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Magnesium in PDB 6dbz: Crystal Structure of Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate

Enzymatic activity of Crystal Structure of Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate

All present enzymatic activity of Crystal Structure of Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate:
3.6.1.22; 3.6.1.55; 3.6.1.67;

Protein crystallography data

The structure of Crystal Structure of Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate, PDB code: 6dbz was solved by J.P.Noel, S.T.Thomas, N.Dudareva, L.K.Henry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.69 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.050, 72.751, 116.390, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate (pdb code 6dbz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate, PDB code: 6dbz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6dbz

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Magnesium binding site 1 out of 7 in the Crystal Structure of Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate


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 Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:49.0
occ:1.00
 O A:HOH324 2.0 38.8 1.0
OE1 A:GLU56 2.1 40.7 1.0
O A:HOH301 2.3 43.1 1.0
OE2 A:GLU60 2.4 40.5 1.0
O14 A:IPR201 2.5 50.8 1.0
CD A:GLU56 3.0 40.1 1.0
CD A:GLU60 3.3 36.0 1.0
HG3 A:GLU60 3.3 35.7 1.0
HG2 A:GLU60 3.3 35.7 1.0
OE2 A:GLU56 3.3 42.8 1.0
MG A:MG204 3.4 54.4 1.0
CG A:GLU60 3.5 29.6 1.0
O A:HOH392 3.6 58.1 1.0
HA3 A:GLY41 3.7 39.7 1.0
MG A:MG203 3.7 52.0 1.0
O A:GLY40 3.7 31.8 1.0
P11 A:IPR201 3.7 58.5 1.0
O12 A:IPR201 3.9 48.3 1.0
OE1 A:GLU107 4.0 44.5 1.0
OE1 A:GLU59 4.0 45.0 1.0
O A:HOH379 4.0 47.2 1.0
HB3 A:GLU56 4.1 33.4 1.0
O13 A:IPR201 4.1 65.5 1.0
OE2 A:GLU107 4.2 45.0 1.0
HZ2 A:LYS110 4.3 72.9 1.0
HA A:GLU56 4.3 27.4 1.0
O A:HOH380 4.3 54.4 1.0
CG A:GLU56 4.3 33.2 1.0
HB2 A:GLU59 4.3 36.4 1.0
OE1 A:GLU60 4.4 28.1 1.0
CD A:GLU107 4.5 46.4 1.0
CA A:GLY41 4.5 33.0 1.0
C A:GLY40 4.6 33.4 1.0
CB A:GLU56 4.6 27.8 1.0
HG3 A:GLU56 4.6 40.0 1.0
HD2 A:LYS110 4.7 65.2 1.0
HZ3 A:LYS110 4.7 72.9 1.0
HA2 A:GLY41 4.7 39.7 1.0
HB3 A:GLU59 4.7 36.4 1.0
O A:GLU56 4.8 25.5 1.0
CA A:GLU56 4.9 22.8 1.0
NZ A:LYS110 4.9 60.7 1.0
N A:GLY41 5.0 32.2 1.0
CB A:GLU60 5.0 23.1 1.0

Magnesium binding site 2 out of 7 in 6dbz

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Magnesium binding site 2 out of 7 in the Crystal Structure of Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate


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 Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:52.0
occ:1.00
 O A:HOH377 2.0 33.1 1.0
O A:HOH379 2.0 47.2 1.0
O8 A:IPR201 2.1 50.8 1.0
OE2 A:GLU60 2.2 40.5 1.0
O A:GLY40 2.4 31.8 1.0
O14 A:IPR201 2.6 50.8 1.0
CD A:GLU60 3.2 36.0 1.0
P7 A:IPR201 3.4 61.6 1.0
O A:HOH301 3.5 43.1 1.0
OE1 A:GLU60 3.5 28.1 1.0
H A:GLY40 3.6 26.5 1.0
C A:GLY40 3.6 33.4 1.0
MG A:MG202 3.7 49.0 1.0
P11 A:IPR201 3.7 58.5 1.0
HA2 A:GLY41 3.8 39.7 1.0
O A:HOH395 3.9 46.8 1.0
O10 A:IPR201 3.9 62.7 1.0
O9 A:IPR201 4.0 60.3 1.0
O A:HOH405 4.1 40.2 1.0
HA3 A:GLY41 4.1 39.7 1.0
N A:GLY40 4.3 22.0 1.0
CA A:GLY41 4.3 33.0 1.0
O13 A:IPR201 4.4 65.5 1.0
N A:GLY41 4.4 32.2 1.0
CG A:GLU60 4.5 29.6 1.0
HG2 A:GLU60 4.5 35.7 1.0
CA A:GLY40 4.6 27.2 1.0
O6 A:IPR201 4.6 62.7 1.0
HH12 A:ARG27 4.7 56.6 1.0
HA A:PRO39 4.8 19.8 1.0
O A:HOH347 4.8 42.8 1.0
HD2 A:LYS110 4.9 65.2 1.0
O12 A:IPR201 4.9 48.3 1.0
O A:HOH401 4.9 36.7 1.0
HG3 A:GLU60 4.9 35.7 1.0
OE1 A:GLU56 4.9 40.7 1.0
HB3 A:LYS110 5.0 51.4 1.0

