Magnesium in PDB 6rme: Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N

Enzymatic activity of Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N

All present enzymatic activity of Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N:
3.1.3.5;

Protein crystallography data

The structure of Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N, PDB code: 6rme was solved by L.Carrique, L.Ballut, S.Violot, N.Aghajari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.25 / 3.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 108.260, 204.610, 115.920, 90.00, 113.19, 90.00
R / Rfree (%) 19.6 / 24.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N (pdb code 6rme). 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 Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N, PDB code: 6rme:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6rme

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Magnesium binding site 1 out of 8 in the Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:60.8
occ:1.00
 O3P A:IMP501 2.0 92.7 1.0
OD1 A:ASP394 2.1 86.2 1.0
OD2 A:ASP170 2.6 80.5 1.0
O A:ASN172 2.8 86.2 1.0
CG A:ASP394 3.2 85.9 1.0
CG A:ASP170 3.4 95.8 1.0
OD1 A:ASP170 3.4 0.1 1.0
P A:IMP501 3.5 0.3 1.0
OD2 A:ASP394 3.6 99.6 1.0
NE2 A:GLN395 3.7 0.3 1.0
CD A:GLN395 3.8 96.1 1.0
C A:ASN172 3.8 83.5 1.0
CG A:GLN395 4.0 0.2 1.0
O1P A:IMP501 4.1 0.3 1.0
CB A:ASN172 4.2 96.4 1.0
OE1 A:GLN395 4.3 88.7 1.0
O5' A:IMP501 4.3 97.4 1.0
O2P A:IMP501 4.4 83.5 1.0
CB A:GLU173 4.4 81.3 1.0
CB A:ASP394 4.5 75.0 1.0
CA A:ASN172 4.5 84.4 1.0
OD2 A:ASP402 4.7 88.8 1.0
CB A:ASP170 4.8 84.4 1.0
N A:ASP394 4.8 73.0 1.0
N A:GLU173 4.8 80.9 1.0
N A:ASN172 4.8 90.2 1.0
N A:GLN395 4.8 72.3 1.0
CB A:GLN395 4.9 89.2 1.0

Magnesium binding site 2 out of 8 in 6rme

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Magnesium binding site 2 out of 8 in the Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:66.3
occ:1.00
 O3P B:IMP501 2.1 0.0 1.0
OD2 B:ASP170 2.2 70.2 1.0
OD1 B:ASP394 2.2 0.4 1.0
O B:ASN172 2.7 87.8 1.0
CG B:ASP170 3.1 89.0 1.0
CG B:GLN395 3.3 86.5 1.0
CG B:ASP394 3.4 79.5 1.0
OD1 B:ASP170 3.4 0.4 1.0
P B:IMP501 3.5 94.0 1.0
NE2 B:GLN395 3.6 0.7 1.0
O1P B:IMP501 3.7 93.9 1.0
CD B:GLN395 3.7 92.0 1.0
C B:ASN172 3.7 0.5 1.0
OD2 B:ASP394 3.9 77.6 1.0
CB B:GLU173 4.1 84.1 1.0
OD2 B:ASP402 4.2 72.6 1.0
O5' B:IMP501 4.3 95.6 1.0
CB B:ASN172 4.4 0.4 1.0
CB B:ASP170 4.5 93.6 1.0
O2P B:IMP501 4.5 88.0 1.0
CA B:ASN172 4.5 96.6 1.0
CB B:ASP394 4.6 65.0 1.0
OE1 B:GLN395 4.6 82.5 1.0
N B:GLU173 4.6 0.4 1.0
CB B:GLN395 4.7 83.4 1.0
CG2 B:THR174 4.7 80.5 1.0
N B:ASN172 4.7 94.5 1.0
N B:ASP394 4.8 77.7 1.0
N B:GLN395 4.8 77.6 1.0
CA B:GLU173 4.9 82.6 1.0

