Atomistry » Magnesium » PDB 5wu3-5x86 » 5wwd
Atomistry »
  Magnesium »
    PDB 5wu3-5x86 »
      5wwd »

Magnesium in PDB 5wwd: Crystal Structure of ATNUDX1

Enzymatic activity of Crystal Structure of ATNUDX1

All present enzymatic activity of Crystal Structure of ATNUDX1:
3.6.1.22; 3.6.1.55; 3.6.1.67;

Protein crystallography data

The structure of Crystal Structure of ATNUDX1, PDB code: 5wwd was solved by J.Liu, Z.Guan, L.Yan, T.Zou, P.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.12 / 1.39
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.522, 83.181, 115.224, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 17.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of ATNUDX1 (pdb code 5wwd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of ATNUDX1, PDB code: 5wwd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5wwd

Go back to Magnesium Binding Sites List in 5wwd
Magnesium binding site 1 out of 6 in the Crystal Structure of ATNUDX1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of ATNUDX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:39.4
occ:1.00
MG A:MG205 2.3 45.7 1.0
O A:HOH342 2.7 63.2 1.0
ND1 A:HIS42 2.9 48.9 1.0
N A:HIS42 3.0 16.1 1.0
O A:HOH355 3.3 45.3 1.0
CA A:GLY41 3.4 17.9 1.0
O A:HOH302 3.6 68.3 1.0
CG A:HIS42 3.7 39.3 1.0
C A:GLY41 3.7 15.1 1.0
CB A:HIS42 3.8 22.3 1.0
CE1 A:HIS42 3.9 49.1 1.0
CA A:HIS42 4.0 14.6 1.0
OE2 A:GLU56 4.1 32.5 1.0
O A:HOH433 4.2 36.8 1.0
OE1 A:GLU56 4.4 27.1 1.0
NZ A:LYS110 4.6 45.6 1.0
CD A:GLU56 4.6 29.7 1.0
O A:HOH455 4.6 47.3 1.0
O A:HOH365 4.8 46.3 1.0
N A:GLY41 4.8 15.9 1.0
O A:GLY40 4.9 18.6 1.0
MG A:MG206 4.9 41.0 1.0
O A:GLY41 4.9 16.5 1.0
CD2 A:HIS42 4.9 49.0 1.0
NE2 A:HIS42 5.0 51.2 1.0

Magnesium binding site 2 out of 6 in 5wwd

Go back to Magnesium Binding Sites List in 5wwd
Magnesium binding site 2 out of 6 in the Crystal Structure of ATNUDX1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of ATNUDX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:45.7
occ:1.00
O A:HOH302 2.1 68.3 1.0
MG A:MG204 2.3 39.4 1.0
O A:HOH365 2.5 46.3 1.0
O A:HOH342 2.7 63.2 1.0
OE2 A:GLU56 3.4 32.5 1.0
O A:HOH455 3.6 47.3 1.0
MG A:MG206 3.6 41.0 1.0
OE1 A:GLU56 4.0 27.1 1.0
CD A:GLU56 4.1 29.7 1.0
N A:HIS42 4.2 16.1 1.0
NH1 A:ARG55 4.5 21.0 1.0
OE1 A:GLU59 4.5 30.8 1.0
CB A:HIS42 4.6 22.3 1.0
ND1 A:HIS42 4.7 48.9 1.0
O A:HOH355 4.8 45.3 1.0
CA A:GLY41 4.8 17.9 1.0
O A:HIS42 4.9 18.4 1.0
CA A:HIS42 5.0 14.6 1.0
C A:GLY41 5.0 15.1 1.0

Magnesium binding site 3 out of 6 in 5wwd

Go back to Magnesium Binding Sites List in 5wwd
Magnesium binding site 3 out of 6 in the Crystal Structure of ATNUDX1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of ATNUDX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:41.0
occ:1.00
O A:HOH342 2.5 63.2 1.0
OE2 A:GLU107 2.6 34.3 1.0
OE1 A:GLU59 2.6 30.8 1.0
OE1 A:GLU56 3.0 27.1 1.0
O A:HOH365 3.3 46.3 1.0
CD A:GLU107 3.4 24.8 1.0
OE1 A:GLU107 3.5 28.6 1.0
OE2 A:GLU60 3.6 25.0 1.0
MG A:MG205 3.6 45.7 1.0
CD A:GLU59 3.8 23.0 1.0
CB A:GLU59 3.8 18.4 1.0
CD A:GLU56 3.9 29.7 1.0
CG A:GLU60 4.0 16.1 1.0
NZ A:LYS110 4.1 45.6 1.0
CD A:GLU60 4.2 20.8 1.0
OE2 A:GLU56 4.3 32.5 1.0
CG A:GLU59 4.4 22.4 1.0
O A:HOH302 4.5 68.3 1.0
O A:HOH355 4.8 45.3 1.0
OE2 A:GLU59 4.8 27.9 1.0
CG A:GLU107 4.8 24.3 1.0
MG A:MG204 4.9 39.4 1.0
O A:GLU56 4.9 14.9 1.0
CA A:GLU56 5.0 14.4 1.0

