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Magnesium in PDB 6no5: Adp Bound to K46BE&K114BD Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase

Enzymatic activity of Adp Bound to K46BE&K114BD Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase

All present enzymatic activity of Adp Bound to K46BE&K114BD Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase:
6.2.1.5;

Protein crystallography data

The structure of Adp Bound to K46BE&K114BD Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase, PDB code: 6no5 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) 36.65 / 2.07
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.052, 82.494, 91.248, 90.00, 118.92, 90.00
R / Rfree (%) 19.4 / 22.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Adp Bound to K46BE&K114BD Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase (pdb code 6no5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Adp Bound to K46BE&K114BD Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase, PDB code: 6no5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6no5

Go back to Magnesium Binding Sites List in 6no5
Magnesium binding site 1 out of 4 in the Adp Bound to K46BE&K114BD 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 K46BE&K114BD Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:37.0
occ:1.00
 HOA2 A:ADP301 1.8 48.5 1.0
O A:HOH427 2.1 40.1 1.0
O A:HOH498 2.1 43.3 1.0
OD2 A:ASP228 2.2 38.0 1.0
O A:ASN210 2.2 33.2 1.0
O3B A:ADP301 2.2 44.8 1.0
O2A A:ADP301 2.3 40.4 1.0
HOB3 A:ADP301 2.5 53.8 1.0
CG A:ASP228 3.2 39.7 1.0
HB3 A:ASP228 3.3 39.8 1.0
HB2 A:ASP228 3.4 39.8 1.0
PA A:ADP301 3.4 39.9 1.0
C A:ASN210 3.4 34.6 1.0
PB A:ADP301 3.5 43.6 1.0
CB A:ASP228 3.5 33.1 1.0
HD3 A:PRO211 3.5 46.7 1.0
O3A A:ADP301 3.5 45.8 1.0
HB3 A:ASN210 3.6 46.3 1.0
O A:HOH466 3.9 46.7 1.0
O1A A:ADP301 4.0 40.7 1.0
O A:HOH467 4.1 51.6 1.0
CD A:PRO211 4.1 38.9 1.0
HD2 A:PRO211 4.2 46.7 1.0
N A:PRO211 4.2 36.2 1.0
HD22 A:ASN210 4.3 56.3 1.0
CB A:ASN210 4.3 38.5 1.0
O A:HOH423 4.3 46.7 1.0
OD1 A:ASP228 4.3 35.3 1.0
O1B A:ADP301 4.4 44.3 1.0
H5'1 A:ADP301 4.4 47.7 1.0
ND2 A:ASN210 4.4 46.9 1.0
CG A:ASN210 4.4 41.0 1.0
O A:HOH470 4.4 33.4 1.0
CA A:ASN210 4.4 38.8 1.0
O2B A:ADP301 4.5 47.4 1.0
HOB2 A:ADP301 4.5 56.9 1.0
HH21 A:ARG58 4.6 42.6 1.0
O5' A:ADP301 4.7 42.4 1.0
H A:ASN210 4.7 41.2 1.0
H3' A:ADP301 4.7 51.8 1.0
O3' A:ADP301 4.7 43.9 1.0
O A:HOH529 4.7 53.0 1.0
HD21 A:ASN210 4.8 56.3 1.0
O A:HOH455 4.8 51.1 1.0

Magnesium binding site 2 out of 4 in 6no5

Go back to Magnesium Binding Sites List in 6no5
Magnesium binding site 2 out of 4 in the Adp Bound to K46BE&K114BD 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 K46BE&K114BD Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:42.6
occ:1.00
 HOA2 B:ADP301 1.7 57.2 1.0
O B:HOH416 2.1 44.7 1.0
OD2 B:ASP228 2.1 39.6 1.0
O B:HOH473 2.1 48.4 1.0
O3B B:ADP301 2.2 50.3 1.0
O B:ASN210 2.2 39.3 1.0
HOB3 B:ADP301 2.2 60.5 1.0
O2A B:ADP301 2.3 47.6 1.0
CG B:ASP228 3.2 43.2 1.0
HB3 B:ASP228 3.3 46.0 1.0
HB2 B:ASP228 3.4 46.0 1.0
PB B:ADP301 3.4 44.2 1.0
PA B:ADP301 3.4 43.3 1.0
C B:ASN210 3.4 42.0 1.0
CB B:ASP228 3.5 38.3 1.0
HB3 B:ASN210 3.5 57.1 1.0
O3A B:ADP301 3.6 47.1 1.0
HD3 B:PRO211 3.6 45.1 1.0
O B:HOH451 3.9 43.9 1.0
O1A B:ADP301 4.1 49.4 1.0
HD22 B:ASN210 4.2 64.0 1.0
CD B:PRO211 4.2 37.5 1.0
CB B:ASN210 4.2 47.5 1.0
O1B B:ADP301 4.2 45.7 1.0
HD2 B:PRO211 4.2 45.1 1.0
N B:PRO211 4.3 41.2 1.0
OD1 B:ASP228 4.3 39.0 1.0
O B:HOH406 4.3 48.8 1.0
ND2 B:ASN210 4.3 53.2 1.0
CG B:ASN210 4.4 48.2 1.0
HH21 B:ARG58 4.4 48.1 1.0
CA B:ASN210 4.4 40.9 1.0
O B:HOH440 4.4 40.1 1.0
O2B B:ADP301 4.5 46.9 1.0
H5'2 B:ADP301 4.6 51.8 1.0
H B:ASN210 4.7 49.4 1.0
HOB2 B:ADP301 4.7 56.4 1.0
O5' B:ADP301 4.7 45.1 1.0
HD21 B:ASN210 4.7 64.0 1.0
H3' B:ADP301 4.8 58.4 1.0
O3' B:ADP301 5.0 52.8 1.0

