Atomistry » Magnesium » PDB 4ogu-4osd » 4okz
Atomistry »
  Magnesium »
    PDB 4ogu-4osd »
      4okz »

Magnesium in PDB 4okz: Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate

Enzymatic activity of Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate

All present enzymatic activity of Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate:
2.5.1.21;

Protein crystallography data

The structure of Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate, PDB code: 4okz 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 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.090, 117.780, 185.590, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 17.7

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate (pdb code 4okz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate, PDB code: 4okz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 4okz

Go back to Magnesium Binding Sites List in 4okz
Magnesium binding site 1 out of 12 in the Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate


Mono view


Stereo pair view

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

b:24.8
occ:1.00
OE2 A:GLU87 1.9 23.2 1.0
O3B A:3E9904 2.0 23.9 1.0
O2A A:3E9904 2.1 22.8 1.0
O A:HOH1274 2.1 28.4 1.0
O A:HOH1281 2.2 23.7 1.0
O A:HOH1231 2.4 24.2 1.0
PB A:3E9904 2.8 21.4 1.0
PA A:3E9904 2.8 20.8 1.0
O3A A:3E9904 2.9 21.2 1.0
CD A:GLU87 3.0 23.6 1.0
MG A:MG902 3.1 23.5 1.0
OE1 A:GLU87 3.5 25.0 1.0
OD2 A:ASP82 3.5 21.6 1.0
O1A A:3E9904 3.6 20.7 1.0
O1B A:3E9904 3.8 19.6 1.0
O A:HOH1258 4.0 25.8 1.0
NZ A:LYS231 4.0 23.5 1.0
O2B A:3E9904 4.1 19.4 1.0
OD2 A:ASP83 4.1 28.8 1.0
NH1 A:ARG310 4.1 24.8 1.0
O1 A:3E9904 4.2 19.8 1.0
CG A:GLU87 4.2 24.1 1.0
OE1 A:GLU232 4.3 23.9 1.0
O A:HOH1045 4.5 25.4 1.0
O A:HOH1257 4.7 23.7 1.0
MG A:MG903 4.7 20.5 1.0
C2 A:3E9904 4.7 25.9 1.0
CG A:ASP82 4.7 20.9 1.0
O A:HOH1015 4.9 20.6 1.0
C1 A:3E9904 4.9 22.6 1.0
CB A:GLU87 5.0 23.4 1.0

Magnesium binding site 2 out of 12 in 4okz

Go back to Magnesium Binding Sites List in 4okz
Magnesium binding site 2 out of 12 in the Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate


Mono view


Stereo pair view

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

b:23.5
occ:1.00
O A:HOH1258 2.1 25.8 1.0
O A:HOH1257 2.1 23.7 1.0
O2A A:3E9904 2.1 22.8 1.0
O A:HOH1015 2.2 20.6 1.0
OD2 A:ASP82 2.2 21.6 1.0
OE2 A:GLU87 2.4 23.2 1.0
MG A:MG901 3.1 24.8 1.0
CG A:ASP82 3.1 20.9 1.0
CD A:GLU87 3.1 23.6 1.0
OD1 A:ASP82 3.4 21.2 1.0
PA A:3E9904 3.4 20.8 1.0
O A:HOH1274 3.7 28.4 1.0
O1 A:3E9904 3.8 19.8 1.0
CG A:GLU87 3.8 24.1 1.0
C2 A:3E9904 3.9 25.9 1.0
OE1 A:GLU87 3.9 25.0 1.0
O A:HOH1281 4.3 23.7 1.0
O A:HOH1045 4.3 25.4 1.0
O1A A:3E9904 4.3 20.7 1.0
OE2 A:GLU159 4.4 24.5 1.0
O3A A:3E9904 4.4 21.2 1.0
CB A:ASP82 4.4 20.1 1.0
OE1 A:GLU159 4.5 21.8 1.0
C1 A:3E9904 4.5 22.6 1.0
O A:ASP181 4.6 20.3 1.0
CD A:GLU159 4.9 22.3 1.0
NH2 A:ARG178 4.9 22.8 1.0
O A:ASP82 5.0 22.0 1.0
O3B A:3E9904 5.0 23.9 1.0
O A:HOH1231 5.0 24.2 1.0
OD2 A:ASP181 5.0 27.0 1.0

