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Magnesium in PDB 6no3: Adp Bound to V113BL Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase

Enzymatic activity of Adp Bound to V113BL Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase

All present enzymatic activity of Adp Bound to V113BL Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase:
6.2.1.5;

Protein crystallography data

The structure of Adp Bound to V113BL Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase, PDB code: 6no3 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) 63.92 / 1.94
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 91.380, 117.345, 127.836, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 21.7

Other elements in 6no3:

The structure of Adp Bound to V113BL Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Adp Bound to V113BL Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase (pdb code 6no3). 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 V113BL Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase, PDB code: 6no3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6no3

Go back to Magnesium Binding Sites List in 6no3
Magnesium binding site 1 out of 3 in the Adp Bound to V113BL Mutant 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 V113BL Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:69.8
occ:1.00
 HOA2 A:ADP301 1.8 89.4 0.9
O A:HOH403 2.1 73.8 1.0
OD2 A:ASP228 2.1 66.5 1.0
O A:ASN210 2.2 59.1 1.0
O2A A:ADP301 2.2 74.4 0.9
O3B A:ADP301 2.2 77.1 0.9
HOB3 A:ADP301 2.4 92.6 0.9
CG A:ASP228 3.1 62.5 1.0
HB3 A:ASP228 3.1 70.5 1.0
HB2 A:ASP228 3.3 70.5 1.0
PA A:ADP301 3.3 71.5 0.9
CB A:ASP228 3.4 58.7 1.0
C A:ASN210 3.4 54.4 1.0
PB A:ADP301 3.4 75.9 0.9
HD3 A:PRO211 3.6 65.5 1.0
O3A A:ADP301 3.6 74.0 0.9
HB3 A:ASN210 3.7 65.0 1.0
O1A A:ADP301 3.9 67.2 0.9
HD2 A:PRO211 4.0 65.5 1.0
O A:HOH480 4.1 76.8 1.0
CD A:PRO211 4.1 54.5 1.0
O1B A:ADP301 4.2 77.3 0.9
N A:PRO211 4.2 52.7 1.0
OD1 A:ASP228 4.3 61.8 1.0
H3' A:ADP301 4.3 88.2 0.9
CB A:ASN210 4.3 54.2 1.0
CA A:ASN210 4.4 52.2 1.0
O A:HOH443 4.5 56.3 1.0
H5'1 A:ADP301 4.5 85.8 0.9
CG A:ASN210 4.6 59.3 1.0
HD22 A:ASN210 4.6 74.0 1.0
HH21 A:ARG58 4.6 75.7 1.0
O2B A:ADP301 4.6 76.6 0.9
HO3' A:ADP301 4.6 91.9 0.9
H A:ASN210 4.6 59.3 1.0
O5' A:ADP301 4.7 70.5 0.9
ND2 A:ASN210 4.7 61.6 1.0
HOB2 A:ADP301 4.7 92.0 0.9
CA A:ASP228 4.9 54.1 1.0

