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Magnesium in PDB 5ivg: Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate

Enzymatic activity of Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate

All present enzymatic activity of Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate:
4.2.3.9;

Protein crystallography data

The structure of Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate, PDB code: 5ivg was solved by M.Chen, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.31 / 1.95
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 123.407, 123.407, 203.455, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 19.9

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate (pdb code 5ivg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate, PDB code: 5ivg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 5ivg

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Magnesium binding site 1 out of 12 in the Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate


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 Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:22.4
occ:1.00
 OD2 A:ASP84 2.1 25.1 1.0
O A:HOH830 2.1 23.0 1.0
O A:HOH980 2.1 24.3 1.0
O1B A:FPS704 2.2 20.8 1.0
O A:HOH852 2.2 20.5 1.0
O2A A:FPS704 2.2 21.2 1.0
CG A:ASP84 3.1 27.1 1.0
MG A:MG702 3.2 27.0 1.0
PA A:FPS704 3.3 21.8 1.0
OD1 A:ASP84 3.4 20.1 1.0
PB A:FPS704 3.4 22.3 1.0
O3A A:FPS704 3.5 20.8 1.0
NZ A:LYS220 3.9 25.0 1.0
O1A A:FPS704 4.0 20.7 1.0
OE2 A:GLU88 4.0 44.8 1.0
NH2 A:ARG308 4.1 21.5 1.0
O2B A:FPS704 4.1 21.4 1.0
OE2 A:GLU221 4.2 22.6 1.0
O A:HOH834 4.3 26.4 1.0
O A:HOH811 4.3 49.4 1.0
O A:HOH837 4.4 26.9 1.0
OD1 A:ASP85 4.4 27.7 1.0
CB A:ASP84 4.5 22.9 1.0
O3B A:FPS704 4.5 20.2 1.0
O A:ASP84 4.7 29.2 1.0
CD A:GLU88 4.8 47.3 1.0
MG A:MG703 4.8 22.4 1.0
O A:HOH940 4.8 32.9 1.0
O A:HOH825 4.9 25.5 1.0
O A:HOH943 4.9 29.5 1.0
O A:HOH1087 4.9 36.1 1.0
C A:ASP84 4.9 25.2 1.0
CE A:LYS220 5.0 26.9 1.0

Magnesium binding site 2 out of 12 in 5ivg

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Magnesium binding site 2 out of 12 in the Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate


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 Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:27.0
occ:1.00
 O A:HOH943 2.0 29.5 1.0
OD1 A:ASP84 2.0 20.1 1.0
O A:HOH940 2.1 32.9 1.0
O A:HOH980 2.1 24.3 1.0
O A:HOH834 2.2 26.4 1.0
O2A A:FPS704 2.3 21.2 1.0
CG A:ASP84 3.0 27.1 1.0
MG A:MG701 3.2 22.4 1.0
OD2 A:ASP84 3.3 25.1 1.0
PA A:FPS704 3.5 21.8 1.0
O A:HOH837 3.8 26.9 1.0
O A:HOH1053 4.1 43.7 1.0
OD1 A:ASP172 4.1 26.8 1.0
OD2 A:ASP172 4.1 27.2 1.0
S1 A:FPS704 4.1 28.5 1.0
O A:HOH830 4.3 23.0 1.0
O1A A:FPS704 4.3 20.7 1.0
NE2 A:GLN151 4.3 26.2 1.0
C1 A:FPS704 4.4 45.1 1.0
O A:HOH1087 4.4 36.1 1.0
CB A:ASP84 4.4 22.9 1.0
NH2 A:ARG169 4.5 28.9 1.0
CG A:ASP172 4.5 25.5 1.0
O A:ASP172 4.6 27.0 1.0
O3A A:FPS704 4.7 20.8 1.0
O A:HOH852 4.9 20.5 1.0
O1B A:FPS704 4.9 20.8 1.0
CG A:GLN151 5.0 27.8 1.0

