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Magnesium in PDB 6rmw: Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase

Enzymatic activity of Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase

All present enzymatic activity of Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase:
3.1.3.5;

Protein crystallography data

The structure of Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase, PDB code: 6rmw 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) 48.07 / 3.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 107.800, 203.900, 115.300, 90.00, 113.40, 90.00
R / Rfree (%) 23.6 / 27.9

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 6rmw

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Magnesium binding site 1 out of 8 in the Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase


Mono view


Stereo pair view

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

b:0.2
occ:1.00
 O3P A:IMP501 2.0 0.3 1.0
OD1 A:ASP394 2.2 0.7 1.0
OD2 A:ASP170 2.2 0.9 1.0
NE2 A:GLN395 2.4 0.4 1.0
O A:ASN172 2.9 0.7 1.0
CG A:ASP170 3.2 1.0 1.0
CG A:ASP394 3.2 0.5 1.0
CD A:GLN395 3.2 0.2 1.0
P A:IMP501 3.5 0.7 1.0
OD1 A:ASP170 3.5 0.6 1.0
OD2 A:ASP394 3.7 0.2 1.0
C A:ASN172 3.9 0.4 1.0
CG A:GLN395 3.9 0.8 1.0
OE1 A:GLN395 4.0 0.1 1.0
O1P A:IMP501 4.1 0.4 1.0
O2P A:IMP501 4.2 0.3 1.0
OD2 A:ASP402 4.2 0.4 1.0
CB A:GLU173 4.2 0.7 1.0
O5' A:IMP501 4.3 0.0 1.0
CB A:ASN172 4.4 0.5 1.0
CB A:ASP170 4.4 0.9 1.0
O A:ASP170 4.5 0.5 1.0
CB A:ASP394 4.5 0.5 1.0
N A:ASP394 4.6 0.2 1.0
N A:GLN395 4.6 0.5 1.0
CA A:ASN172 4.6 0.1 1.0
OD1 A:ASN401 4.7 0.9 1.0
NZ A:LYS371 4.7 1.0 1.0
CB A:GLN395 4.8 0.7 1.0
N A:GLU173 4.8 0.1 1.0
CG A:GLU173 4.9 0.1 1.0
N A:ASN172 4.9 1.0 1.0

Magnesium binding site 2 out of 8 in 6rmw

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Magnesium binding site 2 out of 8 in the Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase


Mono view


Stereo pair view

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

b:0.3
occ:1.00
 OD1 B:ASP394 2.1 0.6 1.0
OD2 B:ASP170 2.2 0.2 1.0
O B:ASN172 2.3 0.3 1.0
O3P B:IMP501 2.3 0.0 1.0
CG B:ASP170 3.1 0.3 1.0
CG B:ASP394 3.2 0.9 1.0
C B:ASN172 3.3 0.5 1.0
OD1 B:ASP170 3.4 0.8 1.0
CB B:GLU173 3.7 0.0 1.0
P B:IMP501 3.7 0.0 1.0
OD2 B:ASP394 3.8 0.7 1.0
CG B:GLN395 3.9 0.1 1.0
O1P B:IMP501 4.1 0.1 1.0
N B:GLU173 4.2 0.6 1.0
CA B:ASN172 4.2 0.7 1.0
CD B:GLN395 4.3 0.5 1.0
CB B:ASN172 4.3 0.9 1.0
NE2 B:GLN395 4.3 0.8 1.0
CB B:ASP170 4.4 0.5 1.0
CB B:ASP394 4.4 0.3 1.0
CG2 B:THR174 4.4 0.8 1.0
OD2 B:ASP402 4.5 0.7 1.0
CA B:GLU173 4.5 0.6 1.0
N B:ASN172 4.5 0.2 1.0
O2P B:IMP501 4.6 0.5 1.0
O5' B:IMP501 4.6 0.2 1.0
N B:ASP394 4.7 0.0 1.0
N B:GLN395 4.9 1.0 1.0
N B:THR174 4.9 0.9 1.0
CG B:GLU173 4.9 0.6 1.0
C B:GLU173 5.0 0.0 1.0
CA B:ASP394 5.0 0.9 1.0

Magnesium binding site 3 out of 8 in 6rmw

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Magnesium binding site 3 out of 8 in the Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:85.7
occ:1.00
 OD2 C:ASP170 2.1 98.0 1.0
NE2 C:GLN395 2.2 0.2 1.0
OD1 C:ASP394 2.2 0.1 1.0
O3P C:IMP501 2.3 0.7 1.0
O C:ASN172 2.5 0.7 1.0
CG C:ASP170 2.9 0.1 1.0
OD1 C:ASP170 3.0 0.7 1.0
CG C:ASP394 3.2 0.7 1.0
CD C:GLN395 3.4 0.0 1.0
C C:ASN172 3.6 0.8 1.0
P C:IMP501 3.8 0.7 1.0
OD2 C:ASP394 3.8 0.0 1.0
CB C:GLU173 4.2 0.7 1.0
OE1 C:GLN395 4.2 0.7 1.0
CB C:ASP170 4.3 0.5 1.0
CG C:GLN395 4.3 0.5 1.0
CB C:ASP394 4.3 0.3 1.0
O2P C:IMP501 4.3 0.0 1.0
CG2 C:THR174 4.3 0.2 1.0
CB C:ASN172 4.3 0.0 1.0
CA C:ASN172 4.4 0.5 1.0
O1P C:IMP501 4.5 0.7 1.0
N C:GLU173 4.5 0.4 1.0
N C:ASP394 4.5 0.4 1.0
N C:ASN172 4.6 0.7 1.0
OD1 C:ASP402 4.6 0.6 1.0
O5' C:IMP501 4.7 0.6 1.0
CA C:GLU173 4.8 0.3 1.0
N C:GLN395 4.9 0.6 1.0
CA C:ASP394 4.9 0.7 1.0
OE1 C:GLU173 4.9 0.8 1.0

Magnesium binding site 4 out of 8 in 6rmw

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Magnesium binding site 4 out of 8 in the Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:0.8
occ:1.00
 O2P D:IMP501 1.9 0.8 1.0
OD2 D:ASP170 2.1 0.1 1.0
O D:ASN172 2.3 0.6 1.0
OD1 D:ASP394 2.5 0.6 1.0
CG D:ASP170 2.9 0.6 1.0
OD1 D:ASP170 3.0 0.5 1.0
CG D:ASP394 3.2 0.0 1.0
P D:IMP501 3.3 0.0 1.0
C D:ASN172 3.4 0.2 1.0
OD2 D:ASP394 3.6 0.2 1.0
NE2 D:GLN395 3.7 0.1 1.0
O5' D:IMP501 4.0 0.7 1.0
CB D:GLU173 4.1 0.4 1.0
CB D:ASN172 4.1 0.0 1.0
CA D:ASN172 4.2 1.0 1.0
O1P D:IMP501 4.2 0.4 1.0
CB D:ASP170 4.3 0.9 1.0
O3P D:IMP501 4.3 0.4 1.0
CD D:GLN395 4.3 0.5 1.0
OD2 D:ASP402 4.3 0.9 1.0
CG D:GLN395 4.4 0.7 1.0
N D:GLU173 4.4 0.6 1.0
CB D:ASP394 4.4 0.3 1.0
N D:ASN172 4.4 0.6 1.0
CG2 D:THR174 4.6 1.0 1.0
CA D:GLU173 4.7 0.8 1.0
N D:ASP394 4.8 0.6 1.0
OD1 D:ASN401 4.8 0.5 1.0
ND2 D:ASN401 5.0 0.8 1.0

Magnesium binding site 5 out of 8 in 6rmw

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Magnesium binding site 5 out of 8 in the Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:0.2
occ:1.00
 O3P E:IMP501 1.9 0.5 1.0
OD2 E:ASP170 2.1 0.8 1.0
OD2 E:ASP394 2.2 0.4 1.0
O E:ASN172 2.2 0.1 1.0
CG E:ASP394 2.5 0.3 1.0
OD1 E:ASP394 2.6 0.8 1.0
CG E:ASP170 3.0 0.4 1.0
C E:ASN172 3.2 0.3 1.0
OD1 E:ASP170 3.3 0.8 1.0
P E:IMP501 3.4 0.7 1.0
CB E:ASN172 3.7 0.9 1.0
CA E:ASN172 3.8 0.6 1.0
CB E:ASP394 3.8 0.6 1.0
O2P E:IMP501 3.9 0.6 1.0
N E:ASN172 3.9 0.8 1.0
NE2 E:GLN395 4.0 0.1 1.0
O1P E:IMP501 4.1 0.4 1.0
OD2 E:ASP402 4.3 0.3 1.0
N E:GLU173 4.3 0.4 1.0
O5' E:IMP501 4.4 0.5 1.0
CB E:ASP170 4.4 0.4 1.0
CB E:GLU173 4.4 0.5 1.0
C5' E:IMP501 4.5 0.3 1.0
ND2 E:ASN401 4.5 0.9 1.0
N E:ASP394 4.7 0.4 1.0
CD E:GLN395 4.7 0.6 1.0
CG2 E:THR174 4.7 0.2 1.0
CA E:ASP394 4.8 0.4 1.0
CA E:GLU173 4.8 0.2 1.0
CG E:GLN395 4.9 0.4 1.0
OD1 E:ASN401 4.9 0.9 1.0
C E:ALA171 5.0 0.2 1.0
CG E:ASN172 5.0 0.1 1.0

Magnesium binding site 6 out of 8 in 6rmw

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Magnesium binding site 6 out of 8 in the Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:0.7
occ:1.00
 O2P F:IMP501 1.8 0.6 1.0
OD1 F:ASP394 2.1 0.1 1.0
O F:ASN172 2.6 0.5 1.0
CG F:ASP394 2.7 0.0 1.0
OD1 F:ASP170 2.8 0.1 1.0
OD2 F:ASP394 2.9 0.2 1.0
P F:IMP501 3.2 0.7 1.0
OD2 F:ASP170 3.4 0.3 1.0
CG F:ASP170 3.5 0.6 1.0
O3P F:IMP501 3.6 0.1 1.0
OE1 F:GLN395 3.7 0.9 1.0
O5' F:IMP501 3.7 0.9 1.0
C F:ASN172 3.7 0.6 1.0
CD F:GLN395 4.0 0.1 1.0
CB F:ASP394 4.1 0.6 1.0
CB F:ASN172 4.1 0.8 1.0
ND2 F:ASN401 4.2 0.5 1.0
CG F:GLN395 4.3 0.1 1.0
CA F:ASN172 4.3 0.2 1.0
O1P F:IMP501 4.4 0.2 1.0
OD1 F:ASN401 4.4 0.0 1.0
CB F:GLU173 4.5 0.8 1.0
N F:ASN172 4.6 0.9 1.0
OD2 F:ASP402 4.6 0.4 1.0
C5' F:IMP501 4.7 0.7 1.0
CG F:ASN401 4.7 1.0 1.0
N F:GLU173 4.8 0.4 1.0
NE2 F:GLN395 4.8 0.4 1.0
CB F:ASP170 4.9 0.6 1.0
N F:ASP394 5.0 0.5 1.0

Magnesium binding site 7 out of 8 in 6rmw

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Magnesium binding site 7 out of 8 in the Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg502

b:0.2
occ:1.00
 O3P G:IMP501 2.1 0.6 1.0
OD2 G:ASP170 2.1 0.1 1.0
OD2 G:ASP394 2.5 0.4 1.0
NE2 G:GLN395 2.6 0.7 1.0
CB G:ASP394 2.8 0.8 1.0
CG G:ASP394 3.0 0.6 1.0
CD G:GLN395 3.1 0.0 1.0
O G:ASN172 3.2 0.2 1.0
CG G:ASP170 3.2 0.5 1.0
OD2 G:ASP402 3.5 0.2 1.0
P G:IMP501 3.5 0.9 1.0
OE1 G:GLN395 3.5 0.4 1.0
OD1 G:ASP170 3.6 0.2 1.0
O1P G:IMP501 3.8 0.3 1.0
CA G:ASP394 3.9 0.9 1.0
N G:GLN395 4.0 0.5 1.0
CG G:GLN395 4.0 0.7 1.0
OD1 G:ASN401 4.1 0.8 1.0
N G:ASP394 4.1 0.8 1.0
OD1 G:ASP394 4.2 0.2 1.0
C G:ASN172 4.3 0.8 1.0
C G:ASP394 4.3 1.0 1.0
O2P G:IMP501 4.4 0.5 1.0
ND2 G:ASN401 4.4 0.4 1.0
O5' G:IMP501 4.5 0.1 1.0
CB G:ASP170 4.5 0.6 1.0
CB G:GLU173 4.6 0.6 1.0
CB G:GLN395 4.7 0.7 1.0
CG G:ASN401 4.7 0.5 1.0
CG G:ASP402 4.7 0.9 1.0
CB G:ASN172 4.9 0.3 1.0
CA G:GLN395 5.0 0.0 1.0

Magnesium binding site 8 out of 8 in 6rmw

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Magnesium binding site 8 out of 8 in the Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of N-Terminal Truncated Imp Bound Plasmodium Falciparum Imp- Nucleotidase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg502

b:0.8
occ:1.00
 O2P H:IMP501 2.1 0.8 1.0
OD2 H:ASP394 2.1 0.5 1.0
OD2 H:ASP170 2.2 0.8 1.0
O H:ASN172 2.3 0.6 1.0
CG H:ASP394 2.5 0.4 1.0
OD1 H:ASP394 2.5 0.5 1.0
CG H:ASP170 3.1 0.5 1.0
OD1 H:ASP170 3.3 0.9 1.0
P H:IMP501 3.4 0.8 1.0
C H:ASN172 3.4 0.3 1.0
CB H:ASP394 3.8 0.2 1.0
O3P H:IMP501 3.8 0.0 1.0
O1P H:IMP501 4.1 0.8 1.0
CB H:ASN172 4.1 0.0 1.0
CA H:ASN172 4.2 0.4 1.0
CB H:GLU173 4.3 0.7 1.0
CG2 H:THR174 4.3 0.0 1.0
N H:ASN172 4.3 0.6 1.0
CB H:ASP170 4.4 0.6 1.0
N H:GLU173 4.5 0.8 1.0
CD H:GLN395 4.5 0.6 1.0
OE1 H:GLN395 4.5 0.4 1.0
N H:ASP394 4.6 0.6 1.0
O5' H:IMP501 4.6 0.7 1.0
OD2 H:ASP402 4.7 0.3 1.0
NE2 H:GLN395 4.7 0.1 1.0
CA H:ASP394 4.7 0.5 1.0
CA H:GLU173 4.8 0.9 1.0
CG H:GLN395 4.8 0.1 1.0
C5' H:IMP501 4.9 0.1 1.0
N H:GLN395 4.9 0.6 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 Oct 1 17:26:38 2024

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