Magnesium in PDB 6hwj: Glucosamine Kinase (Crystal Form A)

The structure of Glucosamine Kinase (Crystal Form A), PDB code: 6hwj was solved by J.A.Manso, P.J.B.Pereira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.74 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.812, 96.070, 80.252, 90.00, 106.69, 90.00
R / Rfree (%)	17.6 / 21.4

The structure of Glucosamine Kinase (Crystal Form A) also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the Glucosamine Kinase (Crystal Form A) (pdb code 6hwj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Glucosamine Kinase (Crystal Form A), PDB code: 6hwj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Glucosamine Kinase (Crystal Form A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Glucosamine Kinase (Crystal Form A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:38.0 occ:1.00 O A:HOH747 2.0 40.3 1.0 OE1 A:GLN305 2.1 31.2 1.0 O A:HOH836 2.2 38.4 1.0 OD2 A:ASP317 2.2 52.8 1.0 O A:HOH737 2.2 44.1 1.0 HE22 A:GLN305 2.8 31.8 1.0 CD A:GLN305 3.0 26.9 1.0 HB2 A:ASP317 3.1 42.5 1.0 CG A:ASP317 3.2 47.9 1.0 NE2 A:GLN305 3.2 26.5 1.0 CB A:ASP317 3.6 35.4 1.0 O A:HOH622 3.7 55.8 1.0 HB3 A:ASP317 3.7 42.5 1.0 O A:HOH627 3.9 40.0 1.0 HA A:GLN305 4.0 28.0 1.0 HE21 A:GLN305 4.1 31.8 1.0 HG23 A:VAL316 4.3 32.5 1.0 OD1 A:ASP317 4.3 53.0 1.0 O A:HOH632 4.4 50.1 1.0 CG A:GLN305 4.4 24.1 1.0 O A:GLY304 4.4 28.2 1.0 HG2 A:GLN305 4.6 28.9 1.0 HE1 A:HIS302 4.6 33.2 1.0 HE2 A:HIS302 4.7 30.0 1.0 CA A:GLN305 4.8 23.3 1.0 HB3 A:GLN305 4.8 26.4 1.0 CB A:GLN305 4.9 22.0 1.0 C A:GLY304 5.0 26.4 1.0

Magnesium binding site 2 out of 7 in the Glucosamine Kinase (Crystal Form A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Glucosamine Kinase (Crystal Form A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:46.4 occ:1.00 O A:HOH795 2.1 37.4 1.0 OE2 A:GLU22 2.1 80.9 1.0 O A:HOH765 2.1 42.0 1.0 O A:HOH623 2.2 49.0 1.0 O A:HOH616 2.2 48.9 1.0 HG3 A:GLU22 3.1 87.8 1.0 CD A:GLU22 3.2 78.2 1.0 HB1 A:ALA28 3.5 66.1 1.0 CG A:GLU22 3.6 73.2 1.0 HB2 A:ALA28 3.6 66.1 1.0 OD2 A:ASP13 3.9 40.8 1.0 HG2 A:GLU22 3.9 87.8 1.0 HA A:ALA25 4.0 57.5 1.0 CB A:ALA28 4.0 55.1 1.0 OD1 A:ASP13 4.0 38.4 1.0 OE1 A:GLU22 4.3 78.3 1.0 O A:HOH834 4.3 28.1 1.0 HB3 A:ALA28 4.4 66.1 1.0 CG A:ASP13 4.4 36.3 1.0 HB2 A:ALA25 4.5 54.9 1.0 O A:HOH862 4.5 41.1 1.0 HB2 A:ALA15 4.6 49.0 1.0 O A:HOH773 4.7 74.0 1.0 HD2 A:PRO14 4.7 46.9 1.0 HB1 A:ALA25 4.8 54.9 1.0 CA A:ALA25 4.9 47.9 1.0 CB A:ALA25 5.0 45.7 1.0 CB A:GLU22 5.0 65.1 1.0 O A:ARG23 5.0 52.2 1.0