Magnesium binding site 3 out of 12 in 5ivg

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Magnesium binding site 3 out of 12 in the Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate


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 Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:22.4
occ:1.00
 O1A A:FPS704 2.0 20.7 1.0
OE2 A:GLU221 2.1 22.6 1.0
OD1 A:ASN213 2.1 21.6 1.0
O A:HOH881 2.1 17.9 1.0
O2B A:FPS704 2.2 21.4 1.0
OG A:SER217 2.2 20.7 1.0
CD A:GLU221 3.0 31.6 1.0
CB A:SER217 3.2 20.8 1.0
CG A:ASN213 3.2 27.2 1.0
PA A:FPS704 3.2 21.8 1.0
PB A:FPS704 3.3 22.3 1.0
OE1 A:GLU221 3.5 27.7 1.0
O3A A:FPS704 3.5 20.8 1.0
ND2 A:ASN213 3.7 27.7 1.0
O A:HOH830 4.0 23.0 1.0
O A:HOH1087 4.0 36.1 1.0
NH1 A:ARG169 4.0 25.8 1.0
O A:ASN213 4.0 18.4 1.0
O1B A:FPS704 4.1 20.8 1.0
O2A A:FPS704 4.2 21.2 1.0
CG A:GLU221 4.3 28.6 1.0
C A:ASN213 4.4 22.0 1.0
CB A:ASN213 4.5 20.1 1.0
O3B A:FPS704 4.5 20.2 1.0
OD1 A:ASP214 4.6 21.6 1.0
CA A:SER217 4.6 21.2 1.0
S1 A:FPS704 4.7 28.5 1.0
N A:ASP214 4.7 19.9 1.0
MG A:MG701 4.8 22.4 1.0
CA A:ASP214 4.9 19.1 1.0
CZ A:ARG169 4.9 28.1 1.0
NH2 A:ARG169 4.9 28.9 1.0
C A:SER217 5.0 22.5 1.0
O A:HOH899 5.0 22.4 1.0

Magnesium binding site 4 out of 12 in 5ivg

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Magnesium binding site 4 out of 12 in the Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate


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 Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:20.2
occ:1.00
 O1B B:FPS704 2.0 18.3 1.0
OD2 B:ASP84 2.0 22.8 1.0
O B:HOH843 2.0 19.8 1.0
O B:HOH879 2.1 17.9 1.0
O B:HOH993 2.2 20.3 1.0
O2A B:FPS704 2.2 17.0 1.0
CG B:ASP84 3.0 28.5 1.0
MG B:MG702 3.1 22.3 1.0
PB B:FPS704 3.2 20.7 1.0
PA B:FPS704 3.3 20.3 1.0
OD1 B:ASP84 3.3 20.9 1.0
O3A B:FPS704 3.4 19.1 1.0
O B:HOH1117 3.9 52.4 1.0
NZ B:LYS220 3.9 21.2 1.0
O1A B:FPS704 3.9 19.1 1.0
OE2 B:GLU88 4.0 45.4 1.0
O2B B:FPS704 4.0 18.4 1.0
NH2 B:ARG308 4.1 20.2 1.0
O B:HOH840 4.2 26.0 1.0
OE2 B:GLU221 4.3 23.0 1.0
O B:HOH852 4.4 24.2 1.0
O3B B:FPS704 4.4 20.6 1.0
CB B:ASP84 4.4 20.3 1.0
OD1 B:ASP85 4.6 27.1 1.0
O B:HOH825 4.6 44.6 1.0
CD B:GLU88 4.8 39.0 1.0
O B:ASP84 4.8 20.3 1.0
O B:HOH1054 4.8 29.9 1.0
MG B:MG703 4.8 19.4 1.0
O B:HOH1114 4.8 33.8 1.0
O B:HOH971 4.9 24.1 1.0
O B:HOH839 4.9 28.1 1.0
C B:ASP84 4.9 22.3 1.0
S1 B:FPS704 5.0 25.0 1.0

