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Magnesium in PDB 5mcp: Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp

Enzymatic activity of Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp

All present enzymatic activity of Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp:
1.1.1.205;

Protein crystallography data

The structure of Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp, PDB code: 5mcp was solved by G.Winter, D.Fernandez-Justel, J.M.De Pereda, J.L.Revuelta, R.M.Buey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 152.04 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 127.891, 152.090, 152.255, 90.00, 93.03, 90.00
R / Rfree (%) 24.9 / 27.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp (pdb code 5mcp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp, PDB code: 5mcp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5mcp

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Magnesium binding site 1 out of 8 in the Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:79.3
occ:1.00
O1G B:ATP605 1.8 0.3 1.0
O3B B:ATP606 2.1 0.5 1.0
OE1 B:GLN170 3.0 0.7 1.0
PG B:ATP605 3.2 0.8 1.0
PB B:ATP606 3.2 0.3 1.0
O3G B:ATP606 3.4 0.1 1.0
PG B:ATP606 3.4 0.5 1.0
O1B B:ATP605 3.4 0.1 1.0
O3A B:ATP606 3.5 0.9 1.0
O2B B:ATP606 3.6 0.8 1.0
PA B:ATP606 3.7 0.0 1.0
O2G B:ATP605 3.7 0.1 1.0
HE22 B:GLN170 3.8 0.5 1.0
O1A B:ATP606 3.8 0.8 1.0
O2G B:ATP606 3.9 0.3 1.0
CD B:GLN170 4.0 0.2 1.0
PB B:ATP605 4.0 0.9 1.0
O3B B:ATP605 4.2 0.5 1.0
NE2 B:GLN170 4.3 0.1 1.0
O3G B:ATP605 4.3 0.1 1.0
O2A B:ATP606 4.3 0.1 1.0
O1B B:ATP606 4.5 0.3 1.0
O1G B:ATP606 4.5 0.0 1.0
O2B B:ATP605 4.7 0.3 1.0
HG F:SER166 4.9 0.4 1.0

Magnesium binding site 2 out of 8 in 5mcp

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Magnesium binding site 2 out of 8 in the Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:89.2
occ:1.00
O2B C:ATP602 1.8 93.3 1.0
O2G C:ATP602 2.4 60.7 1.0
O2G C:ATP601 2.6 70.9 1.0
O2B C:ATP601 2.6 70.2 1.0
HZ3 C:LYS210 2.9 66.9 1.0
PB C:ATP602 3.1 76.1 1.0
HZ1 C:LYS210 3.2 66.9 1.0
HE22 H:GLN170 3.2 0.3 1.0
NZ C:LYS210 3.4 55.7 1.0
HE3 C:LYS210 3.5 65.6 1.0
PB C:ATP601 3.5 71.2 1.0
PG C:ATP602 3.6 63.4 1.0
PG C:ATP601 3.7 72.0 1.0
O C:HOH808 3.7 47.8 1.0
PA C:ATP602 3.8 55.1 1.0
O1A C:ATP602 3.8 53.5 1.0
O3B C:ATP602 3.9 70.7 1.0
O2A C:ATP602 3.9 54.9 1.0
HZ H:PHE171 3.9 0.8 1.0
NE2 H:GLN170 4.0 98.6 1.0
CE C:LYS210 4.0 54.6 1.0
O1G C:ATP601 4.0 71.6 1.0
O3B C:ATP601 4.1 72.2 1.0
O3A C:ATP602 4.1 65.5 1.0
O1B C:ATP602 4.2 72.7 1.0
HZ2 C:LYS210 4.2 66.9 1.0
O C:HOH708 4.2 42.4 1.0
O1B C:ATP601 4.3 71.7 1.0
HA3 C:GLY209 4.4 69.9 1.0
HE21 H:GLN170 4.4 0.3 1.0
O3G C:ATP602 4.4 60.0 1.0
HE2 C:LYS210 4.5 65.6 1.0
HG1 C:THR227 4.6 89.5 1.0
OE1 H:GLN170 4.7 99.4 1.0
CD H:GLN170 4.8 99.1 1.0
O1A C:ATP601 4.8 69.0 1.0
O1G C:ATP602 4.8 61.7 1.0
CZ H:PHE171 4.8 89.7 1.0
PA C:ATP601 4.9 69.7 1.0
HE2 H:PHE171 4.9 0.5 1.0
O C:HOH800 4.9 57.1 1.0
O3A C:ATP601 4.9 71.0 1.0
OG1 C:THR227 4.9 74.5 1.0
HD3 C:LYS210 5.0 62.6 1.0