Magnesium binding site 3 out of 8 in 6rme

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Magnesium binding site 3 out of 8 in the Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N


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 Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:42.0
occ:1.00
 OD2 C:ASP170 2.0 50.1 1.0
OD1 C:ASP394 2.2 79.7 1.0
NE2 C:GLN395 2.3 70.0 1.0
O3P C:IMP501 2.3 84.2 1.0
O C:ASN172 2.4 63.1 1.0
CG C:ASP170 2.9 59.3 1.0
OD1 C:ASP170 3.1 73.7 1.0
CG C:ASP394 3.4 74.9 1.0
CD C:GLN395 3.4 80.5 1.0
C C:ASN172 3.6 59.4 1.0
P C:IMP501 3.7 74.5 1.0
OD2 C:ASP394 4.0 50.3 1.0
O2P C:IMP501 4.1 69.0 1.0
OE1 C:GLN395 4.1 65.3 1.0
CG C:GLN395 4.2 76.2 1.0
CB C:ASP170 4.3 54.5 1.0
CA C:ASN172 4.3 58.2 1.0
CB C:ASN172 4.3 72.7 1.0
CG2 C:THR174 4.3 62.8 1.0
CB C:GLU173 4.4 65.9 1.0
CB C:ASP394 4.4 67.2 1.0
N C:ASN172 4.5 61.2 1.0
OD1 C:ASP402 4.5 66.3 1.0
O1P C:IMP501 4.6 58.0 1.0
N C:GLU173 4.6 59.9 1.0
N C:ASP394 4.7 63.1 1.0
O5' C:IMP501 4.7 59.7 1.0
CA C:GLU173 4.9 60.4 1.0
N C:GLN395 5.0 50.8 1.0

Magnesium binding site 4 out of 8 in 6rme

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Magnesium binding site 4 out of 8 in the Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N


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 Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:71.5
occ:1.00
 O2P D:IMP501 2.1 77.2 1.0
OD2 D:ASP170 2.3 63.7 1.0
OD1 D:ASP394 2.3 88.8 1.0
O D:ASN172 2.4 66.6 1.0
CG D:ASP394 3.0 79.8 1.0
CG D:ASP170 3.1 75.8 1.0
OD1 D:ASP170 3.2 85.2 1.0
OD2 D:ASP394 3.2 83.2 1.0
NE2 D:GLN395 3.3 82.6 1.0
C D:ASN172 3.5 74.2 1.0
P D:IMP501 3.6 64.4 1.0
CB D:GLU173 4.0 63.8 1.0
O5' D:IMP501 4.2 67.4 1.0
CD D:GLN395 4.2 62.0 1.0
CG D:GLN395 4.2 62.0 1.0
CB D:ASP394 4.2 51.9 1.0
CB D:ASN172 4.3 51.7 1.0
O1P D:IMP501 4.3 52.1 1.0
CA D:ASN172 4.4 53.3 1.0
OD2 D:ASP402 4.4 65.6 1.0
CB D:ASP170 4.5 69.4 1.0
N D:GLU173 4.5 85.1 1.0
O3P D:IMP501 4.5 67.2 1.0
N D:ASN172 4.7 68.0 1.0
CA D:GLU173 4.7 66.0 1.0
N D:ASP394 4.7 76.0 1.0
N D:GLN395 5.0 64.7 1.0
OD1 D:ASN401 5.0 68.8 1.0

Magnesium binding site 5 out of 8 in 6rme

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Magnesium binding site 5 out of 8 in the Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N


