Magnesium in PDB 6a2d: Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIGAND1

Protein crystallography data

The structure of Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIGAND1, PDB code: 6a2d was solved by X.Han, T.P.Ko, W.D.Liu, Y.Y.Zheng, C.C.Chen, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.96
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 132.527, 132.527, 141.903, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.5

Other elements in 6a2d:

The structure of Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIGAND1 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIGAND1 (pdb code 6a2d). 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 of A Synthase 2 From Santalum Album in Complex with LIGAND1, PDB code: 6a2d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6a2d

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Magnesium binding site 1 out of 4 in the Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIGAND1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIGAND1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:22.8
occ:1.00
OAE A:6R2900 2.0 22.7 1.0
O A:HOH1299 2.1 23.2 1.0
O A:HOH1107 2.1 27.3 1.0
OD1 A:ASP316 2.1 19.8 1.0
O A:HOH1099 2.1 23.3 1.0
OD1 A:ASP320 2.2 32.8 1.0
MG A:MG902 2.9 25.6 1.0
CG A:ASP320 3.0 38.3 1.0
CG A:ASP316 3.0 19.5 1.0
OD2 A:ASP320 3.1 74.2 1.0
PAY A:6R2900 3.2 31.9 1.0
OD2 A:ASP316 3.3 21.2 1.0
OAG A:6R2900 3.5 28.0 1.0
OE1 A:GLU394 4.0 36.0 1.0
O A:HOH1149 4.2 30.8 1.0
CLJ A:6R2900 4.3 33.2 1.0
OAH A:6R2900 4.3 32.4 1.0
CB A:ASP316 4.3 17.7 1.0
OAF A:6R2900 4.3 32.8 1.0
O A:HOH1021 4.4 32.5 1.0
CB A:ASP320 4.4 28.9 1.0
CAX A:6R2900 4.4 32.3 1.0
O A:ASP316 4.5 16.2 1.0
CE1 A:TYR391 4.5 21.2 1.0
CD1 A:TYR391 4.7 21.6 1.0
CA A:ASP316 4.8 16.5 1.0
C A:ASP316 5.0 17.0 1.0

Magnesium binding site 2 out of 4 in 6a2d

Go back to Magnesium Binding Sites List in 6a2d
Magnesium binding site 2 out of 4 in the Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIGAND1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIGAND1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:25.6
occ:1.00
OD1 A:ASP320 1.8 32.8 1.0
OAE A:6R2900 2.0 22.7 1.0
OAF A:6R2900 2.0 32.8 1.0
O A:HOH1149 2.1 30.8 1.0
OD2 A:ASP316 2.1 21.2 1.0
O A:HOH1194 2.3 21.0 1.0
MG A:MG901 2.9 22.8 1.0
CG A:ASP320 2.9 38.3 1.0
CG A:ASP316 3.0 19.5 1.0
OD1 A:ASP316 3.2 19.8 1.0
PAY A:6R2900 3.2 31.9 1.0
PAZ A:6R2900 3.4 28.9 1.0
CB A:ASP320 3.5 28.9 1.0
OAH A:6R2900 3.7 32.4 1.0
CAX A:6R2900 3.9 32.3 1.0
OD2 A:ASP320 4.0 74.2 1.0
O A:HOH1299 4.0 23.2 1.0
O A:HOH1456 4.1 40.1 1.0
O A:HOH1216 4.2 29.1 1.0
O A:ASP316 4.2 16.2 1.0
CB A:ASP316 4.3 17.7 1.0
CLJ A:6R2900 4.3 33.2 1.0
C A:ASP316 4.5 17.0 1.0
O A:HOH1099 4.5 23.3 1.0
OAI A:6R2900 4.5 33.3 1.0
OAT A:6R2900 4.5 35.9 1.0
OAG A:6R2900 4.6 28.0 1.0
OD1 A:ASP317 4.6 23.1 1.0
O A:HOH1107 4.7 27.3 1.0
N A:ASP317 4.9 17.4 1.0
CA A:ASP316 4.9 16.5 1.0
CA A:ASP320 5.0 24.1 1.0