Magnesium binding site 5 out of 12 in 5ivg

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Magnesium binding site 5 out of 12 in the Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate


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 Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:22.3
occ:1.00
 O B:HOH993 2.0 20.3 1.0
O B:HOH1054 2.1 29.9 1.0
OD1 B:ASP84 2.1 20.9 1.0
O2A B:FPS704 2.1 17.0 1.0
O B:HOH971 2.1 24.1 1.0
O B:HOH840 2.2 26.0 1.0
CG B:ASP84 3.0 28.5 1.0
MG B:MG701 3.1 20.2 1.0
OD2 B:ASP84 3.3 22.8 1.0
PA B:FPS704 3.4 20.3 1.0
O B:HOH852 3.7 24.2 1.0
O B:HOH1117 4.1 52.4 1.0
S1 B:FPS704 4.1 25.0 1.0
OD1 B:ASP172 4.2 23.9 1.0
OD2 B:ASP172 4.2 24.6 1.0
O1A B:FPS704 4.2 19.1 1.0
O B:HOH934 4.2 39.8 1.0
NE2 B:GLN151 4.3 23.4 1.0
O B:HOH879 4.3 17.9 1.0
C1 B:FPS704 4.3 34.7 1.0
O B:HOH1114 4.4 33.8 1.0
CB B:ASP84 4.4 20.3 1.0
CG B:ASP172 4.6 25.9 1.0
O3A B:FPS704 4.6 19.1 1.0
NH2 B:ARG169 4.6 22.1 1.0
O1B B:FPS704 4.7 18.3 1.0
O B:HOH843 4.7 19.8 1.0
O B:ASP172 4.7 24.1 1.0
CG B:GLN151 5.0 25.0 1.0

Magnesium binding site 6 out of 12 in 5ivg

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Magnesium binding site 6 out of 12 in the Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate


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 Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:19.4
occ:1.00
 OE2 B:GLU221 2.0 23.0 1.0
O2B B:FPS704 2.0 18.4 1.0
O1A B:FPS704 2.1 19.1 1.0
ND2 B:ASN213 2.1 13.7 1.0
O B:HOH885 2.1 18.0 1.0
OG B:SER217 2.2 18.8 1.0
CD B:GLU221 3.1 29.1 1.0
CB B:SER217 3.2 17.4 1.0
CG B:ASN213 3.2 25.5 1.0
PB B:FPS704 3.3 20.7 1.0
PA B:FPS704 3.3 20.3 1.0
O3A B:FPS704 3.4 19.1 1.0
OE1 B:GLU221 3.5 25.2 1.0
OD1 B:ASN213 3.6 30.4 1.0
O B:HOH1114 4.0 33.8 1.0
NH1 B:ARG169 4.0 22.4 1.0
O B:ASN213 4.0 18.7 1.0
O B:HOH879 4.0 17.9 1.0
O1B B:FPS704 4.1 18.3 1.0
O2A B:FPS704 4.2 17.0 1.0
CG B:GLU221 4.3 23.7 1.0
C B:ASN213 4.4 22.9 1.0
O3B B:FPS704 4.4 20.6 1.0
CB B:ASN213 4.4 17.8 1.0
OD1 B:ASP214 4.6 17.3 1.0
CA B:SER217 4.6 19.1 1.0
S1 B:FPS704 4.7 25.0 1.0
N B:ASP214 4.8 19.5 1.0
MG B:MG701 4.8 20.2 1.0
CA B:ASP214 4.8 18.6 1.0
O B:HOH821 4.9 39.1 1.0
OH B:TYR309 4.9 17.5 1.0
CZ B:ARG169 4.9 26.8 1.0
C B:SER217 5.0 20.5 1.0
O B:SER217 5.0 18.2 1.0

