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Magnesium in PDB 5myd: Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling.

Enzymatic activity of Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling.

All present enzymatic activity of Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling.:
3.6.1.23;

Protein crystallography data

The structure of Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling., PDB code: 5myd was solved by J.Donderis, J.Bowring, E.Maiques, J.R.Ciges-Tomas, C.Alite, I.Mehmedov, M.A.Tormo-Mas, J.R.Penades, A.Marina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.12 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.890, 81.440, 81.530, 90.00, 106.92, 90.00
R / Rfree (%) 22.4 / 26.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling. (pdb code 5myd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling., PDB code: 5myd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5myd

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Magnesium binding site 1 out of 8 in the Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:45.6
occ:1.00
 OE1 A:GLU42 2.2 78.4 1.0
OE1 A:GLU39 2.3 34.4 1.0
OE1 A:GLU67 2.3 53.9 1.0
OD2 A:ASP70 2.4 47.3 1.0
O1B A:DUP201 2.7 89.5 1.0
CD A:GLU39 3.2 37.2 1.0
CD A:GLU67 3.3 48.1 1.0
CD A:GLU42 3.4 81.8 1.0
CG A:ASP70 3.4 48.4 1.0
OE2 A:GLU39 3.5 46.5 1.0
OE2 A:GLU67 3.7 61.7 1.0
O2G A:DUP201 3.8 58.8 1.0
MG A:MG203 3.9 64.0 1.0
CB A:ASP70 3.9 44.3 1.0
PB A:DUP201 4.0 99.9 1.0
OE2 A:GLU42 4.2 88.5 1.0
O2B A:DUP201 4.3 71.4 1.0
CB A:GLU42 4.3 51.1 1.0
OD1 A:ASP70 4.4 54.1 1.0
CG A:GLU42 4.4 75.3 1.0
O3B A:DUP201 4.4 0.0 1.0
CG A:GLU39 4.6 37.5 1.0
CG A:GLU67 4.7 40.9 1.0
CA A:GLU67 4.7 36.6 1.0
PG A:DUP201 4.8 79.5 1.0
CB A:GLU67 4.9 39.8 1.0

Magnesium binding site 2 out of 8 in 5myd

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Magnesium binding site 2 out of 8 in the Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:64.0
occ:1.00
 O1A A:DUP201 2.3 73.2 1.0
OE2 A:GLU39 2.3 46.5 1.0
OE2 A:GLU42 2.7 88.5 1.0
O1B A:DUP201 2.8 89.5 1.0
O2G A:DUP201 2.8 58.8 1.0
O1G A:DUP201 3.0 63.4 1.0
OE1 A:GLU42 3.2 78.4 1.0
CD A:GLU42 3.3 81.8 1.0
PG A:DUP201 3.3 79.5 1.0
CD A:GLU39 3.3 37.2 1.0
PB A:DUP201 3.7 99.9 1.0
PA A:DUP201 3.7 74.2 1.0
OE1 A:GLU39 3.8 34.4 1.0
MG A:MG202 3.9 45.6 1.0
O3B A:DUP201 3.9 0.0 1.0
N3A A:DUP201 4.2 68.7 1.0
CG A:GLU39 4.5 37.5 1.0
O2A A:DUP201 4.6 83.2 1.0
O5' A:DUP201 4.7 85.8 1.0
C5' A:DUP201 4.8 72.5 1.0
O3G A:DUP201 4.8 66.4 1.0
CG A:GLU42 4.8 75.3 1.0

Magnesium binding site 3 out of 8 in 5myd

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Magnesium binding site 3 out of 8 in the Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:46.9
occ:1.00
 O1B B:DUP201 2.1 50.1 1.0
O2G B:DUP201 2.2 39.6 1.0
OE2 B:GLU39 2.3 45.0 1.0
O1A B:DUP201 2.3 45.8 1.0
OE2 B:GLU42 2.6 80.1 1.0
OE1 B:GLU42 2.9 50.0 1.0
CD B:GLU42 3.1 53.3 1.0
PB B:DUP201 3.2 52.9 1.0
CD B:GLU39 3.2 34.1 1.0
MG B:MG203 3.3 61.5 1.0
PG B:DUP201 3.3 51.7 1.0
O3B B:DUP201 3.5 64.6 1.0
OE1 B:GLU39 3.5 33.1 1.0
PA B:DUP201 3.6 52.8 1.0
N3A B:DUP201 3.7 38.4 1.0
O3G B:DUP201 4.0 43.8 1.0
O B:HOH308 4.4 58.1 1.0
O1G B:DUP201 4.5 50.5 1.0
CG B:GLU39 4.5 31.9 1.0
O2B B:DUP201 4.6 62.0 1.0
C5' B:DUP201 4.6 48.5 1.0
O2A B:DUP201 4.6 43.4 1.0
O5' B:DUP201 4.7 50.4 1.0
CG B:GLU42 4.7 39.5 1.0