Magnesium binding site 3 out of 7 in 6dbz

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Magnesium binding site 3 out of 7 in the Crystal Structure of Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate


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 Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:54.4
occ:1.00
 O12 A:IPR201 2.1 48.3 1.0
O A:HOH365 2.3 43.9 1.0
OE2 A:GLU56 2.4 42.8 1.0
O A:HOH398 2.5 54.5 1.0
O A:HOH380 2.6 54.4 1.0
O A:HOH392 2.8 58.1 1.0
H A:HIS42 3.1 37.0 1.0
P11 A:IPR201 3.2 58.5 1.0
O14 A:IPR201 3.3 50.8 1.0
CD A:GLU56 3.4 40.1 1.0
MG A:MG202 3.4 49.0 1.0
HD1 A:HIS42 3.6 64.1 1.0
O13 A:IPR201 3.6 65.5 1.0
HA3 A:GLY41 3.6 39.7 1.0
HH12 A:ARG55 3.6 44.8 1.0
OE1 A:GLU56 3.7 40.7 1.0
HB2 A:HIS42 3.9 38.4 1.0
N A:HIS42 3.9 30.8 1.0
ND1 A:HIS42 4.4 53.3 1.0
CA A:GLY41 4.4 33.0 1.0
O A:HOH324 4.5 38.8 1.0
NH1 A:ARG55 4.5 37.2 1.0
OE1 A:GLU59 4.5 45.0 1.0
HH22 A:ARG55 4.5 35.2 1.0
O10 A:IPR201 4.6 62.7 1.0
CB A:HIS42 4.7 31.9 1.0
O A:HIS42 4.7 25.2 1.0
C A:GLY41 4.7 30.1 1.0
HA2 A:GLY41 4.7 39.7 1.0
CG A:GLU56 4.8 33.2 1.0
O A:HOH422 4.8 49.5 1.0
CA A:HIS42 4.8 32.0 1.0
O A:HOH301 4.8 43.1 1.0
HG3 A:GLU56 4.9 40.0 1.0
HH11 A:ARG55 4.9 44.8 1.0
CG A:HIS42 5.0 44.6 1.0

Magnesium binding site 4 out of 7 in 6dbz

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Magnesium binding site 4 out of 7 in the Crystal Structure of Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate


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 Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:30.6
occ:1.00
 O A:HOH409 2.1 28.2 1.0
O A:HOH423 2.2 28.4 1.0
O A:HOH330 2.3 24.1 1.0
O A:GLY19 3.7 17.3 1.0
O A:HOH336 4.0 19.7 1.0
O A:HOH378 4.2 32.1 1.0
HD1 A:PHE141 4.3 22.9 1.0
HA2 A:GLY19 4.5 29.5 1.0
C A:GLY19 4.6 20.6 1.0
OD1 A:ASN20 4.8 16.5 1.0
HE1 A:PHE141 4.9 22.7 1.0

Magnesium binding site 5 out of 7 in 6dbz

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Magnesium binding site 5 out of 7 in the Crystal Structure of Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate


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 Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:72.0
occ:1.00
 O B:HOH340 2.0 38.4 1.0
OE2 B:GLU60 2.1 52.8 1.0
CD B:GLU60 2.7 47.3 1.0
O9 B:IPR201 2.8 64.5 1.0
O B:HOH304 2.9 67.0 1.0
OE1 B:GLU60 3.0 35.9 1.0
O B:GLY40 3.1 39.4 1.0
O14 B:IPR201 3.2 66.0 1.0
H B:GLY40 3.7 33.3 1.0
O B:HOH356 3.9 48.2 1.0
HG2 B:GLU60 3.9 55.1 1.0
CG B:GLU60 4.0 45.9 1.0
P7 B:IPR201 4.1 87.1 1.0
MG B:MG204 4.2 74.2 1.0
P11 B:IPR201 4.2 92.8 1.0
O B:HOH352 4.2 39.7 1.0
C B:GLY40 4.3 37.2 1.0
O12 B:IPR201 4.3 82.6 1.0
HB3 B:LYS110 4.3 61.9 1.0
HD2 B:LYS110 4.4 90.6 1.0
N B:GLY40 4.5 27.6 1.0
O8 B:IPR201 4.5 78.0 1.0
HG3 B:GLU60 4.6 55.1 1.0
HA B:PRO39 4.6 27.2 1.0
O10 B:IPR201 4.6 83.7 1.0
HZ2 B:TRP114 4.6 34.8 1.0
OE1 B:GLU107 4.6 68.7 1.0
HB3 B:GLU60 4.7 41.0 1.0
HA2 B:GLY41 4.8 42.4 1.0
HD3 B:LYS110 4.8 90.6 1.0
HB2 B:LYS110 4.8 61.9 1.0
HH2 B:TRP114 4.9 35.0 1.0
HH12 B:ARG27 4.9 57.5 1.0
CB B:GLU60 4.9 34.1 1.0

