Magnesium in PDB 6hwk: Glucosamine Kinase (Crystal Form B)

Protein crystallography data

The structure of Glucosamine Kinase (Crystal Form B), PDB code: 6hwk 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) 47.27 / 2.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.202, 111.216, 150.589, 90.00, 93.21, 90.00
R / Rfree (%) 20.6 / 24.2

Other elements in 6hwk:

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

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 3 in 6hwk

Go back to Magnesium Binding Sites List in 6hwk
Magnesium binding site 1 out of 3 in the Glucosamine Kinase (Crystal Form B)


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 B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:38.1
occ:1.00
OD2 A:ASP317 2.1 59.6 1.0
OE1 A:GLN305 2.1 50.5 1.0
O A:HOH611 2.2 37.2 1.0
O A:HOH646 2.2 52.2 1.0
CD A:GLN305 3.1 42.7 1.0
CG A:ASP317 3.3 57.1 1.0
NE2 A:GLN305 3.6 44.4 1.0
O A:GLY304 4.1 31.6 1.0
OD1 A:ASP317 4.2 60.0 1.0
CB A:ASP317 4.2 46.6 1.0
O A:HOH640 4.3 49.7 1.0
CG A:GLN305 4.3 35.6 1.0
C A:GLY304 4.6 26.5 1.0
CA A:GLN305 4.7 30.1 1.0
CE1 A:HIS302 4.7 27.1 1.0
N A:GLN305 4.8 25.8 1.0
CB A:GLN305 4.9 31.2 1.0
NE2 A:HIS302 4.9 26.2 1.0
CG2 A:VAL316 5.0 23.6 1.0

Magnesium binding site 2 out of 3 in 6hwk

Go back to Magnesium Binding Sites List in 6hwk
Magnesium binding site 2 out of 3 in the Glucosamine Kinase (Crystal Form B)


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 B) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:46.4
occ:1.00
OD2 C:ASP317 2.1 62.7 1.0
OE1 C:GLN305 2.1 52.0 1.0
O C:HOH633 2.1 44.4 1.0
O C:HOH621 2.1 45.8 1.0
O C:HOH604 2.2 34.7 1.0
CD C:GLN305 3.1 40.1 1.0
CG C:ASP317 3.3 59.0 1.0
NE2 C:GLN305 3.7 31.2 1.0
O C:GLY304 4.0 34.7 1.0
CB C:ASP317 4.1 47.1 1.0
OD1 C:ASP317 4.2 61.3 1.0
O C:HOH647 4.3 44.1 1.0
CG C:GLN305 4.3 37.0 1.0
O C:HOH634 4.4 42.8 1.0
C C:GLY304 4.5 36.5 1.0
CA C:GLN305 4.5 37.7 1.0
CE1 C:HIS302 4.6 24.4 1.0
N C:GLN305 4.7 36.0 1.0
CG2 C:VAL316 4.8 27.9 1.0
CB C:GLN305 4.8 39.1 1.0
NE2 C:HIS302 4.9 24.4 1.0

Magnesium binding site 3 out of 3 in 6hwk

Go back to Magnesium Binding Sites List in 6hwk
Magnesium binding site 3 out of 3 in the Glucosamine Kinase (Crystal Form B)


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 B) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:44.1
occ:1.00
OD2 D:ASP317 2.0 56.3 1.0
O D:HOH627 2.1 42.5 1.0
OE1 D:GLN305 2.1 50.6 1.0
O D:HOH649 2.1 46.9 1.0
O D:HOH605 2.2 37.6 1.0
O D:HOH633 2.8 35.2 1.0
CD D:GLN305 3.1 41.2 1.0
CG D:ASP317 3.2 53.2 1.0
NE2 D:GLN305 3.6 41.6 1.0
O D:GLY304 3.9 25.5 1.0
CB D:ASP317 4.0 43.1 1.0
OD1 D:ASP317 4.1 56.2 1.0
CG D:GLN305 4.3 34.3 1.0
C D:GLY304 4.5 29.5 1.0
CA D:GLN305 4.6 32.5 1.0
N D:GLN305 4.8 27.4 1.0
CE1 D:HIS302 4.8 20.3 1.0
CG2 D:VAL316 4.8 24.0 1.0
CB D:GLN305 4.8 34.7 1.0

Reference:

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
Page generated: Mon Dec 14 22:54:42 2020

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