Magnesium binding site 3 out of 7 in the Glucosamine Kinase (Crystal Form A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Glucosamine Kinase (Crystal Form A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:60.5 occ:1.00 O A:HOH648 2.2 56.5 1.0 HB2 A:ASP13 3.6 42.8 1.0 CB A:ASP13 4.5 35.6 1.0 O A:HOH778 4.6 37.5 1.0 OD2 A:ASP13 4.6 40.8 1.0 H A:ASP13 4.6 39.7 1.0 HA A:ASP13 4.9 40.6 1.0 N A:ASP13 5.0 33.1 1.0

Magnesium binding site 4 out of 7 in the Glucosamine Kinase (Crystal Form A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Glucosamine Kinase (Crystal Form A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:45.3 occ:1.00 O A:HOH711 2.0 50.5 1.0 O A:HOH605 2.0 46.0 1.0 OD1 A:ASP319 2.1 47.0 0.5 O A:HOH627 2.1 40.0 1.0 OD1 A:ASP317 2.2 53.0 1.0 O A:HOH601 2.2 39.1 1.0 OD2 A:ASP319 2.2 45.1 0.5 CG A:ASP319 2.4 40.3 0.5 HB2 A:ASP319 2.7 46.5 0.5 CG A:ASP317 3.1 47.9 1.0 OD2 A:ASP317 3.3 52.8 1.0 OD2 A:ASP319 3.6 42.6 0.5 CB A:ASP319 3.7 38.8 0.5 H A:ASP319 3.9 34.7 0.5 H A:ASP319 3.9 34.8 0.5 O A:HOH774 3.9 52.6 1.0 CB A:ASP319 3.9 36.0 0.5 HB3 A:ASP319 4.1 46.5 0.5 CG A:ASP319 4.1 40.3 0.5 HB2 A:ASP319 4.3 43.1 0.5 HB3 A:ASP319 4.4 43.1 0.5 CB A:ASP317 4.5 35.4 1.0 HA A:ASP317 4.5 32.7 1.0 HE22 A:GLN305 4.6 31.8 1.0 N A:ASP319 4.6 28.9 0.5 N A:ASP319 4.6 29.0 0.5 O A:GLY320 4.6 32.5 1.0 OD2 A:ASP300 4.7 33.0 1.0 CA A:ASP319 4.7 32.7 0.5 CA A:ASP319 4.7 32.7 0.5 H A:GLY320 4.9 34.3 0.5 CA A:ASP317 4.9 27.2 1.0 HB3 A:ASP317 5.0 42.5 1.0 HB3 A:PRO322 5.0 53.2 1.0

Magnesium binding site 5 out of 7 in the Glucosamine Kinase (Crystal Form A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Glucosamine Kinase (Crystal Form A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:67.1 occ:1.00 O A:GLU26 2.1 90.4 1.0 O A:HOH713 2.1 71.3 1.0 O A:HOH784 2.2 70.5 1.0 O A:HOH843 2.2 70.1 1.0 C A:GLU26 3.3 67.8 1.0 HA A:VAL27 3.4 68.1 1.0 HG12 A:VAL27 4.0 68.8 1.0 HA A:GLU26 4.0 68.3 1.0 N A:VAL27 4.2 58.8 1.0 CA A:VAL27 4.2 56.8 1.0 CA A:GLU26 4.2 56.9 1.0 HB3 A:GLU26 4.3 60.1 1.0 HG13 A:VAL27 4.4 68.8 1.0 CG1 A:VAL27 4.6 57.3 1.0 CB A:GLU26 4.8 50.1 1.0 H A:ALA28 4.9 64.8 1.0 H A:VAL27 5.0 70.5 1.0

