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Magnesium in PDB 4okm: Selinadiene Synthase Apo and in Complex with Diphosphate

Enzymatic activity of Selinadiene Synthase Apo and in Complex with Diphosphate

All present enzymatic activity of Selinadiene Synthase Apo and in Complex with Diphosphate:
2.5.1.21;

Protein crystallography data

The structure of Selinadiene Synthase Apo and in Complex with Diphosphate, PDB code: 4okm was solved by P.Baer, P.Rabe, K.Fischer, C.A.Citron, T.Klapschinski, M.Groll, J.S.Dickschat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.780, 119.090, 186.100, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Selinadiene Synthase Apo and in Complex with Diphosphate (pdb code 4okm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Selinadiene Synthase Apo and in Complex with Diphosphate, PDB code: 4okm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4okm

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Magnesium binding site 1 out of 9 in the Selinadiene Synthase Apo and in Complex with Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Selinadiene Synthase Apo and in Complex with Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:33.7
occ:1.00
 O31 A:PPV904 1.9 26.6 1.0
O22 A:PPV904 2.1 29.4 1.0
O A:HOH1202 2.1 30.8 1.0
O A:HOH1204 2.1 30.1 1.0
OE2 A:GLU87 2.1 35.1 1.0
O A:HOH1072 2.1 26.0 1.0
CD A:GLU87 3.0 32.8 1.0
P1 A:PPV904 3.2 25.8 1.0
P2 A:PPV904 3.2 27.4 1.0
OPP A:PPV904 3.3 24.2 1.0
MG A:MG902 3.4 29.2 1.0
OE1 A:GLU87 3.4 29.9 1.0
OD2 A:ASP82 3.7 20.8 1.0
NH1 A:ARG310 3.7 25.6 1.0
NZ A:LYS231 3.7 28.5 1.0
OD2 A:ASP83 3.9 32.8 1.0
O32 A:PPV904 3.9 25.6 1.0
O21 A:PPV904 4.0 24.9 1.0
O A:HOH1191 4.2 25.3 1.0
CG A:GLU87 4.3 33.7 1.0
O11 A:PPV904 4.3 24.0 1.0
O12 A:PPV904 4.5 26.4 1.0
OE1 A:GLU232 4.6 30.4 1.0
O A:HOH1020 4.6 22.7 1.0
O A:HOH1203 4.7 26.8 1.0
O A:HOH1053 4.7 37.3 1.0
MG A:MG903 4.8 26.1 1.0
O A:HOH1032 4.9 35.4 1.0
CB A:GLU87 4.9 32.3 1.0
CG A:ASP82 4.9 22.3 1.0
CZ A:ARG310 4.9 24.6 1.0

Magnesium binding site 2 out of 9 in 4okm

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Magnesium binding site 2 out of 9 in the Selinadiene Synthase Apo and in Complex with Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Selinadiene Synthase Apo and in Complex with Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:29.2
occ:1.00
 O A:HOH1203 2.0 26.8 1.0
O A:HOH1191 2.1 25.3 1.0
O A:HOH1125 2.1 25.9 1.0
OD2 A:ASP82 2.1 20.8 1.0
OE2 A:GLU87 2.1 35.1 1.0
O22 A:PPV904 2.3 29.4 1.0
CD A:GLU87 3.0 32.8 1.0
CG A:ASP82 3.1 22.3 1.0
OD1 A:ASP82 3.3 24.6 1.0
MG A:MG901 3.4 33.7 1.0
P2 A:PPV904 3.5 27.4 1.0
O A:HOH1202 3.6 30.8 1.0
O12 A:PPV904 3.7 26.4 1.0
CG A:GLU87 3.7 33.7 1.0
OE1 A:GLU87 3.9 29.9 1.0
OE2 A:GLU159 4.3 26.0 1.0
O A:HOH1020 4.3 22.7 1.0
O A:HOH1204 4.4 30.1 1.0
O A:ASP181 4.4 28.6 1.0
O32 A:PPV904 4.4 25.6 1.0
OE1 A:GLU159 4.4 25.7 1.0
CB A:ASP82 4.5 22.3 1.0
OPP A:PPV904 4.6 24.2 1.0
CD A:GLU159 4.8 25.6 1.0
O31 A:PPV904 4.9 26.6 1.0
O A:HOH1072 5.0 26.0 1.0