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 Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:0.7
occ:1.00
 O3P E:IMP501 1.9 96.5 1.0
OD2 E:ASP170 2.1 0.9 1.0
OD2 E:ASP394 2.2 0.7 1.0
O E:ASN172 2.2 81.1 1.0
CG E:ASP394 2.7 0.1 1.0
OD1 E:ASP394 2.8 0.1 1.0
CG E:ASP170 3.0 80.6 1.0
OD1 E:ASP170 3.2 0.9 1.0
C E:ASN172 3.2 79.1 1.0
P E:IMP501 3.4 83.7 1.0
CB E:ASN172 3.6 88.4 1.0
CA E:ASN172 3.8 78.8 1.0
N E:ASN172 3.9 78.0 1.0
O2P E:IMP501 3.9 96.3 1.0
CB E:ASP394 4.0 66.3 1.0
NE2 E:GLN395 4.0 82.4 1.0
O1P E:IMP501 4.1 0.4 1.0
OD2 E:ASP402 4.3 73.6 1.0
CB E:ASP170 4.4 61.8 1.0
N E:GLU173 4.4 77.5 1.0
O5' E:IMP501 4.4 84.5 1.0
CB E:GLU173 4.5 90.1 1.0
C5' E:IMP501 4.6 97.0 1.0
ND2 E:ASN401 4.7 73.5 1.0
N E:ASP394 4.7 73.1 1.0
CD E:GLN395 4.8 77.7 1.0
C E:ALA171 4.8 80.3 1.0
CG E:GLN395 4.9 99.1 1.0
CA E:GLU173 4.9 78.9 1.0
CG2 E:THR174 4.9 57.2 1.0
CA E:ASP394 5.0 56.3 1.0
CG E:ASN172 5.0 99.3 1.0
N E:ALA171 5.0 65.8 1.0

Magnesium binding site 6 out of 8 in 6rme

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Magnesium binding site 6 out of 8 in the Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N


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 Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:48.8
occ:1.00
 O2P F:IMP501 2.0 90.1 1.0
OD1 F:ASP394 2.0 88.4 1.0
OD2 F:ASP170 2.1 65.8 1.0
O F:ASN172 2.5 74.4 1.0
CG F:ASP170 2.9 80.1 1.0
OD1 F:ASP170 3.0 88.0 1.0
CG F:ASP394 3.2 83.0 1.0
NE2 F:GLN395 3.3 0.3 1.0
P F:IMP501 3.4 65.0 1.0
C F:ASN172 3.6 76.0 1.0
O3P F:IMP501 3.8 85.7 1.0
OD2 F:ASP394 3.8 84.7 1.0
CD F:GLN395 4.0 88.7 1.0
CG F:GLN395 4.1 89.5 1.0
O5' F:IMP501 4.2 65.0 1.0
CB F:ASN172 4.2 73.9 1.0
CB F:ASP170 4.3 79.0 1.0
CA F:ASN172 4.3 72.8 1.0
OD2 F:ASP402 4.3 79.4 1.0
CB F:ASP394 4.4 73.0 1.0
N F:ASN172 4.4 76.7 1.0
O1P F:IMP501 4.5 64.8 1.0
CB F:GLU173 4.6 69.4 1.0
N F:GLU173 4.7 75.6 1.0
N F:ASP394 4.7 63.5 1.0
CG2 F:THR174 4.8 60.0 1.0
CB F:GLN395 4.9 65.3 1.0
O F:ASP170 5.0 94.8 1.0
C F:ASP170 5.0 69.0 1.0
C5' F:IMP501 5.0 77.2 1.0

Magnesium binding site 7 out of 8 in 6rme

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Magnesium binding site 7 out of 8 in the Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N