Magnesium binding site 3 out of 12 in 4okz

Go back to Magnesium Binding Sites List in 4okz
Magnesium binding site 3 out of 12 in the Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate


Mono view


Stereo pair view

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

b:20.5
occ:1.00
O A:HOH1267 2.0 22.1 1.0
O1B A:3E9904 2.1 19.6 1.0
O1A A:3E9904 2.1 20.7 1.0
OG A:SER228 2.1 21.2 1.0
OE1 A:GLU232 2.2 23.9 1.0
OD1 A:ASN224 2.2 20.9 1.0
CD A:GLU232 3.1 23.6 1.0
CB A:SER228 3.1 23.8 1.0
CG A:ASN224 3.1 22.4 1.0
PA A:3E9904 3.4 20.8 1.0
PB A:3E9904 3.4 21.4 1.0
ND2 A:ASN224 3.5 23.3 1.0
OE2 A:GLU232 3.5 23.3 1.0
O3A A:3E9904 3.7 21.2 1.0
O A:HOH1045 3.8 25.4 1.0
NH1 A:ARG178 3.9 23.4 1.0
O A:ASN224 4.0 20.4 1.0
O A:HOH1281 4.0 23.7 1.0
O3B A:3E9904 4.1 23.9 1.0
CG A:GLU232 4.2 24.1 1.0
O2A A:3E9904 4.2 22.8 1.0
C A:ASN224 4.3 20.9 1.0
O2B A:3E9904 4.3 19.4 1.0
CB A:ASN224 4.4 22.5 1.0
O1 A:3E9904 4.5 19.8 1.0
CA A:SER228 4.5 24.0 1.0
OD2 A:ASP225 4.5 19.9 1.0
N A:ASP225 4.6 21.1 1.0
MG A:MG901 4.7 24.8 1.0
CA A:ASP225 4.8 21.9 1.0
C A:SER228 4.9 24.0 1.0
CZ A:ARG178 4.9 22.4 1.0
O A:SER228 5.0 25.0 1.0
CA A:ASN224 5.0 22.4 1.0
CE A:LYS231 5.0 23.6 1.0

Magnesium binding site 4 out of 12 in 4okz

Go back to Magnesium Binding Sites List in 4okz
Magnesium binding site 4 out of 12 in the Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate


Mono view


Stereo pair view

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

b:19.3
occ:1.00
OE2 B:GLU87 1.8 17.3 1.0
O2A B:3E9904 1.9 18.0 1.0
O B:HOH1316 2.0 17.2 1.0
O B:HOH1310 2.2 16.8 1.0
O3B B:3E9904 2.2 20.2 1.0
O B:HOH1294 2.3 18.8 1.0
PA B:3E9904 2.8 18.5 1.0
CD B:GLU87 2.8 17.8 1.0
PB B:3E9904 3.0 17.9 1.0
O3A B:3E9904 3.0 17.4 1.0
MG B:MG902 3.1 17.4 1.0
OE1 B:GLU87 3.3 18.9 1.0
OD2 B:ASP82 3.5 15.8 1.0
O1A B:3E9904 3.6 18.4 1.0
OD2 B:ASP83 3.9 20.9 1.0
NZ B:LYS231 4.0 16.4 1.0
O B:HOH1308 4.0 15.6 1.0
O1B B:3E9904 4.0 16.9 1.0
CG B:GLU87 4.1 18.6 1.0
NH1 B:ARG310 4.1 18.8 1.0
O2B B:3E9904 4.2 16.3 1.0
O1 B:3E9904 4.2 17.9 1.0
OE1 B:GLU232 4.4 17.3 1.0
O B:HOH1030 4.5 18.7 1.0
CG B:ASP82 4.7 15.7 1.0
CB B:GLU87 4.7 17.8 1.0
C2 B:3E9904 4.8 25.5 1.0
MG B:MG903 4.8 17.4 1.0
O B:HOH1272 4.8 14.0 1.0
O B:HOH1013 4.8 22.5 1.0
O B:HOH1183 5.0 31.9 1.0
C1 B:3E9904 5.0 21.3 1.0

