Atomistry » Magnesium » PDB 6xmq-6xz7 » 6xpt
Atomistry »
  Magnesium »
    PDB 6xmq-6xz7 »
      6xpt »

Magnesium in PDB 6xpt: Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Udp

Enzymatic activity of Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Udp

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

Protein crystallography data

The structure of Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Udp, PDB code: 6xpt 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) 46.21 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.648, 126.820, 134.942, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 23.3

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 6xpt

Go back to Magnesium Binding Sites List in 6xpt
Magnesium binding site 1 out of 2 in the Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Udp


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 Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:48.0
occ:1.00
O B:HOH658 2.0 43.3 1.0
O B:HOH611 2.1 40.6 1.0
O B:HOH612 2.1 41.3 1.0
O B:HOH725 2.3 45.8 1.0
O1A B:UDP202 2.3 42.4 1.0
O B:HOH626 2.7 42.9 1.0
O2B B:UDP202 3.5 35.4 1.0
O B:HOH614 3.7 38.4 1.0
OD2 B:ASP120 3.7 45.5 1.0
PA B:UDP202 3.8 43.0 1.0
O B:HOH654 4.0 32.0 1.0
O B:HOH713 4.1 41.4 1.0
OD2 B:ASP53 4.2 50.0 1.0
CG B:ASP120 4.3 42.8 1.0
O5' B:UDP202 4.3 41.3 1.0
O3A B:UDP202 4.4 49.6 1.0
OD1 B:ASP53 4.5 46.7 1.0
PB B:UDP202 4.6 37.4 1.0
CG B:ASP53 4.8 47.7 1.0
OD1 B:ASP120 4.8 38.1 1.0
CB B:ASP120 4.9 40.6 1.0
O2A B:UDP202 4.9 35.6 1.0
CD1 B:LEU54 5.0 43.4 1.0

Magnesium binding site 2 out of 2 in 6xpt

Go back to Magnesium Binding Sites List in 6xpt
Magnesium binding site 2 out of 2 in the Nucleoside Diphosphate Kinase From Aspergillus Fumgiatus AF293 Bound to Udp


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 Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg201

b:41.6
occ:1.00
O1A G:UDP202 2.0 31.0 0.9
O G:HOH336 2.1 37.6 1.0
O G:HOH352 2.1 44.7 1.0
O G:HOH301 2.1 36.9 1.0
O G:HOH410 2.1 47.3 1.0
O G:HOH385 2.3 38.6 1.0
O3B G:UDP202 3.3 34.0 0.9
PA G:UDP202 3.5 37.9 0.9
O G:HOH303 4.0 32.5 1.0
O G:HOH339 4.1 33.3 1.0
O2A G:UDP202 4.2 42.0 0.9
OD2 G:ASP53 4.3 49.4 1.0
OD2 G:ASP120 4.3 40.3 1.0
O3A G:UDP202 4.3 39.2 0.9
O G:HOH348 4.3 46.8 1.0
PB G:UDP202 4.4 36.7 0.9
O5' G:UDP202 4.4 30.6 0.9
C5' G:UDP202 4.5 32.0 0.9
O2B G:UDP202 4.7 33.5 0.9
O G:HOH437 4.7 44.3 1.0
OD1 G:ASP53 4.7 54.1 1.0
CG G:ASP120 4.7 39.0 1.0
CD1 G:LEU54 4.8 39.0 1.0
CG G:ASP53 4.9 56.2 1.0

Reference:

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
Page generated: Tue Oct 1 23:37:17 2024

Last articles

Zn in 1MC5
Zn in 1MFM
Zn in 1MA0
Zn in 1MED
Zn in 1MEA
Zn in 1MBX
Zn in 1MA3
Zn in 1M9O
Zn in 1M9R
Zn in 1M9Q
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy