Magnesium in PDB 6byw: Structure of Goxa From Pseudoalteromonas Luteoviolacea

The structure of Structure of Goxa From Pseudoalteromonas Luteoviolacea, PDB code: 6byw was solved by E.T.Yukl, D.Avalos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.28 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	109.843, 93.236, 188.457, 90.00, 94.88, 90.00
R / Rfree (%)	18.6 / 21.9

The binding sites of Magnesium atom in the Structure of Goxa From Pseudoalteromonas Luteoviolacea (pdb code 6byw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Goxa From Pseudoalteromonas Luteoviolacea, PDB code: 6byw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Goxa From Pseudoalteromonas Luteoviolacea


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Goxa From Pseudoalteromonas Luteoviolacea within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:18.7 occ:1.00 O B:ALA699 2.3 17.1 1.0 O B:ALA362 2.3 17.6 1.0 O B:ILE365 2.4 17.7 1.0 OD1 B:ASN700 2.5 29.9 1.0 O B:HOH1053 2.5 23.4 1.0 OD1 B:ASP360 2.8 18.4 1.0 HA B:ASN700 3.0 20.0 1.0 C B:ALA699 3.2 17.0 1.0 C B:ALA362 3.2 17.6 1.0 OD2 B:ASP360 3.3 21.2 1.0 HB3 B:ALA362 3.4 20.8 1.0 CG B:ASP360 3.4 28.7 1.0 CG B:ASN700 3.5 16.9 1.0 C B:ILE365 3.5 18.0 1.0 H B:ILE365 3.6 21.8 1.0 HB B:ILE365 3.6 21.4 1.0 HA B:PRO363 3.6 21.5 1.0 HB1 B:ALA699 3.6 20.7 1.0 H B:ALA362 3.7 20.6 1.0 CA B:ASN700 3.7 16.7 1.0 N B:ASN700 3.8 16.8 1.0 HD3 B:PRO367 4.0 21.2 1.0 CA B:ALA362 4.0 17.4 1.0 N B:PRO363 4.1 17.8 1.0 CB B:ALA362 4.1 17.4 1.0 CA B:PRO363 4.1 17.9 1.0 N B:ILE365 4.1 18.2 1.0 CB B:ASN700 4.2 16.6 1.0 CA B:ILE365 4.2 18.1 1.0 CA B:ALA699 4.2 17.1 1.0 HA B:GLU366 4.2 21.7 1.0 N B:ALA362 4.3 17.1 1.0 CB B:ALA699 4.3 17.3 1.0 C B:PRO363 4.3 18.2 1.0 HB1 B:ALA362 4.4 20.8 1.0 CB B:ILE365 4.4 17.9 1.0 HA B:ALA699 4.4 20.5 1.0 HB3 B:ALA699 4.4 20.7 1.0 ND2 B:ASN700 4.5 26.1 1.0 O B:PRO363 4.5 18.3 1.0 HD21 B:ASN700 4.5 31.4 1.0 N B:GLU366 4.6 18.1 1.0 H B:ASN700 4.6 20.1 1.0 HB3 B:ASN700 4.6 19.9 1.0 HG22 B:ILE365 4.8 21.4 1.0 CA B:GLU366 4.8 18.1 1.0 N B:GLN364 4.9 18.5 1.0 CD B:PRO367 4.9 17.7 1.0 HG3 B:PRO367 4.9 20.9 1.0 HB2 B:ALA362 4.9 20.8 1.0 CB B:ASP360 4.9 18.4 1.0 HA B:ALA362 4.9 20.9 1.0 HB2 B:ASN700 5.0 19.9 1.0

Magnesium binding site 2 out of 4 in the Structure of Goxa From Pseudoalteromonas Luteoviolacea