Magnesium binding site 3 out of 8 in 5mcp

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Magnesium binding site 3 out of 8 in the Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg605

b:0.2
occ:1.00
O1B H:ATP601 2.3 0.1 1.0
O3B H:ATP602 2.6 97.0 0.9
O2G H:ATP601 2.7 0.6 1.0
PB H:ATP601 2.9 97.8 1.0
O3G H:ATP601 3.0 0.1 1.0
PG H:ATP601 3.2 0.7 1.0
O2G H:ATP602 3.2 0.2 0.9
PG H:ATP602 3.4 98.6 0.9
HE22 C:GLN170 3.4 0.4 1.0
O2B H:ATP601 3.5 98.3 1.0
O3B H:ATP601 3.5 0.5 1.0
PB H:ATP602 3.7 99.3 0.9
O1G H:ATP602 3.7 95.5 0.9
O3A H:ATP602 3.9 98.5 0.9
O2B H:ATP602 4.1 99.4 0.9
NE2 C:GLN170 4.2 0.6 1.0
OE1 C:GLN170 4.3 0.6 1.0
PA H:ATP602 4.3 98.0 0.9
HG H:SER166 4.4 0.2 1.0
O3A H:ATP601 4.4 97.3 1.0
PA H:ATP601 4.6 96.8 1.0
CD C:GLN170 4.7 0.1 1.0
O1G H:ATP601 4.7 0.4 1.0
O3G H:ATP602 4.7 95.7 0.9
O1A H:ATP602 4.7 98.2 0.9
HZ C:PHE171 4.8 0.2 1.0
O2A H:ATP602 4.8 97.3 0.9
HE21 C:GLN170 4.8 0.4 1.0
O1A H:ATP601 4.8 97.7 1.0
HA3 H:GLY209 4.8 0.2 1.0
O2A H:ATP601 4.9 96.2 1.0
OG H:SER166 4.9 0.8 1.0
O1B H:ATP602 5.0 99.9 0.9

Magnesium binding site 4 out of 8 in 5mcp

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Magnesium binding site 4 out of 8 in the Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:87.5
occ:1.00
O3G G:ATP601 1.9 98.0 1.0
O1B G:ATP601 1.9 97.2 1.0
O1G G:ATP602 2.0 0.4 1.0
O1B G:ATP602 2.4 0.7 1.0
PB G:ATP601 2.8 89.3 1.0
PG G:ATP601 3.3 91.6 1.0
HE22 D:GLN170 3.3 0.8 1.0
PG G:ATP602 3.4 0.5 1.0
O2B G:ATP601 3.5 84.1 1.0
O3B G:ATP601 3.6 90.2 1.0
PB G:ATP602 3.6 1.0 1.0
O3B G:ATP602 4.1 1.0 1.0
O3A G:ATP602 4.1 0.5 1.0
O2G G:ATP602 4.1 0.9 1.0
NE2 D:GLN170 4.2 0.9 1.0
O3A G:ATP601 4.2 85.1 1.0
O1G G:ATP601 4.2 94.5 1.0
O1A G:ATP602 4.2 0.3 1.0
O2G G:ATP601 4.3 93.7 1.0
PA G:ATP601 4.3 84.8 1.0
O1A G:ATP601 4.5 83.0 1.0
PA G:ATP602 4.5 0.6 1.0
O3G G:ATP602 4.5 0.8 1.0
OE1 D:GLN170 4.6 0.8 1.0
HZ D:PHE171 4.6 0.7 1.0
HA3 G:GLY209 4.7 0.4 1.0
HE21 D:GLN170 4.7 0.8 1.0
O2A G:ATP601 4.8 86.3 1.0
CD D:GLN170 4.8 0.0 1.0
HB G:THR165 4.9 0.1 1.0
O2B G:ATP602 5.0 0.9 1.0