Magnesium binding site 3 out of 9 in 4okm

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Magnesium binding site 3 out of 9 in the Selinadiene Synthase Apo and in Complex with Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Selinadiene Synthase Apo and in Complex with Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:26.1
occ:1.00
 O32 A:PPV904 2.0 25.6 1.0
O21 A:PPV904 2.0 24.9 1.0
OE1 A:GLU232 2.1 30.4 1.0
OD1 A:ASN224 2.1 25.6 1.0
O A:HOH1196 2.2 26.9 1.0
OG A:SER228 2.3 25.0 1.0
CD A:GLU232 3.2 30.2 1.0
CG A:ASN224 3.2 26.6 1.0
P2 A:PPV904 3.3 27.4 1.0
P1 A:PPV904 3.3 25.8 1.0
CB A:SER228 3.3 25.8 1.0
OPP A:PPV904 3.5 24.2 1.0
ND2 A:ASN224 3.6 28.6 1.0
O A:HOH1020 3.6 22.7 1.0
OE2 A:GLU232 3.7 31.1 1.0
NH1 A:ARG178 3.8 27.7 1.0
O A:HOH1204 3.9 30.1 1.0
O31 A:PPV904 4.0 26.6 1.0
O A:ASN224 4.1 24.7 1.0
O22 A:PPV904 4.2 29.4 1.0
O12 A:PPV904 4.3 26.4 1.0
CG A:GLU232 4.3 30.6 1.0
C A:ASN224 4.4 23.6 1.0
OD2 A:ASP225 4.4 23.9 1.0
O11 A:PPV904 4.5 24.0 1.0
CB A:ASN224 4.5 24.4 1.0
CA A:SER228 4.7 25.7 1.0
N A:ASP225 4.7 22.0 1.0
MG A:MG901 4.8 33.7 1.0
CA A:ASP225 4.8 23.1 1.0
NZ A:LYS231 4.9 28.5 1.0
CZ A:ARG178 4.9 28.2 1.0

Magnesium binding site 4 out of 9 in 4okm

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Magnesium binding site 4 out of 9 in the Selinadiene Synthase Apo and in Complex with Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Selinadiene Synthase Apo and in Complex with Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:25.1
occ:1.00
 OE2 B:GLU87 1.9 20.4 1.0
O22 B:PPV904 2.0 18.5 1.0
O31 B:PPV904 2.1 23.4 1.0
O B:HOH1213 2.1 21.5 1.0
O B:HOH1230 2.1 22.4 1.0
O B:HOH1218 2.2 17.2 1.0
CD B:GLU87 2.8 22.7 1.0
MG B:MG902 3.1 19.2 1.0
P2 B:PPV904 3.2 19.9 1.0
OE1 B:GLU87 3.2 22.0 1.0
P1 B:PPV904 3.3 23.1 1.0
OPP B:PPV904 3.4 21.0 1.0
OD2 B:ASP82 3.7 16.7 1.0
O32 B:PPV904 3.7 20.3 1.0
NZ B:LYS231 3.8 29.5 1.0
OD2 B:ASP83 4.0 23.4 1.0
NH1 B:ARG310 4.0 21.5 1.0
CG B:GLU87 4.1 24.3 1.0
O21 B:PPV904 4.1 20.0 1.0
O B:HOH1017 4.2 18.1 1.0
O11 B:PPV904 4.4 23.3 1.0
OE1 B:GLU232 4.4 20.0 1.0
O12 B:PPV904 4.5 16.9 1.0
O B:HOH1047 4.5 25.5 1.0
O B:HOH1107 4.6 24.6 1.0
O B:HOH1034 4.7 27.9 1.0
CB B:GLU87 4.7 22.9 1.0
MG B:MG903 4.8 23.3 1.0
O B:HOH1014 4.8 26.2 1.0
O B:HOH1003 4.9 15.9 1.0
CG B:ASP82 4.9 17.6 1.0