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 Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg502

b:0.3
occ:1.00
 O3P G:IMP501 2.0 0.8 1.0
OD2 G:ASP394 2.3 0.9 1.0
OD2 G:ASP170 2.3 99.7 1.0
OD1 G:ASP394 2.6 0.2 1.0
CG G:ASP394 2.7 0.8 1.0
O G:ASN172 3.1 0.6 1.0
CG G:ASP170 3.4 0.8 1.0
P G:IMP501 3.4 0.8 1.0
CG G:GLN395 3.6 0.2 1.0
OD2 G:ASP402 3.6 0.7 1.0
OD1 G:ASP170 3.7 0.5 1.0
O1P G:IMP501 3.7 0.0 1.0
CD G:GLN395 3.9 0.5 1.0
CB G:ASP394 4.2 93.2 1.0
N G:GLN395 4.2 98.8 1.0
O5' G:IMP501 4.2 0.7 1.0
NE2 G:GLN395 4.2 0.2 1.0
OE1 G:GLN395 4.3 0.1 1.0
C G:ASN172 4.3 0.5 1.0
OD1 G:ASN401 4.3 100.0 1.0
CB G:GLN395 4.4 0.6 1.0
O2P G:IMP501 4.4 98.5 1.0
N G:ASP394 4.6 0.3 1.0
CB G:ASP170 4.7 0.4 1.0
CB G:ASN172 4.7 0.5 1.0
CA G:ASP394 4.8 92.2 1.0
C G:ASP394 4.8 93.7 1.0
CG G:ASP402 4.9 98.0 1.0
CB G:GLU173 4.9 97.2 1.0
CA G:GLN395 4.9 0.8 1.0
ND2 G:ASN401 4.9 89.8 1.0
CA G:ASN172 5.0 0.5 1.0

Magnesium binding site 8 out of 8 in 6rme

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Magnesium binding site 8 out of 8 in the Structure of Imp Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N


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 Bound Plasmodium Falciparum Imp-Nucleotidase Mutant D172N within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg502

b:55.8
occ:1.00
 OD2 H:ASP170 2.1 66.3 1.0
O2P H:IMP501 2.2 96.2 1.0
OD2 H:ASP394 2.2 78.9 1.0
OD1 H:ASP394 2.2 0.7 1.0
CG H:ASP394 2.4 96.8 1.0
O H:ASN172 3.0 75.0 1.0
CG H:ASP170 3.0 84.6 1.0
OD1 H:ASP170 3.3 98.6 1.0
P H:IMP501 3.3 93.3 1.0
O1P H:IMP501 3.6 71.0 1.0
CB H:ASP394 3.9 78.6 1.0
O3P H:IMP501 4.1 72.3 1.0
CD H:GLN395 4.1 85.9 1.0
C H:ASN172 4.2 88.7 1.0
OE1 H:GLN395 4.3 65.1 1.0
CG H:GLN395 4.3 93.8 1.0
OD2 H:ASP402 4.4 84.7 1.0
CB H:ASP170 4.4 77.5 1.0
NE2 H:GLN395 4.5 99.6 1.0
N H:ASP394 4.5 71.4 1.0
O5' H:IMP501 4.5 73.7 1.0
N H:GLN395 4.6 91.8 1.0
ND2 H:ASN401 4.6 85.9 1.0
CB H:ASN172 4.7 81.9 1.0
C5' H:IMP501 4.7 76.8 1.0
CA H:ASP394 4.7 68.0 1.0
CG2 H:THR174 4.7 72.2 1.0
CA H:ASN172 4.8 81.7 1.0
OD1 H:ASP402 4.8 86.4 1.0
OD1 H:ASN401 4.8 62.1 1.0
NZ H:LYS371 4.9 78.0 1.0
CB H:GLN395 4.9 68.8 1.0
N H:ASN172 4.9 87.7 1.0
CG H:ASP402 5.0 69.3 1.0

Reference:

L.Carrique, L.Ballut, A.Shukla, N.Varma, R.Ravi, S.Violot, B.Srinivasan, U.T.Ganeshappa, S.Kulkarni, H.Balaram, N.Aghajari. Structure and Catalytic Regulation of Plasmodium Falciparum Imp Specific Nucleotidase. Nat Commun V. 11 3228 2020.
ISSN: ESSN 2041-1723
PubMed: 32591529
DOI: 10.1038/S41467-020-17013-X
Page generated: Tue Dec 15 00:00:22 2020

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