Magnesium binding site 3 out of 4 in 6no5

Go back to Magnesium Binding Sites List in 6no5
Magnesium binding site 3 out of 4 in the Adp Bound to K46BE&K114BD 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 K46BE&K114BD Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:46.0
occ:1.00
 HOA2 C:ADP301 1.7 54.8 1.0
O C:HOH468 2.1 49.8 1.0
O C:HOH423 2.1 49.3 1.0
O C:ASN210 2.1 38.5 1.0
O3B C:ADP301 2.1 50.0 1.0
HOB3 C:ADP301 2.1 60.1 1.0
OD2 C:ASP228 2.2 41.7 1.0
O2A C:ADP301 2.2 45.6 1.0
CG C:ASP228 3.2 44.0 1.0
C C:ASN210 3.3 42.4 1.0
PA C:ADP301 3.3 40.4 1.0
PB C:ADP301 3.4 49.2 1.0
HB3 C:ASP228 3.4 46.0 1.0
HB2 C:ASP228 3.5 46.0 1.0
HB3 C:ASN210 3.5 56.6 1.0
HD3 C:PRO211 3.5 50.0 1.0
O3A C:ADP301 3.5 48.6 1.0
CB C:ASP228 3.6 38.3 1.0
O C:HOH440 3.7 50.5 1.0
HD22 C:ASN210 3.9 66.7 1.0
O C:HOH443 4.0 48.7 1.0
O1A C:ADP301 4.0 41.9 1.0
ND2 C:ASN210 4.1 55.6 1.0
CB C:ASN210 4.1 47.1 1.0
CD C:PRO211 4.1 41.6 1.0
O C:HOH430 4.1 50.1 1.0
N C:PRO211 4.2 39.8 1.0
CG C:ASN210 4.2 48.9 1.0
HD2 C:PRO211 4.2 50.0 1.0
CA C:ASN210 4.3 41.3 1.0
OD1 C:ASP228 4.3 40.5 1.0
H5'1 C:ADP301 4.4 57.5 1.0
O2B C:ADP301 4.4 48.0 1.0
O1B C:ADP301 4.4 42.4 1.0
HOB2 C:ADP301 4.4 57.6 1.0
HD21 C:ASN210 4.5 66.7 1.0
HH21 C:ARG58 4.5 54.1 1.0
H C:ASN210 4.6 46.3 1.0
O C:HOH448 4.6 41.4 1.0
HO3' C:ADP301 4.6 59.4 1.0
O5' C:ADP301 4.6 44.0 1.0
H3' C:ADP301 4.8 54.7 1.0
OD1 C:ASN210 4.8 53.1 1.0
N C:ASN210 4.9 38.5 1.0
O3' C:ADP301 5.0 49.4 1.0
HB2 C:ASN210 5.0 56.6 1.0

Magnesium binding site 4 out of 4 in 6no5

Go back to Magnesium Binding Sites List in 6no5
Magnesium binding site 4 out of 4 in the Adp Bound to K46BE&K114BD 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 4 of Adp Bound to K46BE&K114BD Mutant Atp-Grasp Fold of Blastocystis Hominis Succinyl-Coa Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:39.3
occ:1.00
 HOA2 D:ADP301 1.7 51.0 1.0
O D:HOH412 2.1 38.2 1.0
O3B D:ADP301 2.1 39.5 1.0
O D:HOH461 2.1 46.2 1.0
OD2 D:ASP228 2.1 35.5 1.0
O D:ASN210 2.1 39.6 1.0
O2A D:ADP301 2.2 42.5 1.0
HOB3 D:ADP301 2.3 47.5 1.0
CG D:ASP228 3.2 39.2 1.0
PA D:ADP301 3.3 37.2 1.0
PB D:ADP301 3.3 42.8 1.0
HB2 D:ASP228 3.3 41.6 1.0
C D:ASN210 3.4 38.0 1.0
O3A D:ADP301 3.4 39.4 1.0
HB3 D:ASP228 3.4 41.6 1.0
HD3 D:PRO211 3.4 45.2 1.0
HB3 D:ASN210 3.5 46.3 1.0
CB D:ASP228 3.5 34.6 1.0
O1A D:ADP301 3.9 37.5 1.0
O D:HOH451 3.9 45.1 1.0
O D:HOH463 3.9 56.4 1.0
CD D:PRO211 4.1 37.6 1.0
O D:HOH439 4.1 46.3 1.0
HD22 D:ASN210 4.1 58.9 1.0
HD2 D:PRO211 4.2 45.2 1.0
N D:PRO211 4.2 38.5 1.0
CB D:ASN210 4.2 38.5 1.0
O1B D:ADP301 4.2 43.1 1.0
OD1 D:ASP228 4.3 38.9 1.0
H5'1 D:ADP301 4.3 52.9 1.0
HOB2 D:ADP301 4.3 54.0 1.0
ND2 D:ASN210 4.3 49.0 1.0
O2B D:ADP301 4.3 45.0 1.0
CA D:ASN210 4.4 40.3 1.0
O D:HOH443 4.4 37.4 1.0
CG D:ASN210 4.4 41.9 1.0
HH21 D:ARG58 4.4 48.6 1.0
HO3' D:ADP301 4.5 53.8 1.0
O5' D:ADP301 4.6 42.0 1.0
H D:ASN210 4.6 42.6 1.0
H3' D:ADP301 4.6 54.1 1.0
HD21 D:ASN210 4.8 58.9 1.0
O3' D:ADP301 4.8 44.7 1.0
C5' D:ADP301 5.0 44.0 1.0

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 12:50:25 2024

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