Magnesium in PDB 6a2c: Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIG2

Protein crystallography data

The structure of Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIG2, PDB code: 6a2c 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 / 1.94
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.052, 133.052, 142.328, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIG2 (pdb code 6a2c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIG2, PDB code: 6a2c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6a2c

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Magnesium binding site 1 out of 6 in the Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIG2


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 LIG2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:33.4
occ:1.00
O1B A:FPP900 2.1 29.6 1.0
OD1 A:ASP316 2.1 25.7 1.0
O A:HOH1169 2.2 32.5 1.0
O A:HOH1092 2.2 35.3 1.0
O A:HOH1302 2.2 29.5 1.0
OD1 A:ASP320 2.3 52.0 1.0
MG A:MG902 2.8 38.9 1.0
CG A:ASP316 3.0 23.9 1.0
OD2 A:ASP316 3.3 27.6 1.0
PB A:FPP900 3.3 36.3 1.0
CG A:ASP320 3.4 42.4 1.0
O2B A:FPP900 3.4 31.8 1.0
CB A:ASP320 4.0 41.0 1.0
O A:HOH1358 4.1 38.8 1.0
O A:HOH1094 4.2 32.1 1.0
O A:HOH1426 4.2 53.1 1.0
O3B A:FPP900 4.4 33.6 1.0
OE1 A:GLU394 4.4 29.2 1.0
O2A A:FPP900 4.4 38.6 1.0
OD2 A:ASP320 4.4 76.1 1.0
CB A:ASP316 4.4 20.8 1.0
CE1 A:TYR391 4.4 24.5 1.0
O3A A:FPP900 4.5 39.3 1.0
O A:ASP316 4.5 22.3 1.0
NZ A:LYS476 4.5 66.8 1.0
O A:HOH1071 4.7 33.6 1.0
CD1 A:TYR391 4.7 23.4 1.0
O A:HOH1068 4.7 25.9 1.0
CA A:ASP316 4.8 18.0 1.0
C A:ASP316 4.9 21.4 1.0

Magnesium binding site 2 out of 6 in 6a2c

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Magnesium binding site 2 out of 6 in the Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIG2


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 LIG2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:38.9
occ:1.00
O2A A:FPP900 2.0 38.6 1.0
O1B A:FPP900 2.1 29.6 1.0
OD2 A:ASP316 2.2 27.6 1.0
O A:HOH1094 2.2 32.1 1.0
O A:HOH1071 2.2 33.6 1.0
OD1 A:ASP320 2.3 52.0 1.0
MG A:MG901 2.8 33.4 1.0
CG A:ASP316 3.0 23.9 1.0
CG A:ASP320 3.2 42.4 1.0
OD1 A:ASP316 3.2 25.7 1.0
PB A:FPP900 3.3 36.3 1.0
OD2 A:ASP320 3.4 76.1 1.0
PA A:FPP900 3.4 38.4 1.0
O3A A:FPP900 3.6 39.3 1.0
O A:HOH1282 3.8 42.6 1.0
O A:HOH1302 3.8 29.5 1.0
O A:HOH1426 4.0 53.1 1.0
O A:HOH1264 4.2 37.3 1.0
O3B A:FPP900 4.2 33.6 1.0
CB A:ASP316 4.4 20.8 1.0
O2B A:FPP900 4.4 31.8 1.0
O1A A:FPP900 4.5 37.5 1.0
CB A:ASP320 4.5 41.0 1.0
O A:HOH1169 4.6 32.5 1.0
O1 A:FPP900 4.6 40.2 1.0
O A:HOH1092 4.7 35.3 1.0
O A:ASP316 4.7 22.3 1.0
OD1 A:ASP317 4.8 29.2 1.0
C A:ASP316 4.8 21.4 1.0
MG A:MG903 4.8 43.0 1.0

Magnesium binding site 3 out of 6 in 6a2c

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Magnesium binding site 3 out of 6 in the Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIG2


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 LIG2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:43.0
occ:1.00
O1A A:FPP900 1.9 37.5 1.0
O3B A:FPP900 2.1 33.6 1.0
O A:HOH1282 2.2 42.6 1.0
O A:HOH1017 2.2 35.3 1.0
O A:HOH1082 2.2 38.1 1.0
OD1 A:ASN460 2.4 38.5 1.0
PA A:FPP900 3.0 38.4 1.0
PB A:FPP900 3.1 36.3 1.0
O3A A:FPP900 3.2 39.3 1.0
CG A:ASN460 3.3 30.4 1.0
O2A A:FPP900 3.5 38.6 1.0
ND2 A:ASN460 3.7 32.3 1.0
O1B A:FPP900 4.0 29.6 1.0
NZ A:LYS476 4.0 66.8 1.0
NH1 A:ARG457 4.1 23.6 1.0
O1 A:FPP900 4.2 40.2 1.0
O2B A:FPP900 4.3 31.8 1.0
O A:HOH1094 4.3 32.1 1.0
CE A:LYS476 4.4 65.0 1.0
OD1 A:ASP461 4.7 21.7 1.0
CB A:ASN460 4.7 22.8 1.0
MG A:MG902 4.8 38.9 1.0
O A:HOH1081 4.9 51.3 1.0
CG2 A:THR464 5.0 55.7 1.0