Magnesium binding site 4 out of 6 in 5wwd

Go back to Magnesium Binding Sites List in 5wwd
Magnesium binding site 4 out of 6 in the Crystal Structure of ATNUDX1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of ATNUDX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:51.6
occ:1.00
MG B:MG205 2.3 42.6 1.0
O B:HOH363 3.1 38.3 1.0
OE2 B:GLU56 3.4 28.8 1.0
MG B:MG206 3.8 44.5 1.0
OE1 B:GLU56 3.9 29.9 1.0
ND1 B:HIS42 4.0 56.0 1.0
CD B:GLU56 4.1 28.5 1.0
N B:HIS42 4.1 16.9 1.0
NZ B:LYS110 4.5 40.1 1.0
CA B:GLY41 4.5 18.9 1.0
CB B:HIS42 4.7 19.1 1.0
CG B:HIS42 4.7 46.4 1.0
C B:GLY41 4.8 15.4 1.0
OE1 B:GLU59 4.9 30.3 1.0
CE1 B:HIS42 4.9 58.2 1.0
CA B:HIS42 5.0 15.7 1.0

Magnesium binding site 5 out of 6 in 5wwd

Go back to Magnesium Binding Sites List in 5wwd
Magnesium binding site 5 out of 6 in the Crystal Structure of ATNUDX1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of ATNUDX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:42.6
occ:1.00
MG B:MG204 2.3 51.6 1.0
ND1 B:HIS42 2.6 56.0 1.0
N B:HIS42 3.1 16.9 1.0
CE1 B:HIS42 3.1 58.2 1.0
CG B:HIS42 3.2 46.4 1.0
CA B:GLY41 3.6 18.9 1.0
CB B:HIS42 3.7 19.1 1.0
C B:GLY41 3.8 15.4 1.0
NE2 B:HIS42 4.0 56.5 1.0
CA B:HIS42 4.0 15.7 1.0
CD2 B:HIS42 4.0 55.3 1.0
OE2 B:GLU56 4.4 28.8 1.0
NZ B:LYS110 4.6 40.1 1.0
OE1 B:GLU56 4.8 29.9 1.0
CD B:GLU56 4.9 28.5 1.0
N B:GLY41 5.0 16.8 1.0

Magnesium binding site 6 out of 6 in 5wwd

Go back to Magnesium Binding Sites List in 5wwd
Magnesium binding site 6 out of 6 in the Crystal Structure of ATNUDX1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of ATNUDX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg206

b:44.5
occ:1.00
OE2 B:GLU107 2.6 35.3 1.0
OE1 B:GLU59 2.9 30.3 1.0
OE1 B:GLU56 3.0 29.9 1.0
CD B:GLU107 3.4 26.6 1.0
OE1 B:GLU107 3.4 29.2 1.0
NZ B:LYS110 3.6 40.1 1.0
CG B:GLU60 3.7 17.4 1.0
O B:HOH363 3.8 38.3 1.0
CB B:GLU59 3.8 20.8 1.0
MG B:MG204 3.8 51.6 1.0
OE2 B:GLU60 4.0 40.6 1.0
CD B:GLU59 4.0 26.1 1.0
CD B:GLU56 4.1 28.5 1.0
CD B:GLU60 4.3 29.1 1.0
OE2 B:GLU56 4.5 28.8 1.0
CG B:GLU59 4.5 24.4 1.0
CE B:LYS110 4.7 43.4 1.0
CG B:GLU107 4.8 21.0 1.0
O B:GLU56 4.8 15.4 1.0
C B:GLU59 4.9 16.6 1.0
N B:GLU60 4.9 14.7 1.0
CA B:GLU59 5.0 17.6 1.0

Reference:

J.Liu, Z.Guan, H.Liu, L.Qi, D.Zhang, T.Zou, P.Yin. Structural Insights Into the Substrate Recognition Mechanism of Arabidopsis Gpp-Bound NUDX1 For Noncanonical Monoterpene Biosynthesis. Mol Plant V. 11 218 2018.
ISSN: ESSN 1752-9867
PubMed: 29066356
DOI: 10.1016/J.MOLP.2017.10.006
Page generated: Mon Sep 30 08:57:43 2024

Last articles

Cl in 2WU6
Cl in 2WTV
Cl in 2WTP
Cl in 2WTW
Cl in 2WTO
Cl in 2WRT
Cl in 2WTU
Cl in 2WQL
Cl in 2WTA
Cl in 2WSM
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy