Magnesium in PDB 5z79: Crystal Structure Analysis of the Hppk-Dhps in Complex with Substrates

All present enzymatic activity of Crystal Structure Analysis of the Hppk-Dhps in Complex with Substrates:
2.5.1.15; 2.7.6.3;

The structure of Crystal Structure Analysis of the Hppk-Dhps in Complex with Substrates, PDB code: 5z79 was solved by Y.Manickam, H.Karl, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.82 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	136.049, 113.892, 172.387, 90.00, 94.24, 90.00
R / Rfree (%)	24.2 / 28.5

The binding sites of Magnesium atom in the Crystal Structure Analysis of the Hppk-Dhps in Complex with Substrates (pdb code 5z79). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure Analysis of the Hppk-Dhps in Complex with Substrates, PDB code: 5z79:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure Analysis of the Hppk-Dhps in Complex with Substrates


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Analysis of the Hppk-Dhps in Complex with Substrates within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1104 b:31.9 occ:1.00 OD1 A:ASN342 2.1 34.8 1.0 O2P A:HH21101 2.2 56.1 1.0 O4P A:HH21101 2.2 32.6 1.0 CG A:ASN342 3.3 35.4 1.0 P2 A:HH21101 3.3 48.6 1.0 O6P A:HH21101 3.5 46.8 1.0 NH2 A:ARG697 3.5 31.6 1.0 P1 A:HH21101 3.6 33.6 1.0 OD2 A:ASP454 3.8 31.4 1.0 ND2 A:ASN342 3.8 35.3 1.0 O3P A:HH21101 3.9 51.1 1.0 C3 A:HH21101 4.0 25.2 1.0 O A:GLU380 4.4 35.2 1.0 OG A:SER347 4.4 37.1 1.0 CA A:GLY378 4.5 33.8 1.0 CB A:ASN342 4.5 36.5 1.0 O4 A:HH21101 4.5 53.9 1.0 O1P A:HH21101 4.6 30.4 1.0 O5P A:HH21101 4.7 27.9 1.0 N4 A:HH21101 4.7 25.3 1.0 C11 A:HH21101 4.8 42.2 1.0 CZ A:ARG697 4.8 31.1 1.0 O A:GLY378 4.9 35.7 1.0 C2 A:HH21101 4.9 30.5 1.0 CG A:ASP454 4.9 31.1 1.0 C A:GLY378 4.9 35.0 1.0 CA A:ASN342 5.0 36.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure Analysis of the Hppk-Dhps in Complex with Substrates


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure Analysis of the Hppk-Dhps in Complex with Substrates within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1104 b:32.2 occ:1.00 O5P C:HH21101 2.2 52.5 1.0 O2P C:HH21101 2.2 35.7 1.0 OD1 C:ASN342 2.3 31.0 1.0 CG C:ASN342 3.3 31.3 1.0 P2 C:HH21101 3.4 42.9 1.0 P1 C:HH21101 3.6 39.3 1.0 O6P C:HH21101 3.8 39.5 1.0 ND2 C:ASN342 3.8 31.0 1.0 NH2 C:ARG697 3.8 27.8 1.0 OD2 C:ASP454 4.0 28.1 1.0 O3P C:HH21101 4.0 35.1 1.0 O C:GLU380 4.0 32.4 1.0 OG C:SER347 4.3 33.7 1.0 CA C:GLY378 4.4 29.9 1.0 C3 C:HH21101 4.4 37.9 1.0 O4 C:HH21101 4.6 43.0 1.0 CB C:ASN342 4.6 32.1 1.0 O4P C:HH21101 4.7 41.3 1.0 O1P C:HH21101 4.7 33.5 1.0 O C:GLY378 4.7 31.7 1.0 C C:GLY378 4.8 31.2 1.0 ND2 C:ASN344 4.9 36.0 1.0 C11 C:HH21101 4.9 51.4 1.0 CG C:ASP454 5.0 27.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure Analysis of the Hppk-Dhps in Complex with Substrates


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure Analysis of the Hppk-Dhps in Complex with Substrates within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1104 b:27.1 occ:1.00 OD1 D:ASN342 2.1 32.7 1.0 O4P D:HH21101 2.2 41.7 1.0 O D:HOH1239 2.6 28.1 1.0 O1P D:HH21101 3.2 31.0 1.0 CG D:ASN342 3.3 32.9 1.0 P2 D:HH21101 3.5 44.8 1.0 OD2 D:ASP454 3.7 30.6 1.0 O D:GLU380 3.7 34.0 1.0 O6P D:HH21101 3.9 28.5 1.0 ND2 D:ASN342 3.9 32.5 1.0 NH2 D:ARG697 4.0 30.1 1.0 P1 D:HH21101 4.1 34.8 1.0 CA D:GLY378 4.2 33.2 1.0 O3P D:HH21101 4.3 32.3 1.0 O D:GLY378 4.3 34.6 1.0 O4 D:HH21101 4.4 34.2 1.0 OG D:SER347 4.5 34.4 1.0 C3 D:HH21101 4.5 38.8 1.0 CB D:ASN342 4.5 33.9 1.0 C D:GLY378 4.5 34.3 1.0 O5P D:HH21101 4.7 33.1 1.0 CG D:ASP454 4.7 30.6 1.0 C D:GLU380 4.8 34.9 1.0 CA D:ASN342 4.9 34.1 1.0 N D:GLY378 5.0 33.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure Analysis of the Hppk-Dhps in Complex with Substrates


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure Analysis of the Hppk-Dhps in Complex with Substrates within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1103 b:28.8 occ:1.00 OD1 E:ASN342 2.1 44.3 1.0 O3P E:HH21101 2.2 48.5 1.0 O5P E:HH21101 2.8 60.2 1.0 P2 E:HH21101 3.0 60.0 1.0 CG E:ASN342 3.3 44.5 1.0 O2P E:HH21101 3.3 56.2 1.0 P1 E:HH21101 3.4 40.4 1.0 O4P E:HH21101 3.6 33.7 1.0 OD2 E:ASP454 3.6 42.3 1.0 O E:GLU380 3.7 46.8 1.0 NH2 E:ARG697 3.8 41.2 1.0 ND2 E:ASN342 3.8 44.1 1.0 C3 E:HH21101 4.2 45.0 1.0 O6P E:HH21101 4.3 53.7 1.0 O1P E:HH21101 4.4 27.7 1.0 O4 E:HH21101 4.4 47.9 1.0 CA E:GLY378 4.5 43.5 1.0 CB E:ASN342 4.5 45.2 1.0 OG E:SER347 4.5 47.7 1.0 C11 E:HH21101 4.7 51.5 1.0 CG E:ASP454 4.7 42.0 1.0 C E:GLU380 4.8 48.1 1.0 C2 E:HH21101 4.8 42.5 1.0 O E:GLY378 4.9 45.5 1.0 CG2 E:ILE340 5.0 41.4 1.0 N4 E:HH21101 5.0 39.8 1.0 CA E:SER381 5.0 49.1 1.0 ND2 E:ASN344 5.0 48.0 1.0 CZ E:ARG697 5.0 40.6 1.0

M.Yogavel, J.E.Nettleship, A.Sharma, K.Harlos, A.Jamwal, R.Chaturvedi, M.Sharma, V.Jain, J.Chhibber-Goel, A.Sharma. Structure of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase-Dihydropteroate Synthase Fromplasmodium Vivaxsheds Light on Drug Resistance J. Biol. Chem. V. 293 14962 2018.
ISSN: ESSN 1083-351X
PubMed: 30104413
DOI: 10.1074/JBC.RA118.004558