Magnesium binding site 6 out of 7 in the Glucosamine Kinase (Crystal Form A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Glucosamine Kinase (Crystal Form A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:52.2 occ:1.00 O B:HOH691 2.0 58.3 1.0 OD2 B:ASP317 2.1 79.9 1.0 O B:HOH700 2.1 49.5 1.0 OE1 B:GLN305 2.2 62.6 1.0 O B:HOH729 2.2 57.3 1.0 O B:HOH740 2.3 78.0 1.0 HE22 B:GLN305 2.8 54.9 1.0 CD B:GLN305 3.0 49.2 1.0 HB2 B:ASP317 3.1 69.3 1.0 CG B:ASP317 3.2 74.0 1.0 NE2 B:GLN305 3.2 45.7 1.0 CB B:ASP317 3.5 57.8 1.0 HB3 B:ASP317 3.6 69.3 1.0 O B:HOH620 3.7 60.2 1.0 HE21 B:GLN305 4.1 54.9 1.0 HA B:GLN305 4.1 41.4 1.0 O B:HOH615 4.2 68.5 1.0 HE1 B:HIS302 4.2 42.4 1.0 HG23 B:VAL316 4.3 43.2 1.0 OD1 B:ASP317 4.3 84.3 1.0 O B:GLY304 4.4 31.9 1.0 HE2 B:HIS302 4.4 43.2 1.0 CG B:GLN305 4.4 40.7 1.0 O B:HOH754 4.6 43.3 1.0 O B:HOH695 4.6 54.2 1.0 HG2 B:GLN305 4.7 48.8 1.0 O B:HOH774 4.7 71.5 1.0 CE1 B:HIS302 4.8 35.4 1.0 NE2 B:HIS302 4.8 36.0 1.0 CA B:GLN305 4.9 34.5 1.0 C B:GLY304 4.9 34.9 1.0

Magnesium binding site 7 out of 7 in the Glucosamine Kinase (Crystal Form A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Glucosamine Kinase (Crystal Form A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:65.2 occ:1.00 OD2 B:ASP319 2.1 0.3 1.0 OD1 B:ASP319 2.1 99.8 1.0 OD1 B:ASP317 2.2 84.3 1.0 O B:HOH604 2.2 68.5 1.0 O B:HOH620 2.2 60.2 1.0 CG B:ASP319 2.4 94.9 1.0 CG B:ASP317 3.0 74.0 1.0 HZ1 B:LYS133 3.1 68.1 1.0 OD2 B:ASP317 3.2 79.9 1.0 CB B:ASP319 3.9 78.9 1.0 H B:ASP319 3.9 59.9 1.0 NZ B:LYS133 4.0 56.8 1.0 HZ3 B:LYS133 4.2 68.1 1.0 HB3 B:ASP319 4.2 94.7 1.0 HE2 B:LYS133 4.3 66.4 1.0 HB2 B:ASP319 4.3 94.7 1.0 OD2 B:ASP300 4.4 41.3 1.0 HE22 B:GLN305 4.4 54.9 1.0 O B:GLY320 4.4 48.1 1.0 CB B:ASP317 4.4 57.8 1.0 HZ2 B:LYS133 4.5 68.1 1.0 CE B:LYS133 4.6 55.3 1.0 HA B:ASP317 4.6 53.1 1.0 N B:ASP319 4.6 49.9 1.0 HE3 B:LYS133 4.6 66.4 1.0 HD3 B:PRO322 4.7 69.1 1.0 CA B:ASP319 4.7 58.9 1.0 HB3 B:PRO322 4.8 73.0 1.0 O B:ASP317 4.8 40.9 1.0 HB3 B:ASP317 4.8 69.3 1.0 C B:ASP317 4.9 42.6 1.0 CA B:ASP317 4.9 44.3 1.0 H B:GLY320 4.9 56.2 1.0

J.A.Manso, D.Nunes-Costa, S.Macedo-Ribeiro, N.Empadinhas, P.J.B.Pereira. Molecular Fingerprints For A Novel Enzyme Family Inactinobacteriawith Glucosamine Kinase Activity. Mbio V. 10 2019.
ISSN: ESSN 2150-7511
PubMed: 31088917
DOI: 10.1128/MBIO.00239-19