Magnesium binding site 4 out of 6 in 6a2c

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Magnesium binding site 4 out of 6 in the Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIG2


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 LIG2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:58.1
occ:1.00
O1A B:FPP601 1.9 62.9 1.0
O3B B:FPP601 2.0 75.6 1.0
O B:HOH789 2.2 75.6 1.0
O B:HOH741 2.2 56.1 1.0
O B:HOH705 2.2 55.5 1.0
OD1 B:ASN460 2.4 54.9 1.0
PA B:FPP601 2.9 67.8 1.0
PB B:FPP601 3.1 57.1 1.0
O3A B:FPP601 3.2 71.6 1.0
CG B:ASN460 3.4 51.2 1.0
O2A B:FPP601 3.6 59.8 1.0
NH1 B:ARG457 3.6 46.7 1.0
ND2 B:ASN460 3.8 43.8 1.0
O1B B:FPP601 3.8 54.4 1.0
O2B B:FPP601 4.3 53.4 1.0
O1 B:FPP601 4.4 62.6 1.0
O B:HOH838 4.4 63.0 1.0
OD1 B:ASP461 4.5 43.5 1.0
MG B:MG603 4.5 43.8 1.0
CB B:ASN460 4.7 52.4 1.0
CZ B:ARG457 4.8 43.0 1.0
O B:HOH709 5.0 58.4 1.0

Magnesium binding site 5 out of 6 in 6a2c

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Magnesium binding site 5 out of 6 in the Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIG2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIG2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:43.8
occ:1.00
O2A B:FPP601 2.0 59.8 1.0
O1B B:FPP601 2.1 54.4 1.0
O B:HOH772 2.2 54.3 1.0
O B:HOH838 2.2 63.0 1.0
OD2 B:ASP320 2.2 41.1 1.0
OD2 B:ASP316 2.3 39.6 1.0
O3A B:FPP601 3.0 71.6 1.0
PA B:FPP601 3.0 67.8 1.0
CG B:ASP316 3.1 41.8 1.0
PB B:FPP601 3.1 57.1 1.0
MG B:MG604 3.2 50.7 1.0
CG B:ASP320 3.2 45.7 1.0
OD1 B:ASP316 3.3 46.2 1.0
O B:HOH709 3.4 58.4 1.0
O B:HOH705 3.5 55.5 1.0
OD1 B:ASP320 3.5 47.9 1.0
O1 B:FPP601 4.0 62.6 1.0
O3B B:FPP601 4.0 75.6 1.0
O1A B:FPP601 4.2 62.9 1.0
O2B B:FPP601 4.3 53.4 1.0
OD1 B:ASP317 4.5 49.3 1.0
CB B:ASP316 4.5 40.2 1.0
MG B:MG602 4.5 58.1 1.0
CB B:ASP320 4.5 45.0 1.0
O B:HOH724 4.9 47.1 1.0
O B:HOH852 5.0 45.9 1.0

Magnesium binding site 6 out of 6 in 6a2c

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Magnesium binding site 6 out of 6 in the Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIG2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of A Synthase 2 From Santalum Album in Complex with LIG2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:50.7
occ:1.00
O1B B:FPP601 2.0 54.4 1.0
O B:HOH724 2.1 47.1 1.0
O B:HOH709 2.2 58.4 1.0
O B:HOH852 2.2 45.9 1.0
OD1 B:ASP316 2.3 46.2 1.0
OD2 B:ASP320 2.3 41.1 1.0
CG B:ASP320 3.2 45.7 1.0
PB B:FPP601 3.2 57.1 1.0
MG B:MG603 3.2 43.8 1.0
CG B:ASP316 3.3 41.8 1.0
CB B:ASP320 3.3 45.0 1.0
O2B B:FPP601 3.4 53.4 1.0
OD2 B:ASP316 3.6 39.6 1.0
OE1 B:GLU394 3.9 74.4 1.0
O B:HOH838 4.1 63.0 1.0
O3B B:FPP601 4.1 75.6 1.0
O3A B:FPP601 4.2 71.6 1.0
OD1 B:ASP320 4.3 47.9 1.0
CE1 B:TYR391 4.3 56.3 1.0
O B:HOH705 4.4 55.5 1.0
CB B:ASP316 4.5 40.2 1.0
O B:ASP316 4.6 65.3 1.0
CD1 B:TYR391 4.7 57.6 1.0
CA B:ASP320 4.8 52.7 1.0
O B:HOH772 4.8 54.3 1.0
O2A B:FPP601 4.9 59.8 1.0
CA B:ASP316 5.0 38.0 1.0
C B:ASP316 5.0 42.9 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 in Complex with LIG2 To Be Published.
Page generated: Mon Dec 14 22:18:51 2020

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