Magnesium binding site 5 out of 8 in 5mcp

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Magnesium binding site 5 out of 8 in the Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg604

b:86.7
occ:1.00
O1B A:ATP602 1.9 62.1 1.0
O3G A:ATP602 1.9 64.5 1.0
O3G A:ATP601 2.2 64.0 1.0
O1B A:ATP601 2.2 66.1 1.0
HE22 E:GLN170 2.9 0.9 1.0
PB A:ATP602 3.1 60.6 1.0
HZ1 A:LYS210 3.1 94.1 1.0
HZ2 A:LYS210 3.2 94.1 1.0
PB A:ATP601 3.2 65.1 1.0
PG A:ATP602 3.3 67.4 1.0
PG A:ATP601 3.6 64.9 1.0
NZ A:LYS210 3.6 78.4 1.0
O3B A:ATP602 3.6 61.7 1.0
NE2 E:GLN170 3.7 0.7 1.0
O1A A:ATP602 3.7 55.2 1.0
O3B A:ATP601 3.9 64.5 1.0
O A:HOH724 3.9 49.5 1.0
HE3 A:LYS210 3.9 92.7 1.0
O2B A:ATP601 4.0 63.4 1.0
O1G A:ATP602 4.0 66.0 1.0
HE21 E:GLN170 4.1 0.9 1.0
HZ E:PHE171 4.1 99.0 1.0
PA A:ATP602 4.1 52.5 1.0
O2B A:ATP602 4.2 59.3 1.0
O3A A:ATP602 4.2 58.8 1.0
HZ3 A:LYS210 4.3 94.1 1.0
O2G A:ATP601 4.3 64.7 1.0
CE A:LYS210 4.4 77.2 1.0
OE1 E:GLN170 4.4 99.6 1.0
CD E:GLN170 4.5 0.3 1.0
O2G A:ATP602 4.5 68.9 1.0
HA3 A:GLY209 4.5 75.2 1.0
O3A A:ATP601 4.5 61.4 1.0
O1G A:ATP601 4.7 66.3 1.0
PA A:ATP601 4.7 58.1 1.0
O2A A:ATP602 4.8 53.7 1.0
HG23 A:THR227 4.8 84.2 1.0
HG21 A:THR227 4.8 84.2 1.0
O2A A:ATP601 4.9 59.0 1.0
HE2 A:LYS210 4.9 92.7 1.0
CZ E:PHE171 5.0 82.4 1.0

Magnesium binding site 6 out of 8 in 5mcp

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Magnesium binding site 6 out of 8 in the Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg605

b:93.4
occ:1.00
O2G E:ATP602 1.8 0.5 1.0
O1G E:ATP601 2.0 95.5 1.0
O2B E:ATP602 2.0 0.3 1.0
O2B E:ATP601 2.1 94.4 1.0
PG E:ATP602 3.2 0.5 1.0
PB E:ATP602 3.2 0.6 1.0
PG E:ATP601 3.2 92.0 1.0
PB E:ATP601 3.3 91.1 1.0
O3B E:ATP602 3.7 0.7 1.0
O3B E:ATP601 3.7 91.7 1.0
O2G E:ATP601 3.7 89.6 1.0
O E:HOH725 3.8 51.2 1.0
O3A E:ATP601 3.9 88.9 1.0
O3G E:ATP602 4.2 0.2 1.0
O1G E:ATP602 4.2 0.5 1.0
O2A E:ATP602 4.2 0.5 1.0
O1B E:ATP602 4.3 0.8 1.0
PA E:ATP602 4.3 0.3 1.0
O3A E:ATP602 4.4 0.9 1.0
O3G E:ATP601 4.5 90.6 1.0
O1B E:ATP601 4.7 90.6 1.0
O1A E:ATP602 4.7 0.6 1.0
HG E:SER166 4.7 0.1 1.0
O1A E:ATP601 4.8 87.0 1.0
PA E:ATP601 4.9 85.9 1.0
HA3 E:GLY209 4.9 0.7 1.0

Magnesium binding site 7 out of 8 in 5mcp

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Magnesium binding site 7 out of 8 in the Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg602