Magnesium binding site 5 out of 9 in 4okm

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Magnesium binding site 5 out of 9 in the Selinadiene Synthase Apo and in Complex with Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Selinadiene Synthase Apo and in Complex with Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:19.2
occ:1.00
 OE2 B:GLU87 2.0 20.4 1.0
O B:HOH1107 2.0 24.6 1.0
O22 B:PPV904 2.1 18.5 1.0
OD2 B:ASP82 2.1 16.7 1.0
O B:HOH1003 2.2 15.9 1.0
O B:HOH1017 2.2 18.1 1.0
CD B:GLU87 3.0 22.7 1.0
MG B:MG901 3.1 25.1 1.0
CG B:ASP82 3.1 17.6 1.0
P2 B:PPV904 3.3 19.9 1.0
OD1 B:ASP82 3.4 19.1 1.0
O B:HOH1218 3.4 17.2 1.0
CG B:GLU87 3.7 24.3 1.0
O12 B:PPV904 3.7 16.9 1.0
OE1 B:GLU87 3.9 22.0 1.0
O B:HOH1047 4.3 25.5 1.0
O32 B:PPV904 4.3 20.3 1.0
O B:HOH1230 4.3 22.4 1.0
OPP B:PPV904 4.4 21.0 1.0
CB B:ASP82 4.4 18.1 1.0
O B:ASP181 4.5 20.3 1.0
OE2 B:GLU159 4.5 19.8 1.0
OE1 B:GLU159 4.5 20.8 1.0
O31 B:PPV904 4.7 23.4 1.0
O B:HOH1213 4.7 21.5 1.0
O B:ASP82 4.9 20.1 1.0
CD B:GLU159 5.0 20.4 1.0

Magnesium binding site 6 out of 9 in 4okm

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Magnesium binding site 6 out of 9 in the Selinadiene Synthase Apo and in Complex with Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Selinadiene Synthase Apo and in Complex with Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg903

b:23.3
occ:1.00
 O32 B:PPV904 2.0 20.3 1.0
OE1 B:GLU232 2.0 20.0 1.0
O21 B:PPV904 2.0 20.0 1.0
O B:HOH1236 2.1 17.4 1.0
OD1 B:ASN224 2.1 16.8 1.0
OG B:SER228 2.2 22.8 1.0
CD B:GLU232 3.1 21.0 1.0
CG B:ASN224 3.2 17.0 1.0
P1 B:PPV904 3.2 23.1 1.0
CB B:SER228 3.3 24.3 1.0
P2 B:PPV904 3.3 19.9 1.0
OPP B:PPV904 3.4 21.0 1.0
OE2 B:GLU232 3.6 23.9 1.0
ND2 B:ASN224 3.6 17.1 1.0
O B:HOH1047 3.8 25.5 1.0
NH1 B:ARG178 3.9 24.0 1.0
O B:HOH1230 3.9 22.4 1.0
O31 B:PPV904 4.0 23.4 1.0
O B:ASN224 4.0 21.2 1.0
O22 B:PPV904 4.2 18.5 1.0
O12 B:PPV904 4.3 16.9 1.0
CG B:GLU232 4.3 21.5 1.0
C B:ASN224 4.3 19.9 1.0
OD2 B:ASP225 4.4 19.9 1.0
CB B:ASN224 4.5 18.5 1.0
O11 B:PPV904 4.5 23.3 1.0
CA B:SER228 4.6 24.6 1.0
N B:ASP225 4.7 19.9 1.0
CA B:ASP225 4.8 19.4 1.0
MG B:MG901 4.8 25.1 1.0
C B:SER228 4.9 24.0 1.0
CZ B:ARG178 5.0 21.9 1.0
O B:SER228 5.0 24.0 1.0

Magnesium binding site 7 out of 9 in 4okm

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Magnesium binding site 7 out of 9 in the Selinadiene Synthase Apo and in Complex with Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Selinadiene Synthase Apo and in Complex with Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg901

b:33.0
occ:1.00
 O31 C:PPV904 2.0 25.7 1.0
OE2 C:GLU87 2.0 25.1 1.0
O C:HOH1010 2.1 29.9 1.0
O22 C:PPV904 2.1 26.8 1.0
O C:HOH1206 2.1 25.9 1.0
O C:HOH1186 2.2 23.8 1.0
CD C:GLU87 2.9 22.9 1.0
P1 C:PPV904 3.2 28.7 1.0
P2 C:PPV904 3.2 27.3 1.0
MG C:MG902 3.3 26.2 1.0
OPP C:PPV904 3.3 26.6 1.0
OE1 C:GLU87 3.3 23.0 1.0
OD2 C:ASP82 3.7 19.7 1.0
NZ C:LYS231 3.8 31.4 1.0
NH1 C:ARG310 3.8 25.9 1.0
OD2 C:ASP83 3.8 25.9 1.0
O32 C:PPV904 3.9 26.8 1.0
O21 C:PPV904 4.1 26.6 1.0
CG C:GLU87 4.1 22.7 1.0
O C:HOH1086 4.3 28.9 1.0
O11 C:PPV904 4.3 24.6 1.0
OE1 C:GLU232 4.3 25.4 1.0
O12 C:PPV904 4.5 25.4 1.0
O C:HOH1016 4.6 23.0 1.0
O C:HOH1205 4.8 24.5 1.0
CB C:GLU87 4.8 22.1 1.0
O C:HOH1012 4.8 29.1 1.0
MG C:MG903 4.8 29.0 1.0
CG C:ASP82 4.9 20.6 1.0
O C:HOH1188 5.0 32.7 1.0
O C:HOH1030 5.0 34.5 1.0