Magnesium binding site 6 out of 7 in 6dbz

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Magnesium binding site 6 out of 7 in the Crystal Structure of Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate


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 Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:63.3
occ:1.00
 O B:HOH322 2.3 46.9 1.0
O13 B:IPR201 2.5 74.7 1.0
OE2 B:GLU56 2.6 48.0 1.0
O B:HOH328 2.8 52.9 1.0
H B:HIS42 2.9 35.9 1.0
MG B:MG204 3.1 74.2 1.0
HD1 B:HIS42 3.2 75.1 1.0
HA3 B:GLY41 3.5 42.4 1.0
O14 B:IPR201 3.5 66.0 1.0
CD B:GLU56 3.5 49.5 1.0
HB2 B:HIS42 3.6 43.0 1.0
HH12 B:ARG55 3.6 62.0 1.0
P11 B:IPR201 3.6 92.8 1.0
OE1 B:GLU56 3.7 50.7 1.0
N B:HIS42 3.7 29.9 1.0
ND1 B:HIS42 4.0 62.5 1.0
CA B:GLY41 4.3 35.3 1.0
O B:HOH362 4.3 53.7 1.0
CB B:HIS42 4.4 35.8 1.0
HA2 B:GLY41 4.4 42.4 1.0
NH1 B:ARG55 4.4 51.6 1.0
O12 B:IPR201 4.4 82.6 1.0
C B:GLY41 4.5 35.7 1.0
CA B:HIS42 4.6 30.8 1.0
OE1 B:GLU59 4.6 50.4 1.0
O B:HIS42 4.6 26.4 1.0
CG B:HIS42 4.7 51.7 1.0
HH11 B:ARG55 4.7 62.0 1.0
HH22 B:ARG55 4.7 48.9 1.0
O B:HOH317 4.8 51.3 1.0
O10 B:IPR201 4.8 83.7 1.0
CG B:GLU56 4.9 37.7 1.0

Magnesium binding site 7 out of 7 in 6dbz

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Magnesium binding site 7 out of 7 in the Crystal Structure of Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Nudix 1 From Arabidopsis Thaliana Complexed with Isopentenyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:74.2
occ:1.00
 OE1 B:GLU56 2.2 50.7 1.0
O B:HOH317 2.3 51.3 1.0
O14 B:IPR201 2.5 66.0 1.0
OE2 B:GLU60 2.8 52.8 1.0
O B:HOH304 2.8 67.0 1.0
MG B:MG203 3.1 63.3 1.0
CD B:GLU56 3.2 49.5 1.0
OE2 B:GLU56 3.5 48.0 1.0
HG3 B:GLU60 3.7 55.1 1.0
HA3 B:GLY41 3.7 42.4 1.0
P11 B:IPR201 3.7 92.8 1.0
O13 B:IPR201 3.7 74.7 1.0
CD B:GLU60 3.7 47.3 1.0
HG2 B:GLU60 3.8 55.1 1.0
OE1 B:GLU59 3.9 50.4 1.0
OE1 B:GLU107 3.9 68.7 1.0
CG B:GLU60 3.9 45.9 1.0
O B:HOH328 4.0 52.9 1.0
O B:GLY40 4.0 39.4 1.0
O12 B:IPR201 4.1 82.6 1.0
MG B:MG202 4.2 72.0 1.0
OE2 B:GLU107 4.2 79.6 1.0
HA B:GLU56 4.5 38.0 1.0
HB2 B:GLU59 4.5 46.4 1.0
CD B:GLU107 4.5 73.3 1.0
CA B:GLY41 4.5 35.3 1.0
HB3 B:GLU56 4.5 34.6 1.0
HA2 B:GLY41 4.6 42.4 1.0
CG B:GLU56 4.6 37.7 1.0
HB3 B:GLU59 4.7 46.4 1.0
HD2 B:LYS110 4.7 90.6 1.0
HH12 B:ARG55 4.7 62.0 1.0
OE1 B:GLU60 4.8 35.9 1.0
H B:HIS42 4.9 35.9 1.0
C B:GLY40 4.9 37.2 1.0
CB B:GLU56 5.0 28.8 1.0

Reference:

L.K.Henry, S.T.Thomas, J.R.Widhalm, J.H.Lynch, T.C.Davis, S.A.Kessler, J.Bohlmann, J.P.Noel, N.Dudareva. Contribution of Isopentenyl Phosphate to Plant Terpenoid Metabolism. Nat Plants V. 4 721 2018.
ISSN: ESSN 2055-0278
PubMed: 30127411
DOI: 10.1038/S41477-018-0220-Z
Page generated: Mon Sep 30 23:05:59 2024

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