Magnesium binding site 7 out of 12 in 5ivg

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Magnesium binding site 7 out of 12 in the Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:29.3
occ:1.00
 O1B C:FPS704 1.9 26.3 1.0
OD2 C:ASP84 2.0 31.5 1.0
O2A C:FPS704 2.1 24.0 1.0
O C:HOH889 2.2 29.0 1.0
O C:HOH809 2.2 32.5 1.0
O C:HOH968 2.2 33.9 1.0
CG C:ASP84 3.0 31.0 1.0
MG C:MG702 3.1 36.8 1.0
PA C:FPS704 3.2 28.6 1.0
PB C:FPS704 3.2 31.8 1.0
OD1 C:ASP84 3.3 33.8 1.0
O3A C:FPS704 3.4 29.5 1.0
O1A C:FPS704 3.9 32.5 1.0
OE2 C:GLU88 4.0 63.7 1.0
O2B C:FPS704 4.0 28.9 1.0
NZ C:LYS220 4.0 33.3 1.0
NH2 C:ARG308 4.1 31.7 1.0
O C:HOH822 4.2 39.8 1.0
OE2 C:GLU221 4.3 31.9 1.0
O C:HOH837 4.3 33.0 1.0
CB C:ASP84 4.4 29.3 1.0
O3B C:FPS704 4.4 30.9 1.0
OD1 C:ASP85 4.6 41.9 1.0
O C:HOH906 4.6 42.4 1.0
O C:HOH930 4.7 34.6 1.0
O C:HOH1025 4.8 43.0 1.0
O C:ASP84 4.8 30.6 1.0
MG C:MG703 4.8 26.8 1.0
C1 C:FPS704 4.9 55.7 1.0
CD C:GLU88 4.9 56.8 1.0
S1 C:FPS704 4.9 32.7 1.0
CE C:LYS220 4.9 26.3 1.0
C C:ASP84 5.0 35.3 1.0

Magnesium binding site 8 out of 12 in 5ivg

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Magnesium binding site 8 out of 12 in the Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:36.8
occ:1.00
 O C:HOH930 2.0 34.6 1.0
O C:HOH906 2.1 42.4 1.0
O2A C:FPS704 2.1 24.0 1.0
O C:HOH822 2.2 39.8 1.0
OD1 C:ASP84 2.2 33.8 1.0
O C:HOH968 2.2 33.9 1.0
MG C:MG701 3.1 29.3 1.0
CG C:ASP84 3.1 31.0 1.0
OD2 C:ASP84 3.3 31.5 1.0
PA C:FPS704 3.4 28.6 1.0
O C:HOH837 3.8 33.0 1.0
S1 C:FPS704 4.0 32.7 1.0
OD1 C:ASP172 4.0 30.7 1.0
O C:HOH1028 4.1 53.5 1.0
NE2 C:GLN151 4.1 37.9 1.0
OD2 C:ASP172 4.2 33.2 1.0
O C:HOH889 4.2 29.0 1.0
C1 C:FPS704 4.2 55.7 1.0
O1A C:FPS704 4.3 32.5 1.0
O C:HOH1025 4.4 43.0 1.0
CG C:ASP172 4.5 33.4 1.0
NH2 C:ARG169 4.5 29.3 1.0
CB C:ASP84 4.5 29.3 1.0
O C:ASP172 4.6 31.1 1.0
O1B C:FPS704 4.6 26.3 1.0
O3A C:FPS704 4.6 29.5 1.0
O C:HOH809 4.8 32.5 1.0
CG C:GLN151 4.9 28.7 1.0
C2 C:FPS704 5.0 45.2 1.0

Magnesium binding site 9 out of 12 in 5ivg

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Magnesium binding site 9 out of 12 in the Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg703