Magnesium binding site 4 out of 8 in 5myd

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Magnesium binding site 4 out of 8 in the Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:61.5
occ:1.00
 O1B B:DUP201 2.2 50.1 1.0
OE1 B:GLU42 2.4 50.0 1.0
OD2 B:ASP70 2.4 45.9 1.0
OE1 B:GLU39 2.6 33.1 1.0
O B:HOH308 2.7 58.1 1.0
OE1 B:GLU67 2.7 39.3 1.0
PB B:DUP201 3.1 52.9 1.0
MG B:MG202 3.3 46.9 1.0
O2B B:DUP201 3.3 62.0 1.0
O3B B:DUP201 3.4 64.6 1.0
CG B:ASP70 3.4 41.6 1.0
CD B:GLU39 3.5 34.1 1.0
OE2 B:GLU39 3.5 45.0 1.0
CD B:GLU42 3.6 53.3 1.0
CD B:GLU67 3.6 37.5 1.0
OE2 B:GLU67 3.8 43.8 1.0
CB B:ASP70 4.1 34.9 1.0
OE2 B:GLU42 4.2 80.1 1.0
OD1 B:ASP70 4.2 46.4 1.0
O2G B:DUP201 4.3 39.6 1.0
PG B:DUP201 4.4 51.7 1.0
NZ B:LYS154 4.4 41.9 1.0
O3G B:DUP201 4.4 43.8 1.0
N3A B:DUP201 4.7 38.4 1.0
CB B:GLU42 4.7 34.1 1.0
CG B:GLU42 4.7 39.5 1.0
O1A B:DUP201 4.8 45.8 1.0
CG B:GLU39 4.9 31.9 1.0
CG B:GLU67 5.0 36.2 1.0

Magnesium binding site 5 out of 8 in 5myd

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Magnesium binding site 5 out of 8 in the Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:55.4
occ:1.00
 OD2 C:ASP70 2.4 51.0 1.0
OE1 C:GLU42 2.4 66.2 1.0
OE1 C:GLU67 2.5 49.7 1.0
O2B C:DUP201 2.5 60.5 1.0
OE1 C:GLU39 2.6 47.5 1.0
MG C:MG203 3.1 74.5 1.0
CG C:ASP70 3.4 39.0 1.0
CD C:GLU67 3.4 42.2 1.0
CD C:GLU39 3.5 35.7 1.0
OE2 C:GLU39 3.6 46.7 1.0
CD C:GLU42 3.6 78.7 1.0
OE2 C:GLU67 3.7 46.8 1.0
PB C:DUP201 3.9 91.8 1.0
O2G C:DUP201 4.0 44.1 1.0
CB C:ASP70 4.1 36.8 1.0
OD1 C:ASP70 4.3 46.0 1.0
OE2 C:GLU42 4.3 0.7 1.0
O3B C:DUP201 4.4 0.3 1.0
NZ C:LYS154 4.5 69.5 1.0
O C:HOH325 4.5 46.7 1.0
CB C:GLU42 4.6 42.2 1.0
O1B C:DUP201 4.7 0.2 1.0
CG C:GLU42 4.7 59.2 1.0
CG C:GLU67 4.8 42.1 1.0
CA C:GLU67 4.9 37.2 1.0
CG C:GLU39 4.9 30.9 1.0
PG C:DUP201 5.0 62.7 1.0