Magnesium binding site 2 out of 3 in 6no3

Go back to Magnesium Binding Sites List in 6no3
Magnesium binding site 2 out of 3 in the Adp Bound to V113BL Mutant 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 V113BL Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:0.2
occ:1.00
 O B:HOH447 2.1 70.9 1.0
OD1 A:ASP220 2.1 81.3 1.0
OD1 B:ASP220 2.2 74.0 1.0
OE1 A:GLU216 3.0 79.7 1.0
CG B:ASP220 3.1 71.2 1.0
CG A:ASP220 3.3 72.8 1.0
OD2 B:ASP220 3.4 76.2 1.0
HD2 A:LYS114 3.7 96.1 1.0
HD3 A:LYS114 3.8 96.1 1.0
HZ1 A:LYS114 3.9 1.0 1.0
HA A:ASP220 3.9 71.7 1.0
OD2 A:ASP220 4.0 78.1 1.0
HZ2 B:LYS114 4.1 0.0 1.0
HZ2 A:LYS114 4.1 1.0 1.0
HB3 A:GLU216 4.1 74.1 1.0
CD A:LYS114 4.2 80.0 1.0
CD A:GLU216 4.2 77.2 1.0
O B:PRO218 4.2 53.1 1.0
OE1 B:GLU216 4.4 80.6 1.0
CB A:ASP220 4.4 65.2 1.0
NZ A:LYS114 4.4 89.9 1.0
HB2 A:GLU216 4.4 74.1 1.0
CA A:ASP220 4.5 59.7 1.0
H A:ASP220 4.5 69.4 1.0
O A:THR217 4.5 49.8 1.0
CB B:ASP220 4.5 63.5 1.0
HB3 A:ASP220 4.6 78.3 1.0
HD2 B:LYS114 4.6 1.0 1.0
HZ3 B:LYS114 4.6 0.0 1.0
HA B:ASP220 4.6 70.9 1.0
CB A:GLU216 4.7 61.7 1.0
N A:ASP220 4.7 57.8 1.0
NZ B:LYS114 4.8 95.0 1.0
H B:ASP220 4.8 67.2 1.0
HD3 B:LYS114 4.9 1.0 1.0
O A:PRO218 4.9 49.7 1.0
N B:ASP220 4.9 55.9 1.0
HB3 B:ASP220 4.9 76.2 1.0
CA B:ASP220 4.9 59.1 1.0
CE A:LYS114 5.0 86.0 1.0
C B:PRO218 5.0 55.2 1.0
O B:THR217 5.0 50.6 1.0

Magnesium binding site 3 out of 3 in 6no3

Go back to Magnesium Binding Sites List in 6no3
Magnesium binding site 3 out of 3 in the Adp Bound to V113BL Mutant 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 V113BL Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:61.9
occ:1.00
 HOA2 B:ADP301 1.8 73.8 0.9
O1B B:ADP301 2.0 64.3 0.9
O B:HOH448 2.1 70.2 1.0
O B:HOH439 2.1 66.1 1.0
O B:ASN210 2.1 55.0 1.0
O2A B:ADP301 2.2 61.4 0.9
OD2 B:ASP228 2.2 56.2 1.0
PB B:ADP301 3.2 61.6 0.9
PA B:ADP301 3.2 57.7 0.9
CG B:ASP228 3.3 51.2 1.0
O3A B:ADP301 3.3 59.6 0.9
C B:ASN210 3.4 51.7 1.0
HB3 B:ASP228 3.5 60.0 1.0
HB2 B:ASP228 3.5 60.0 1.0
HD3 B:PRO211 3.5 63.9 1.0
HB3 B:ASN210 3.6 66.4 1.0
CB B:ASP228 3.7 50.0 1.0
O B:HOH449 3.9 57.1 1.0
O1A B:ADP301 4.0 53.5 0.9
O B:HOH419 4.0 70.6 1.0
CD B:PRO211 4.1 53.2 1.0
HD2 B:PRO211 4.1 63.9 1.0
N B:PRO211 4.2 51.3 1.0
O3B B:ADP301 4.2 66.0 0.9
H5'1 B:ADP301 4.2 68.1 0.9
CB B:ASN210 4.3 55.3 1.0
O2B B:ADP301 4.3 56.5 0.9
CG B:ASN210 4.4 58.7 1.0
CA B:ASN210 4.4 52.7 1.0
OD1 B:ASP228 4.4 49.6 1.0
O B:HOH459 4.4 67.3 1.0
HD22 B:ASN210 4.4 72.0 1.0
ND2 B:ASN210 4.5 60.0 1.0
HH21 B:ARG58 4.5 65.2 1.0
HOB2 B:ADP301 4.5 67.8 0.9
O5' B:ADP301 4.5 60.5 0.9
H3' B:ADP301 4.6 74.6 0.9
HOB3 B:ADP301 4.6 79.3 0.9
O B:HOH441 4.6 50.4 1.0
HE1 B:MET142 4.7 0.2 1.0
H B:ASN210 4.7 57.6 1.0
HO3' B:ADP301 4.8 75.2 0.9
OD1 B:ASN210 4.8 57.9 1.0
HD21 B:ASN210 4.9 72.0 1.0
O3' B:ADP301 4.9 62.7 0.9
C5' B:ADP301 4.9 56.7 0.9

Reference:

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
Page generated: Tue Oct 1 12:49:46 2024

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