Magnesium binding site 8 out of 9 in 4okm

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Magnesium binding site 8 out of 9 in the Selinadiene Synthase Apo and in Complex with Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Selinadiene Synthase Apo and in Complex with Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg902

b:26.2
occ:1.00
 O C:HOH1205 2.0 24.5 1.0
O C:HOH1086 2.1 28.9 1.0
O22 C:PPV904 2.2 26.8 1.0
OD2 C:ASP82 2.2 19.7 1.0
OE2 C:GLU87 2.2 25.1 1.0
O C:HOH1023 2.2 21.2 1.0
CD C:GLU87 3.1 22.9 1.0
CG C:ASP82 3.1 20.6 1.0
MG C:MG901 3.3 33.0 1.0
P2 C:PPV904 3.3 27.3 1.0
OD1 C:ASP82 3.4 21.7 1.0
O C:HOH1206 3.6 25.9 1.0
O12 C:PPV904 3.6 25.4 1.0
CG C:GLU87 3.8 22.7 1.0
OE1 C:GLU87 3.9 23.0 1.0
O C:HOH1016 4.1 23.0 1.0
O32 C:PPV904 4.3 26.8 1.0
OE2 C:GLU159 4.4 27.7 1.0
O C:ASP181 4.4 26.7 1.0
OPP C:PPV904 4.4 26.6 1.0
O C:HOH1186 4.5 23.8 1.0
OE1 C:GLU159 4.5 25.8 1.0
CB C:ASP82 4.5 20.1 1.0
O31 C:PPV904 4.8 25.7 1.0
O C:HOH1010 4.9 29.9 1.0
NH2 C:ARG178 4.9 26.4 1.0
CD C:GLU159 4.9 24.9 1.0

Magnesium binding site 9 out of 9 in 4okm

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Magnesium binding site 9 out of 9 in the Selinadiene Synthase Apo and in Complex with Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Selinadiene Synthase Apo and in Complex with Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg903

b:29.0
occ:1.00
 O32 C:PPV904 2.0 26.8 1.0
O21 C:PPV904 2.0 26.6 1.0
O C:HOH1202 2.0 26.8 1.0
OD1 C:ASN224 2.1 27.9 1.0
OE1 C:GLU232 2.2 25.4 1.0
OG C:SER228 2.2 28.4 1.0
CG C:ASN224 3.1 26.1 1.0
CD C:GLU232 3.1 23.8 1.0
P1 C:PPV904 3.2 28.7 1.0
P2 C:PPV904 3.2 27.3 1.0
CB C:SER228 3.2 27.8 1.0
ND2 C:ASN224 3.4 24.8 1.0
OPP C:PPV904 3.4 26.6 1.0
OE2 C:GLU232 3.6 25.5 1.0
O C:HOH1016 3.7 23.0 1.0
NH1 C:ARG178 3.8 32.0 1.0
O31 C:PPV904 3.9 25.7 1.0
O C:HOH1186 4.0 23.8 1.0
O C:ASN224 4.0 28.3 1.0
O22 C:PPV904 4.2 26.8 1.0
O12 C:PPV904 4.3 25.4 1.0
C C:ASN224 4.3 25.5 1.0
CG C:GLU232 4.3 24.8 1.0
CB C:ASN224 4.4 24.7 1.0
OD2 C:ASP225 4.4 27.6 1.0
O11 C:PPV904 4.5 24.6 1.0
N C:ASP225 4.6 24.5 1.0
CA C:SER228 4.6 29.2 1.0
CA C:ASP225 4.7 25.8 1.0
MG C:MG901 4.8 33.0 1.0
CZ C:ARG178 4.9 29.7 1.0
NZ C:LYS231 4.9 31.4 1.0
C C:SER228 5.0 31.2 1.0
CA C:ASN224 5.0 26.0 1.0

Reference:

P.Baer, P.Rabe, K.Fischer, C.A.Citron, T.A.Klapschinski, M.Groll, J.S.Dickschat. Induced-Fit Mechanism in Class I Terpene Cyclases. Angew.Chem.Int.Ed.Engl. V. 53 7652 2014.
ISSN: ISSN 1433-7851
PubMed: 24890698
DOI: 10.1002/ANIE.201403648
Page generated: Tue Aug 20 00:54:05 2024

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