Magnesium binding site 3 out of 4 in 6a2d

Go back to Magnesium Binding Sites List in 6a2d
Magnesium binding site 3 out of 4 in the Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIGAND1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIGAND1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:44.7
occ:1.00
OD2 B:ASP320 2.0 30.0 1.0
OAE B:6R2900 2.0 40.6 1.0
O B:HOH1016 2.0 32.4 1.0
O B:HOH1046 2.1 40.9 1.0
OD1 B:ASP316 2.2 36.5 1.0
O B:HOH1201 2.3 46.1 1.0
OD1 B:ASP320 2.4 30.0 1.0
CG B:ASP320 2.5 30.0 1.0
MG B:MG902 3.1 37.1 1.0
CG B:ASP316 3.1 31.2 1.0
PAY B:6R2900 3.4 49.2 1.0
OD2 B:ASP316 3.5 31.6 1.0
OE1 B:GLU394 3.6 76.1 1.0
OAG B:6R2900 3.9 48.2 1.0
CB B:ASP320 3.9 30.0 1.0
O B:HOH1099 4.0 45.5 1.0
OE2 B:GLU394 4.0 63.2 1.0
CD B:GLU394 4.3 68.8 1.0
O B:ASP316 4.3 36.0 1.0
OAH B:6R2900 4.4 47.6 1.0
CB B:ASP316 4.4 35.7 1.0
O B:HOH1095 4.5 46.1 1.0
CE1 B:TYR391 4.6 42.5 1.0
CLJ B:6R2900 4.7 46.8 1.0
OAF B:6R2900 4.7 39.5 1.0
CA B:ASP316 4.8 32.1 1.0
O B:HOH1049 4.8 38.4 1.0
C B:ASP316 4.8 36.3 1.0
CAX B:6R2900 4.8 52.5 1.0
CA B:ASP320 4.8 30.0 1.0
CD1 B:TYR391 4.9 43.2 1.0

Magnesium binding site 4 out of 4 in 6a2d

Go back to Magnesium Binding Sites List in 6a2d
Magnesium binding site 4 out of 4 in the Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIGAND1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIGAND1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:37.1
occ:1.00
O B:HOH1095 2.0 46.1 1.0
OAF B:6R2900 2.0 39.5 1.0
OAE B:6R2900 2.0 40.6 1.0
OD2 B:ASP320 2.1 30.0 1.0
O B:HOH1099 2.1 45.5 1.0
OD2 B:ASP316 2.2 31.6 1.0
PAY B:6R2900 3.0 49.2 1.0
CG B:ASP316 3.0 31.2 1.0
MG B:MG901 3.1 44.7 1.0
OD1 B:ASP316 3.2 36.5 1.0
PAZ B:6R2900 3.2 50.9 1.0
CG B:ASP320 3.2 30.0 1.0
OAH B:6R2900 3.4 47.6 1.0
CAX B:6R2900 3.6 52.5 1.0
CB B:ASP320 3.9 30.0 1.0
CLJ B:6R2900 4.1 46.8 1.0
OAI B:6R2900 4.2 55.7 1.0
OD1 B:ASP320 4.2 30.0 1.0
O B:HOH1201 4.3 46.1 1.0
O B:HOH1046 4.4 40.9 1.0
OD1 B:ASP317 4.4 43.6 1.0
OAT B:6R2900 4.4 50.8 1.0
CB B:ASP316 4.4 35.7 1.0
OAG B:6R2900 4.5 48.2 1.0
O B:ASP316 4.7 36.0 1.0
C B:ASP316 4.8 36.3 1.0
O B:HOH1016 5.0 32.4 1.0

Reference:

X.Han, T.P.Ko, W.D.Liu, Y.Y.Zheng, C.C.Chen, R.T.Guo. Crystal Structure of A Synthase 2 From Santalum Album To Be Published.
Page generated: Mon Dec 14 22:18:50 2020

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