Magnesium in PDB 5oyn: Crystal Structure of D-Xylonate Dehydratase in Holo-Form

The structure of Crystal Structure of D-Xylonate Dehydratase in Holo-Form, PDB code: 5oyn was solved by M.M.Rahman, J.Rouvinen, N.Hakulinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.94 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	270.420, 236.130, 65.160, 90.00, 97.38, 90.00
R / Rfree (%)	17.7 / 21.8

The structure of Crystal Structure of D-Xylonate Dehydratase in Holo-Form also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Magnesium atom in the Crystal Structure of D-Xylonate Dehydratase in Holo-Form (pdb code 5oyn). 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 D-Xylonate Dehydratase in Holo-Form, PDB code: 5oyn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of D-Xylonate Dehydratase in Holo-Form


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 D-Xylonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:79.5 occ:1.00 OE1 A:GLU92 2.1 78.1 1.0 OE2 A:GLU463 2.1 74.3 1.0 OQ1 A:KCX130 2.1 79.5 1.0 OD2 A:ASP129 2.1 80.5 1.0 O A:HOH718 2.2 56.3 1.0 CD A:GLU92 2.7 81.9 1.0 CG A:ASP129 3.1 74.8 1.0 CD A:GLU463 3.1 73.7 1.0 CX A:KCX130 3.2 80.3 1.0 CG A:GLU92 3.3 72.7 1.0 OE1 A:GLU463 3.4 73.5 1.0 OE2 A:GLU92 3.6 83.6 1.0 NZ A:KCX130 3.6 81.3 1.0 CB A:ASP129 3.8 70.1 1.0 OG1 A:THR206 3.8 55.3 1.0 OD1 A:ASP129 3.9 72.7 1.0 O A:HOH753 4.0 52.7 1.0 ND2 A:ASN279 4.0 64.2 1.0 OQ2 A:KCX130 4.3 75.9 1.0 NH2 A:ARG488 4.3 67.6 1.0 CB A:GLU92 4.4 66.3 1.0 CB A:THR206 4.4 56.2 1.0 CG A:GLU463 4.4 64.9 1.0 OG A:SER490 4.9 60.3 1.0 CA A:SER490 4.9 58.5 1.0 N A:GLY491 4.9 52.3 1.0 CG2 A:THR206 5.0 52.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of D-Xylonate Dehydratase in Holo-Form


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 D-Xylonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:86.8 occ:1.00 OE2 B:GLU92 2.1 90.9 1.0 OD2 B:ASP129 2.1 88.8 1.0 OE2 B:GLU463 2.1 89.7 1.0 OQ2 B:KCX130 2.1 85.3 1.0 O B:HOH714 2.2 71.8 1.0 CD B:GLU92 2.7 91.9 1.0 CD B:GLU463 3.1 90.7 1.0 CX B:KCX130 3.2 86.8 1.0 CG B:ASP129 3.3 80.9 1.0 OE1 B:GLU92 3.4 91.4 1.0 OE1 B:GLU463 3.5 92.3 1.0 NZ B:KCX130 3.6 84.6 1.0 OG1 B:THR206 3.6 66.7 1.0 CG B:GLU92 3.6 86.1 1.0 CB B:ASP129 4.1 73.6 1.0 OD1 B:ASP129 4.2 80.6 1.0 OQ1 B:KCX130 4.2 83.5 1.0 O B:HOH706 4.2 73.5 1.0 CB B:THR206 4.3 69.8 1.0 CG B:GLU463 4.4 86.2 1.0 NH2 B:ARG488 4.5 80.7 1.0 CA B:SER490 4.5 80.7 1.0 N B:GLY491 4.5 77.7 1.0 ND2 B:ASN279 4.6 75.2 1.0 CB B:GLU92 4.8 81.2 1.0 CG2 B:THR206 4.9 69.6 1.0 CG B:ASN279 5.0 75.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of D-Xylonate Dehydratase in Holo-Form


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 D-Xylonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:72.0 occ:1.00 OD2 C:ASP129 2.1 73.9 1.0 OQ1 C:KCX130 2.1 67.6 1.0 OE1 C:GLU92 2.1 74.4 1.0 OE1 C:GLU463 2.1 64.8 1.0 O C:HOH726 2.2 54.9 1.0 CD C:GLU92 2.9 80.7 1.0 CX C:KCX130 3.1 69.9 1.0 CD C:GLU463 3.1 61.3 1.0 CG C:ASP129 3.3 67.1 1.0 CG C:GLU92 3.4 68.0 1.0 OE2 C:GLU463 3.4 68.3 1.0 NZ C:KCX130 3.5 67.4 1.0 OE2 C:GLU92 3.8 75.5 1.0 OG1 C:THR206 3.9 56.0 1.0 OQ2 C:KCX130 4.0 68.4 1.0 CB C:ASP129 4.0 59.7 1.0 O C:HOH753 4.1 48.4 1.0 OD1 C:ASP129 4.2 61.9 1.0 ND2 C:ASN279 4.4 54.4 1.0 NH1 C:ARG488 4.4 48.4 1.0 CG C:GLU463 4.4 55.1 1.0 CB C:THR206 4.5 53.9 1.0 CB C:GLU92 4.6 62.9 1.0 CA C:SER490 4.8 54.3 1.0 N C:GLY491 4.9 50.9 1.0 CE C:KCX130 5.0 64.1 1.0 CG C:ASN279 5.0 57.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of D-Xylonate Dehydratase in Holo-Form


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 D-Xylonate Dehydratase in Holo-Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:93.8 occ:1.00 OE2 D:GLU92 2.1 94.6 1.0 OD1 D:ASP129 2.1 80.2 1.0 OQ2 D:KCX130 2.1 78.0 1.0 OE2 D:GLU463 2.1 67.3 1.0 O D:HOH711 2.2 59.7 1.0 CD D:GLU92 2.3 85.0 1.0 CD D:GLU463 2.8 68.3 1.0 OE1 D:GLU92 2.8 81.2 1.0 OE1 D:GLU463 2.9 70.6 1.0 CG D:GLU92 3.0 69.3 1.0 CX D:KCX130 3.2 75.2 1.0 CG D:ASP129 3.4 72.2 1.0 NZ D:KCX130 3.7 78.5 1.0 O D:HOH764 4.0 71.9 1.0 CG D:GLU463 4.1 62.3 1.0 CB D:ASP129 4.2 68.1 1.0 OQ1 D:KCX130 4.2 68.7 1.0 OD2 D:ASP129 4.2 63.8 1.0 CB D:GLU92 4.3 66.1 1.0 O D:HOH778 4.4 45.6 1.0 OG1 D:THR206 4.4 48.4 1.0 ND2 D:ASN279 4.5 61.0 1.0 NH2 D:ARG488 4.5 58.2 1.0 NE2 C:HIS591 4.8 68.8 1.0 OG D:SER490 4.8 56.9 1.0 CA D:SER490 4.8 52.6 1.0 CB D:THR206 5.0 54.1 1.0

M.M.Rahman, M.Andberg, A.Koivula, J.Rouvinen, N.Hakulinen. The Crystal Structure of D-Xylonate Dehydratase Reveals Functional Features of Enzymes From the Ilv/Ed Dehydratase Family. Sci Rep V. 8 865 2018.
ISSN: ESSN 2045-2322
PubMed: 29339766
DOI: 10.1038/S41598-018-19192-6