Magnesium in PDB 6xps: Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Gdp

All present enzymatic activity of Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Gdp:
2.7.4.6;

The structure of Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Gdp, PDB code: 6xps was solved by S.Nguyen, J.B.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.45 / 1.64
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	53.023, 70.287, 119.166, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 20.8

The binding sites of Magnesium atom in the Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Gdp (pdb code 6xps). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Gdp, PDB code: 6xps:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:52.3 occ:1.00 O A:HOH369 2.0 35.4 1.0 O A:HOH382 2.0 38.7 1.0 O3B A:GDP201 2.1 33.7 0.9 O A:HOH388 2.2 35.7 1.0 O A:HOH349 2.4 49.8 1.0 O2A A:GDP201 2.4 32.5 0.9 PB A:GDP201 3.4 31.6 0.9 O A:HOH368 3.6 24.5 1.0 PA A:GDP201 3.7 33.0 0.9 O A:HOH523 3.7 34.2 1.0 O A:HOH493 3.7 35.6 1.0 NH1 A:ARG87 3.7 29.0 1.0 O3A A:GDP201 3.9 33.4 0.9 O2B A:GDP201 4.1 31.1 0.9 CE1 A:HIS117 4.1 21.8 1.0 O A:HOH425 4.2 31.4 1.0 O A:HOH496 4.2 39.9 1.0 OD2 A:ASP120 4.3 45.1 1.0 CG A:ASP120 4.4 27.1 1.0 CB A:ASP120 4.5 22.1 1.0 O A:HOH305 4.5 48.8 1.0 O1B A:GDP201 4.5 28.5 0.9 C5' A:GDP201 4.6 23.8 0.9 O A:GLY118 4.6 18.8 1.0 ND1 A:HIS117 4.6 19.2 1.0 O1A A:GDP201 4.6 38.5 0.9 CZ A:ARG87 4.7 32.4 1.0 O5' A:GDP201 4.7 23.6 0.9 O A:HOH375 4.7 58.0 1.0 NH2 A:ARG87 4.7 30.3 1.0 O A:HOH340 4.9 25.1 1.0 OD1 A:ASP120 4.9 28.1 1.0 O A:HOH327 4.9 27.3 1.0

Magnesium binding site 2 out of 3 in the Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:22.6 occ:0.59 O B:HOH457 2.1 33.1 1.0 O2A B:GDP201 2.1 29.6 1.0 O B:HOH325 2.1 30.2 1.0 O B:HOH304 2.1 30.5 1.0 O B:HOH395 2.2 26.8 1.0 O B:HOH352 2.3 31.0 1.0 PA B:GDP201 3.5 27.8 1.0 O2B B:GDP201 3.7 29.2 1.0 O B:HOH376 3.7 39.4 1.0 O B:HOH309 3.8 36.0 1.0 OD2 B:ASP120 3.9 45.3 1.0 OD2 B:ASP53 3.9 53.3 1.0 O1A B:GDP201 4.1 27.5 1.0 O B:HOH341 4.1 43.3 1.0 O B:HOH423 4.1 29.1 1.0 O B:HOH372 4.2 23.3 1.0 O B:HOH492 4.2 35.0 1.0 OD1 B:ASP53 4.3 59.7 1.0 O3A B:GDP201 4.5 31.5 1.0 CG B:ASP53 4.5 49.3 1.0 O5' B:GDP201 4.5 24.2 1.0 PB B:GDP201 4.6 30.8 1.0 CG B:ASP120 4.7 27.3 1.0 C5' B:GDP201 4.7 23.9 1.0 CD1 B:LEU54 4.8 27.0 1.0 O B:HOH524 4.8 35.8 1.0

Magnesium binding site 3 out of 3 in the Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Gdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:32.7 occ:0.59 O C:HOH305 2.2 31.6 1.0 O C:HOH361 2.2 37.6 1.0 O1A C:GDP201 2.2 35.5 0.9 O C:HOH335 2.2 34.7 1.0 O C:HOH368 2.4 36.1 1.0 O C:HOH475 2.5 39.9 1.0 O C:HOH313 3.6 44.1 1.0 PA C:GDP201 3.7 34.5 0.9 O C:HOH348 3.7 41.2 1.0 O1B C:GDP201 3.8 29.2 0.9 O C:HOH403 3.9 35.5 1.0 OD2 C:ASP53 4.1 31.4 0.6 O C:HOH353 4.2 41.0 1.0 OD1 C:ASP53 4.2 35.4 0.6 O C:HOH328 4.3 29.1 1.0 O2A C:GDP201 4.3 32.7 0.9 OD2 C:ASP120 4.4 54.5 1.0 O C:HOH449 4.4 34.6 1.0 O C:HOH309 4.4 48.9 1.0 CG C:ASP53 4.6 40.0 0.6 O5' C:GDP201 4.6 25.9 0.9 C5' C:GDP201 4.6 25.8 0.9 O3A C:GDP201 4.6 29.4 0.9 CD1 C:LEU54 4.7 32.4 1.0 PB C:GDP201 4.8 31.9 0.9 CG C:ASP120 4.9 31.2 1.0

S.Nguyen, B.Jovcevski, T.L.Pukala, J.B.Bruning. Nucleoside Selectivity of Aspergillus Fumigatus Nucleoside-Diphosphate Kinase. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 33089641
DOI: 10.1111/FEBS.15607