D:GLY470 3.3 81.5 1.0 CG D:ASP441 3.4 85.4 1.0 H D:GLY442 3.4 0.6 1.0 H D:ASP441 3.4 0.5 1.0 H D:GLY470 3.5 0.7 1.0 OG1 D:THR472 3.5 0.5 1.0 HA D:TYR471 3.7 0.7 1.0 O3A D:TPP602 3.7 82.2 1.0 N D:THR472 3.8 0.3 1.0 HA3 D:GLY440 3.9 93.9 1.0 OD2 D:ASP441 3.9 85.0 1.0 H D:ASN468 3.9 99.0 1.0 HB D:THR472 4.0 0.6 1.0 N D:ASP441 4.0 91.2 1.0 HD22 D:ASN468 4.1 0.5 1.0 O7 D:TPP602 4.1 0.0 1.0 N D:GLY470 4.2 83.9 1.0 N D:TYR471 4.2 0.7 1.0 O1A D:TPP602 4.2 81.5 1.0 CB D:THR472 4.2 0.3 1.0 N D:GLY442 4.3 0.5 1.0 CA D:TYR471 4.3 0.1 1.0 CA D:GLY470 4.4 82.0 1.0 CB D:ASN468 4.4 90.1 1.0 O D:ILE466 4.4 82.3 1.0 HA2 D:GLY440 4.5 93.9 1.0 CA D:GLY440 4.6 78.3 1.0 CB D:ASP441 4.6 89.9 1.0 C D:TYR471 4.6 1.0 1.0 N D:ASN468 4.6 82.5 1.0 O1B D:TPP602 4.6 84.5 1.0 CA D:THR472 4.7 0.8 1.0 C D:GLY440 4.7 78.2 1.0 HD1 D:TYR471 4.7 0.8 1.0 CA D:ASP441 4.8 93.8 1.0 HA3 D:GLY442 4.8 0.0 1.0 HB2 D:ASN468 4.8 0.1 1.0 HB3 D:ASP441 4.8 0.8 1.0 CA D:ASN468 4.9 82.1 1.0 C D:ASN468 4.9 80.4 1.0 HA3 D:GLY470 4.9 98.4 1.0 H D:ARG469 5.0 0.3 1.0 N D:ARG469 5.0 91.1 1.0

L.Buddrus, E.S.V.Andrews, D.J.Leak, M.J.Danson, V.L.Arcus, S.J.Crennell. Crystal Structure of An Inferred Ancestral Bacterial Pyruvate Decarboxylase. Acta Crystallogr F Struct V. 74 179 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 29497023
DOI: 10.1107/S2053230X18002819