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Goxa From Pseudoalteromonas Luteoviolacea within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:24.1 occ:1.00 O A:ALA699 2.2 23.4 1.0 O A:ILE365 2.2 24.1 1.0 O A:ALA362 2.4 24.0 1.0 O A:HOH1048 2.4 33.5 1.0 OD1 A:ASN700 2.5 35.2 1.0 OD1 A:ASP360 2.9 25.2 1.0 HA A:ASN700 3.1 26.7 1.0 C A:ALA699 3.2 23.2 1.0 C A:ALA362 3.3 24.0 1.0 OD2 A:ASP360 3.3 35.8 1.0 C A:ILE365 3.4 24.4 1.0 HB3 A:ALA362 3.4 27.5 1.0 HB A:ILE365 3.4 28.4 1.0 CG A:ASP360 3.5 29.6 1.0 H A:ILE365 3.5 29.6 1.0 HB1 A:ALA699 3.6 28.5 1.0 CG A:ASN700 3.6 29.5 1.0 HA A:PRO363 3.7 30.0 1.0 H A:ALA362 3.8 27.6 1.0 CA A:ASN700 3.8 22.3 1.0 N A:ASN700 3.8 22.2 1.0 HD3 A:PRO367 3.9 29.3 1.0 N A:ILE365 4.1 24.7 1.0 CA A:ILE365 4.1 24.4 1.0 CB A:ALA362 4.1 22.9 1.0 CA A:ALA362 4.1 23.4 1.0 CB A:ILE365 4.2 23.7 1.0 CA A:ALA699 4.2 22.9 1.0 N A:PRO363 4.2 24.4 1.0 HA A:GLU366 4.2 30.8 1.0 CA A:PRO363 4.2 25.1 1.0 CB A:ALA699 4.2 23.8 1.0 HA A:ALA699 4.3 27.5 1.0 CB A:ASN700 4.3 22.5 1.0 N A:ALA362 4.3 23.1 1.0 HB1 A:ALA362 4.4 27.5 1.0 C A:PRO363 4.4 25.4 1.0 HB3 A:ALA699 4.4 28.5 1.0 N A:GLU366 4.4 25.5 1.0 HG22 A:ILE365 4.4 28.0 1.0 O A:PRO363 4.5 27.6 1.0 ND2 A:ASN700 4.6 24.2 1.0 H A:ASN700 4.6 26.6 1.0 HD21 A:ASN700 4.6 29.0 1.0 CA A:GLU366 4.8 25.6 1.0 HB3 A:ASN700 4.8 27.0 1.0 CD A:PRO367 4.8 24.4 1.0 HG3 A:PRO367 4.9 28.8 1.0 CG2 A:ILE365 4.9 23.4 1.0 N A:GLN364 4.9 25.3 1.0 HB2 A:ALA362 4.9 27.5 1.0 CB A:ASP360 5.0 26.1 1.0 HA A:ILE365 5.0 29.2 1.0

Magnesium binding site 3 out of 4 in the Structure of Goxa From Pseudoalteromonas Luteoviolacea


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Goxa From Pseudoalteromonas Luteoviolacea within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg901 b:20.1 occ:1.00 O C:ALA699 2.2 17.8 1.0 O C:ALA362 2.3 18.3 1.0 O C:HOH1036 2.3 24.8 1.0 O C:ILE365 2.3 18.6 1.0 OD1 C:ASN700 2.6 23.2 1.0 OD1 C:ASP360 2.9 17.9 1.0 HA C:ASN700 3.1 20.9 1.0 C C:ALA699 3.2 17.7 1.0 C C:ALA362 3.2 18.2 1.0 HB3 C:ALA362 3.3 21.3 1.0 C C:ILE365 3.5 18.8 1.0 OD2 C:ASP360 3.5 18.4 1.0 HB C:ILE365 3.5 22.2 1.0 H C:ILE365 3.5 22.6 1.0 HB1 C:ALA699 3.5 21.7 1.0 CG C:ASP360 3.6 21.2 1.0 CG C:ASN700 3.6 21.4 1.0 HA C:PRO363 3.7 22.3 1.0 H C:ALA362 3.7 21.1 1.0 CA C:ASN700 3.8 17.4 1.0 N C:ASN700 3.8 17.5 1.0 HD3 C:PRO367 3.9 22.6 1.0 CB C:ALA362 4.0 17.8 1.0 CA C:ALA362 4.0 17.9 1.0 N C:ILE365 4.1 18.8 1.0 N C:PRO363 4.1 18.3 1.0 CA C:ILE365 4.1 18.8 1.0 CA C:PRO363 4.1 18.6 1.0 CA C:ALA699 4.2 17.8 1.0 CB C:ALA699 4.2 18.1 1.0 HA C:GLU366 4.2 22.9 1.0 CB C:ILE365 4.2 18.5 1.0 N C:ALA362 4.3 17.6 1.0 HB1 C:ALA362 4.3 21.3 1.0 HA C:ALA699 4.3 21.4 1.0 CB C:ASN700 4.3 17.5 1.0 C C:PRO363 4.3 18.9 1.0 HB3 C:ALA699 4.4 21.7 1.0 O C:HOH1340 4.4 33.7 1.0 O C:PRO363 4.5 19.1 1.0 N C:GLU366 4.6 19.1 1.0 HG22 C:ILE365 4.6 22.2 1.0 ND2 C:ASN700 4.6 34.0 1.0 H C:ASN700 4.6 21.0 1.0 HD21 C:ASN700 4.7 40.8 1.0 HB3 C:ASN700 4.8 21.0 1.0 CD C:PRO367 4.8 18.8 1.0 CA C:GLU366 4.8 19.1 1.0 N C:GLN364 4.8 18.9 1.0 HB2 C:ALA362 4.9 21.3 1.0 HG3 C:PRO367 4.9 22.3 1.0 HA C:ALA362 4.9 21.4 1.0

