Magnesium in PDB 6no0: Adp Bound to Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase

All present enzymatic activity of Adp Bound to Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase:
6.2.1.5;

The structure of Adp Bound to Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase, PDB code: 6no0 was solved by J.Huang, M.E.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.32 / 2.21
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	92.203, 116.981, 127.161, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 23.9

The structure of Adp Bound to Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Adp Bound to Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase (pdb code 6no0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Adp Bound to Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase, PDB code: 6no0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Adp Bound to Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Adp Bound to Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:0.7 occ:1.00 HOA2 A:ADP301 1.7 0.4 0.9 OD2 A:ASP228 2.1 97.2 1.0 O A:ASN210 2.1 88.2 1.0 O3B A:ADP301 2.2 0.3 0.9 O2A A:ADP301 2.3 0.1 0.9 HOB3 A:ADP301 2.4 0.2 0.9 CG A:ASP228 3.1 90.0 1.0 HB3 A:ASP228 3.1 0.5 1.0 HB2 A:ASP228 3.2 0.5 1.0 HD3 A:PRO211 3.3 97.4 1.0 PB A:ADP301 3.3 0.8 0.9 PA A:ADP301 3.3 0.6 0.9 CB A:ASP228 3.3 83.8 1.0 C A:ASN210 3.3 80.4 1.0 O3A A:ADP301 3.5 0.2 0.9 HB3 A:ASN210 3.7 99.2 1.0 O1B A:ADP301 3.8 0.9 0.9 O1A A:ADP301 3.8 0.7 0.9 HD2 A:PRO211 3.8 97.4 1.0 CD A:PRO211 3.9 81.2 1.0 N A:PRO211 4.1 81.6 1.0 HD22 A:ASN210 4.2 0.5 1.0 OD1 A:ASP228 4.2 88.7 1.0 CB A:ASN210 4.3 82.7 1.0 ND2 A:ASN210 4.4 94.6 1.0 CA A:ASN210 4.4 80.0 1.0 CG A:ASN210 4.4 88.8 1.0 HH21 A:ARG58 4.5 0.0 1.0 HO3' A:ADP301 4.5 0.7 0.9 O2B A:ADP301 4.6 0.0 0.9 H5'2 A:ADP301 4.6 0.7 0.9 O5' A:ADP301 4.7 0.1 0.9 H3' A:ADP301 4.7 0.7 0.9 H A:ASN210 4.7 93.3 1.0 HD21 A:ASN210 4.7 0.5 1.0 CA A:ASP228 4.9 73.4 1.0 O3' A:ADP301 4.9 0.4 0.9 HOB2 A:ADP301 5.0 0.6 0.9

Magnesium binding site 2 out of 3 in the Adp Bound to Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Adp Bound to Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:0.1 occ:1.00 OD1 A:ASP220 2.1 0.4 1.0 OD2 B:ASP220 2.2 0.1 1.0 OD1 B:ASP220 2.2 96.7 1.0 OE1 A:GLU216 2.2 0.9 1.0 CG B:ASP220 2.5 91.0 1.0 CG A:ASP220 3.3 98.4 1.0 CD A:GLU216 3.4 0.2 1.0 HD3 A:LYS114 3.5 0.1 1.0 HD2 A:LYS114 3.6 0.1 1.0 OD2 A:ASP220 3.9 0.1 1.0 HB3 A:GLU216 4.0 0.7 1.0 CD A:LYS114 4.0 0.6 1.0 CB B:ASP220 4.0 84.8 1.0 HA A:ASP220 4.0 0.4 1.0 OE2 A:GLU216 4.1 0.4 1.0 HZ3 A:LYS114 4.1 0.0 1.0 HZ2 A:LYS114 4.2 0.0 1.0 HB2 A:GLU216 4.2 0.7 1.0 O B:PRO218 4.2 71.6 1.0 CB A:ASP220 4.3 93.4 1.0 HB2 B:ASP220 4.4 0.8 1.0 HB3 A:ASP220 4.4 0.0 1.0 HB3 B:ASP220 4.4 0.8 1.0 CB A:GLU216 4.4 85.6 1.0 HB2 A:LYS114 4.5 0.3 1.0 NZ A:LYS114 4.5 0.8 1.0 CG A:GLU216 4.5 96.7 1.0 HB3 A:LYS114 4.6 0.3 1.0 CA A:ASP220 4.6 87.8 1.0 HA B:ASP220 4.7 94.2 1.0 N B:ASP220 4.8 70.4 1.0 CA B:ASP220 4.8 78.5 1.0 H B:ASP220 4.9 84.5 1.0 CB A:LYS114 4.9 95.2 1.0 CE A:LYS114 4.9 0.0 1.0 HA B:THR219 4.9 87.4 1.0 OE1 B:GLU216 4.9 0.4 1.0 O A:THR217 5.0 69.6 1.0 H A:ASP220 5.0 98.8 1.0

Magnesium binding site 3 out of 3 in the Adp Bound to Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Adp Bound to Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:0.4 occ:1.00 HOA2 B:ADP301 1.7 0.5 0.9 O1B B:ADP301 2.0 0.2 0.9 O B:ASN210 2.1 75.2 1.0 OD2 B:ASP228 2.1 86.2 1.0 O2A B:ADP301 2.2 92.1 0.9 CG B:ASP228 3.1 73.8 1.0 PB B:ADP301 3.2 0.2 0.9 PA B:ADP301 3.2 87.3 0.9 HB3 B:ASP228 3.3 82.7 1.0 HB2 B:ASP228 3.3 82.7 1.0 C B:ASN210 3.3 67.5 1.0 O3A B:ADP301 3.3 96.2 0.9 CB B:ASP228 3.5 68.9 1.0 HD3 B:PRO211 3.5 83.8 1.0 HB3 B:ASN210 3.6 92.7 1.0 O1A B:ADP301 3.7 77.8 0.9 O B:HOH421 3.9 75.1 1.0 HD2 B:PRO211 4.0 83.8 1.0 HD22 B:ASN210 4.0 0.1 1.0 CD B:PRO211 4.0 69.8 1.0 O2B B:ADP301 4.1 99.0 0.9 N B:PRO211 4.2 67.4 1.0 CB B:ASN210 4.2 77.2 1.0 ND2 B:ASN210 4.2 91.8 1.0 OD1 B:ASP228 4.3 73.1 1.0 HOB2 B:ADP301 4.3 0.8 0.9 O B:HOH412 4.3 63.0 1.0 CG B:ASN210 4.3 84.2 1.0 O3B B:ADP301 4.3 0.6 0.9 CA B:ASN210 4.3 70.4 1.0 HH21 B:ARG58 4.4 81.4 1.0 H5'1 B:ADP301 4.6 0.7 0.9 H B:ASN210 4.6 80.3 1.0 O5' B:ADP301 4.6 92.9 0.9 HD21 B:ASN210 4.6 0.1 1.0 H3' B:ADP301 4.7 0.8 0.9 HO3' B:ADP301 4.8 0.4 0.9 HOB3 B:ADP301 5.0 0.1 0.9 N B:ASN210 5.0 66.9 1.0 CA B:ASP228 5.0 63.9 1.0

J.Huang, V.H.Nguyen, K.A.Hamblin, R.Maytum, M.Van Der Giezen, M.E.Fraser. Atp-Specificity of Succinyl-Coa Synthetase From Blastocystis Hominis. Acta Crystallogr D Struct V. 75 647 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31282474
DOI: 10.1107/S2059798319007976