b:95.8
occ:1.00
O2B B:ATP602 1.9 62.8 1.0
O1G B:ATP601 2.0 71.1 1.0
O2G B:ATP602 2.1 68.0 1.0
O2B B:ATP601 2.7 70.1 1.0
HE21 F:GLN170 2.9 0.9 1.0
HZ1 B:LYS210 3.0 80.5 1.0
PB B:ATP602 3.0 64.0 1.0
PG B:ATP602 3.3 67.5 1.0
PG B:ATP601 3.5 71.4 1.0
O3B B:ATP602 3.5 66.8 1.0
PB B:ATP601 3.5 67.8 1.0
HE3 B:LYS210 3.6 78.7 1.0
HZ2 B:LYS210 3.6 80.5 1.0
NZ B:LYS210 3.6 67.0 1.0
NE2 F:GLN170 3.7 90.7 1.0
O B:HOH774 4.0 29.3 1.0
O1B B:ATP602 4.1 66.4 1.0
O3B B:ATP601 4.1 70.0 1.0
CE B:LYS210 4.1 65.5 1.0
PA B:ATP602 4.1 59.7 1.0
O1B B:ATP601 4.1 66.3 1.0
O2A B:ATP602 4.2 62.5 1.0
HE22 F:GLN170 4.2 0.9 1.0
O3A B:ATP602 4.2 61.4 1.0
O1G B:ATP602 4.2 67.7 1.0
O1A B:ATP602 4.3 58.8 1.0
O2G B:ATP601 4.3 72.0 1.0
HZ F:PHE171 4.4 94.0 1.0
HZ3 B:LYS210 4.4 80.5 1.0
O3G B:ATP601 4.4 72.2 1.0
O3G B:ATP602 4.4 68.4 1.0
HE2 B:LYS210 4.4 78.7 1.0
OE1 F:GLN170 4.4 91.8 1.0
CD F:GLN170 4.5 91.3 1.0
O B:HOH727 4.5 52.0 1.0
HG21 B:THR227 4.7 85.7 1.0
HG23 B:THR227 4.8 85.7 1.0
HA3 B:GLY209 4.9 80.8 1.0
O3A B:ATP601 5.0 66.2 1.0

Magnesium binding site 8 out of 8 in 5mcp

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Magnesium binding site 8 out of 8 in the Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Imp Dehydrogenase From Ashbya Gossypii Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg604

b:64.2
occ:1.00
O3B D:ATP602 2.3 68.2 1.0
O2B D:ATP601 2.3 75.8 1.0
O1G D:ATP602 2.7 62.7 1.0
O2G D:ATP601 2.7 53.9 1.0
PB D:ATP602 2.9 59.1 1.0
O1B D:ATP602 3.0 60.4 1.0
HZ2 D:LYS210 3.1 77.3 1.0
PG D:ATP602 3.1 64.5 1.0
O3A D:ATP602 3.1 56.0 1.0
PB D:ATP601 3.3 65.3 1.0
HZ3 D:LYS210 3.5 77.3 1.0
NZ D:LYS210 3.7 64.3 1.0
O3B D:ATP601 3.7 61.1 1.0
PG D:ATP601 3.8 55.8 1.0
PA D:ATP602 3.9 49.2 1.0
O3G D:ATP602 4.0 63.5 1.0
O D:HOH838 4.0 29.2 1.0
HE3 D:LYS210 4.0 75.6 1.0
O2A D:ATP602 4.1 48.1 1.0
O2G D:ATP602 4.1 64.5 1.0
HE22 G:GLN170 4.1 0.8 1.0
OE1 G:GLN170 4.2 92.4 1.0
O2B D:ATP602 4.3 57.0 1.0
HZ1 D:LYS210 4.4 77.3 1.0
O1B D:ATP601 4.4 63.5 1.0
CE D:LYS210 4.5 62.9 1.0
O3A D:ATP601 4.6 59.6 1.0
O2A D:ATP601 4.6 50.0 1.0
O1G D:ATP601 4.7 55.5 1.0
HZ G:PHE171 4.7 0.2 1.0
O D:HOH787 4.8 50.2 1.0
HG D:SER166 4.8 0.2 1.0
NE2 G:GLN170 4.8 92.6 1.0
O1A D:ATP602 4.8 49.4 1.0
HE2 D:LYS210 4.9 75.6 1.0
O3G D:ATP601 4.9 56.4 1.0
CD G:GLN170 4.9 92.6 1.0
PA D:ATP601 4.9 51.5 1.0
HG23 D:THR227 5.0 93.3 1.0

Reference:

R.M.Buey, D.Fernandez-Justel, I.Marcos-Alcalde, G.Winter, P.Gomez-Puertas, J.M.De Pereda, J.Luis Revuelta. A Nucleotide-Controlled Conformational Switch Modulates the Activity of Eukaryotic Imp Dehydrogenases. Sci Rep V. 7 2648 2017.
ISSN: ESSN 2045-2322
PubMed: 28572600
DOI: 10.1038/S41598-017-02805-X
Page generated: Mon Dec 14 20:51:09 2020

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