b:26.8
occ:1.00
 ND2 C:ASN213 1.9 18.1 1.0
O1A C:FPS704 1.9 32.5 1.0
OE2 C:GLU221 2.0 31.9 1.0
O2B C:FPS704 2.1 28.9 1.0
O C:HOH878 2.2 29.0 1.0
OG C:SER217 2.2 36.5 1.0
CD C:GLU221 3.0 47.5 1.0
CG C:ASN213 3.1 30.8 1.0
CB C:SER217 3.2 37.1 1.0
PA C:FPS704 3.2 28.6 1.0
PB C:FPS704 3.3 31.8 1.0
O3A C:FPS704 3.5 29.5 1.0
OE1 C:GLU221 3.5 39.6 1.0
OD1 C:ASN213 3.6 39.4 1.0
O C:ASN213 3.9 28.6 1.0
O C:HOH1025 4.0 43.0 1.0
NH1 C:ARG169 4.0 31.5 1.0
O1B C:FPS704 4.0 26.3 1.0
O C:HOH889 4.1 29.0 1.0
O2A C:FPS704 4.1 24.0 1.0
CG C:GLU221 4.3 38.1 1.0
C C:ASN213 4.3 33.8 1.0
CB C:ASN213 4.3 27.4 1.0
O3B C:FPS704 4.4 30.9 1.0
CA C:SER217 4.6 34.5 1.0
OD1 C:ASP214 4.6 28.8 1.0
S1 C:FPS704 4.6 32.7 1.0
N C:ASP214 4.7 30.7 1.0
CA C:ASP214 4.8 29.5 1.0
MG C:MG701 4.8 29.3 1.0
OH C:TYR309 4.9 29.4 1.0
CZ C:ARG169 4.9 38.2 1.0
NH2 C:ARG169 4.9 29.3 1.0
O C:SER217 5.0 31.0 1.0
CA C:ASN213 5.0 31.1 1.0
C C:SER217 5.0 34.5 1.0

Magnesium binding site 10 out of 12 in 5ivg

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Magnesium binding site 10 out of 12 in the Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Aspergillus Terreus Aristolochene Synthase N299A Complexed with Farnesyl Thiolodiphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:29.9
occ:1.00
 O1B D:FPS704 2.0 29.7 1.0
O D:HOH843 2.0 29.2 1.0
O D:HOH848 2.1 31.3 1.0
OD2 D:ASP84 2.1 28.8 1.0
O2A D:FPS704 2.2 28.2 1.0
O D:HOH844 2.3 26.8 1.0
CG D:ASP84 3.1 41.7 1.0
PA D:FPS704 3.2 32.5 1.0
PB D:FPS704 3.3 32.1 1.0
MG D:MG702 3.3 37.8 1.0
O3A D:FPS704 3.4 27.1 1.0
OD1 D:ASP84 3.5 34.4 1.0
NZ D:LYS220 4.0 31.2 1.0
O1A D:FPS704 4.0 35.1 1.0
OE2 D:GLU88 4.1 61.2 1.0
NH2 D:ARG308 4.1 29.9 1.0
O2B D:FPS704 4.1 32.8 1.0
OE2 D:GLU221 4.2 33.4 1.0
O D:HOH823 4.3 37.4 1.0
O D:HOH907 4.4 42.0 1.0
OD1 D:ASP85 4.4 45.4 1.0
O3B D:FPS704 4.5 29.8 1.0
CB D:ASP84 4.5 28.3 1.0
MG D:MG703 4.8 32.4 1.0
CD D:GLU88 4.8 57.5 1.0
O D:ASP84 4.9 35.9 1.0
O D:HOH969 4.9 43.8 1.0
O D:HOH839 4.9 35.7 1.0
O D:HOH944 4.9 49.7 1.0
CE D:LYS220 4.9 25.1 1.0
S1 D:FPS704 4.9 38.8 1.0
O D:HOH873 5.0 44.6 1.0
C D:ASP84 5.0 34.5 1.0

Reference:

M.Chen, W.K.Chou, N.Al-Lami, J.A.Faraldos, R.K.Allemann, D.E.Cane, D.W.Christianson. Probing the Role of Active Site Water in the Sesquiterpene Cyclization Reaction Catalyzed By Aristolochene Synthase. Biochemistry V. 55 2864 2016.
ISSN: ISSN 0006-2960
PubMed: 27172425
DOI: 10.1021/ACS.BIOCHEM.6B00343
Page generated: Sun Sep 29 16:58:05 2024

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