Magnesium binding site 6 out of 8 in 5myd

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Magnesium binding site 6 out of 8 in the Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg203

b:74.5
occ:1.00
 O3B C:DUP201 2.3 0.3 1.0
O2B C:DUP201 2.6 60.5 1.0
OE2 C:GLU39 2.6 46.7 1.0
O2A C:DUP201 2.8 61.2 1.0
OE1 C:GLU42 2.8 66.2 1.0
OE2 C:GLU42 2.8 0.7 1.0
O2G C:DUP201 2.9 44.1 1.0
PG C:DUP201 2.9 62.7 1.0
O1G C:DUP201 2.9 89.7 1.0
PB C:DUP201 3.0 91.8 1.0
MG C:MG202 3.1 55.4 1.0
CD C:GLU42 3.2 78.7 1.0
CD C:GLU39 3.5 35.7 1.0
OE1 C:GLU39 3.6 47.5 1.0
PA C:DUP201 3.9 72.6 1.0
N3A C:DUP201 4.0 75.3 1.0
O1B C:DUP201 4.3 0.2 1.0
O3G C:DUP201 4.3 52.9 1.0
C5' C:DUP201 4.7 74.9 1.0
CG C:GLU42 4.8 59.2 1.0
CG C:GLU39 4.8 30.9 1.0
O5' C:DUP201 4.9 80.5 1.0
OD2 C:ASP70 4.9 51.0 1.0
O1A C:DUP201 4.9 53.1 1.0

Magnesium binding site 7 out of 8 in 5myd

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Magnesium binding site 7 out of 8 in the Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:46.0
occ:1.00
 O1B D:DUP201 2.3 42.8 1.0
OE1 D:GLU42 2.3 43.9 1.0
OD2 D:ASP70 2.4 41.4 1.0
OE1 D:GLU39 2.4 48.5 1.0
OE1 D:GLU67 2.6 46.2 1.0
CD D:GLU39 3.3 33.5 1.0
CG D:ASP70 3.4 38.4 1.0
MG D:MG203 3.4 62.0 1.0
OE2 D:GLU39 3.4 35.6 1.0
CD D:GLU42 3.5 52.6 1.0
CD D:GLU67 3.5 38.5 1.0
PB D:DUP201 3.5 71.2 1.0
OE2 D:GLU67 3.8 53.5 1.0
O3G D:DUP201 3.8 35.9 1.0
O2B D:DUP201 3.9 84.6 1.0
CB D:ASP70 4.0 34.6 1.0
OE2 D:GLU42 4.0 79.9 1.0
O3B D:DUP201 4.3 70.5 1.0
OD1 D:ASP70 4.4 45.5 1.0
CB D:GLU42 4.6 31.0 1.0
NZ D:LYS154 4.6 51.3 1.0
CG D:GLU42 4.6 36.1 1.0
CG D:GLU39 4.7 34.3 1.0
PG D:DUP201 4.7 50.1 1.0
CG D:GLU67 4.9 39.2 1.0
O1A D:DUP201 4.9 70.2 1.0
CA D:GLU67 4.9 33.2 1.0
N3A D:DUP201 5.0 57.3 1.0

Magnesium binding site 8 out of 8 in 5myd

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Magnesium binding site 8 out of 8 in the Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Convergent Evolution Involving Dimeric and Trimeric Dutpases in Signalling. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:62.0
occ:1.00
 OE2 D:GLU39 2.5 35.6 1.0
O1A D:DUP201 2.7 70.2 1.0
OE1 D:GLU42 2.8 43.9 1.0
O1B D:DUP201 2.8 42.8 1.0
O3G D:DUP201 2.8 35.9 1.0
O2G D:DUP201 3.1 89.5 1.0
CD D:GLU42 3.3 52.6 1.0
CD D:GLU39 3.4 33.5 1.0
PG D:DUP201 3.4 50.1 1.0
MG D:MG202 3.4 46.0 1.0
OE2 D:GLU42 3.4 79.9 1.0
OE1 D:GLU39 3.7 48.5 1.0
PB D:DUP201 3.8 71.2 1.0
O3B D:DUP201 4.0 70.5 1.0
PA D:DUP201 4.1 52.1 1.0
N3A D:DUP201 4.4 57.3 1.0
CG D:GLU42 4.6 36.1 1.0
CG D:GLU39 4.6 34.3 1.0
O1G D:DUP201 4.8 92.7 1.0
C5' D:DUP201 4.9 69.0 1.0
O5' D:DUP201 4.9 77.9 1.0

Reference:

J.Donderis, J.Bowring, E.Maiques, J.R.Ciges-Tomas, C.Alite, I.Mehmedov, M.A.Tormo-Mas, J.R.Penades, A.Marina. Convergent Evolution Involving Dimeric and Trimeric Dutpases in Pathogenicity Island Mobilization. Plos Pathog. V. 13 06581 2017.
ISSN: ESSN 1553-7374
PubMed: 28892519
DOI: 10.1371/JOURNAL.PPAT.1006581
Page generated: Sun Sep 29 23:02:27 2024

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