Magnesium binding site 4 out of 4 in the Structure of Goxa From Pseudoalteromonas Luteoviolacea


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Goxa From Pseudoalteromonas Luteoviolacea within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg901 b:23.3 occ:1.00 O D:HOH1059 2.2 24.9 1.0 O D:ILE365 2.3 21.8 1.0 O D:ALA362 2.3 21.9 1.0 O D:ALA699 2.3 21.3 1.0 OD1 D:ASN700 2.6 34.5 1.0 OD1 D:ASP360 2.8 21.9 1.0 HA D:ASN700 3.1 24.3 1.0 C D:ALA362 3.2 21.9 1.0 C D:ALA699 3.3 20.9 1.0 OD2 D:ASP360 3.3 29.7 1.0 HB3 D:ALA362 3.4 25.2 1.0 C D:ILE365 3.5 22.0 1.0 CG D:ASP360 3.5 22.4 1.0 H D:ILE365 3.5 26.8 1.0 HA D:PRO363 3.6 28.8 1.0 HB D:ILE365 3.6 25.7 1.0 CG D:ASN700 3.6 29.9 1.0 HB1 D:ALA699 3.7 25.4 1.0 H D:ALA362 3.7 26.3 1.0 CA D:ASN700 3.9 20.3 1.0 HD3 D:PRO367 3.9 44.1 1.0 N D:ASN700 4.0 20.1 1.0 N D:PRO363 4.0 23.5 1.0 N D:ILE365 4.1 22.4 1.0 CA D:PRO363 4.1 24.0 1.0 CA D:ALA362 4.1 21.4 1.0 CB D:ALA362 4.1 21.0 1.0 CA D:ILE365 4.2 22.0 1.0 HA D:GLU366 4.2 27.4 1.0 O D:HOH1242 4.2 39.9 1.0 C D:PRO363 4.2 24.2 1.0 N D:ALA362 4.3 21.9 1.0 CB D:ILE365 4.3 21.4 1.0 CA D:ALA699 4.3 20.8 1.0 CB D:ASN700 4.4 20.4 1.0 HB1 D:ALA362 4.4 25.2 1.0 CB D:ALA699 4.4 21.1 1.0 O D:PRO363 4.4 24.5 1.0 HA D:ALA699 4.5 25.0 1.0 N D:GLU366 4.5 22.8 1.0 HB3 D:ALA699 4.6 25.4 1.0 ND2 D:ASN700 4.6 24.0 1.0 HD21 D:ASN700 4.6 28.8 1.0 HG22 D:ILE365 4.7 25.3 1.0 H D:ASN700 4.7 24.1 1.0 N D:GLN364 4.8 23.5 1.0 CA D:GLU366 4.8 22.9 1.0 HB3 D:ASN700 4.8 24.5 1.0 CD D:PRO367 4.8 36.8 1.0 HG3 D:PRO367 4.9 30.3 1.0 HB2 D:ALA362 4.9 25.2 1.0 CB D:ASP360 5.0 22.5 1.0 HA D:ALA362 5.0 25.7 1.0 H D:GLN364 5.0 28.3 1.0

A.Andreo-Vidal, K.J.Mamounis, E.Sehanobish, D.Avalos, J.C.Campillo-Brocal, A.Sanchez-Amat, E.T.Yukl, V.L.Davidson. Structure and Enzymatic Properties of An Unusual Cysteine Tryptophylquinone-Dependent Glycine Oxidase From Pseudoalteromonas Luteoviolacea. Biochemistry V. 57 1155 2018.
ISSN: ISSN 1520-4995
PubMed: 29381339
DOI: 10.1021/ACS.BIOCHEM.8B00009