Magnesium binding site 5 out of 12 in 4okz

Go back to Magnesium Binding Sites List in 4okz
Magnesium binding site 5 out of 12 in the Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate


Mono view


Stereo pair view

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

b:17.4
occ:1.00
O2A B:3E9904 1.9 18.0 1.0
O B:HOH1308 2.0 15.6 1.0
O B:HOH1272 2.1 14.0 1.0
OD2 B:ASP82 2.2 15.8 1.0
OE2 B:GLU87 2.2 17.3 1.0
O B:HOH1322 2.5 32.9 1.0
CD B:GLU87 3.0 17.8 1.0
MG B:MG901 3.1 19.3 1.0
CG B:ASP82 3.1 15.7 1.0
PA B:3E9904 3.2 18.5 1.0
OD1 B:ASP82 3.3 15.7 1.0
O B:HOH1316 3.6 17.2 1.0
CG B:GLU87 3.7 18.6 1.0
O1 B:3E9904 3.7 17.9 1.0
OE1 B:GLU87 3.8 18.9 1.0
C2 B:3E9904 3.9 25.5 1.0
O1A B:3E9904 4.2 18.4 1.0
O B:HOH1030 4.2 18.7 1.0
O B:HOH1310 4.3 16.8 1.0
OE2 B:GLU159 4.3 21.8 1.0
OE1 B:GLU159 4.4 18.6 1.0
CB B:ASP82 4.5 15.6 1.0
O3A B:3E9904 4.5 17.4 1.0
C1 B:3E9904 4.5 21.3 1.0
O B:ASP181 4.6 18.1 1.0
CD B:GLU159 4.8 20.2 1.0
NH2 B:ARG178 4.9 16.6 1.0
O B:HOH1180 4.9 39.6 1.0
O B:HOH1294 4.9 18.8 1.0
O B:ASP82 4.9 17.1 1.0

Magnesium binding site 6 out of 12 in 4okz

Go back to Magnesium Binding Sites List in 4okz
Magnesium binding site 6 out of 12 in the Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate


Mono view


Stereo pair view

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

b:17.4
occ:1.00
O1B B:3E9904 2.1 16.9 1.0
O1A B:3E9904 2.1 18.4 1.0
OG B:SER228 2.1 16.6 1.0
O B:HOH1309 2.1 18.4 1.0
OE1 B:GLU232 2.2 17.3 1.0
OD1 B:ASN224 2.2 16.7 1.0
CD B:GLU232 3.1 17.9 1.0
CB B:SER228 3.1 16.9 1.0
CG B:ASN224 3.1 17.4 1.0
PB B:3E9904 3.4 17.9 1.0
PA B:3E9904 3.5 18.5 1.0
ND2 B:ASN224 3.5 17.3 1.0
OE2 B:GLU232 3.5 18.9 1.0
O3A B:3E9904 3.6 17.4 1.0
O B:HOH1030 3.8 18.7 1.0
NH1 B:ARG178 3.9 16.9 1.0
O B:ASN224 3.9 17.4 1.0
O B:HOH1310 4.0 16.8 1.0
O3B B:3E9904 4.1 20.2 1.0
CG B:GLU232 4.2 18.7 1.0
C B:ASN224 4.3 17.0 1.0
O2B B:3E9904 4.3 16.3 1.0
O1 B:3E9904 4.4 17.9 1.0
CB B:ASN224 4.5 16.5 1.0
OD2 B:ASP225 4.5 18.0 1.0
CA B:SER228 4.5 17.6 1.0
O2A B:3E9904 4.5 18.0 1.0
N B:ASP225 4.7 17.4 1.0
CA B:ASP225 4.8 17.3 1.0
MG B:MG901 4.8 19.3 1.0
C B:SER228 4.9 18.1 1.0
CE B:LYS231 4.9 18.5 1.0
CZ B:ARG178 5.0 17.1 1.0
CA B:ASN224 5.0 17.2 1.0
O B:SER228 5.0 19.2 1.0

Magnesium binding site 7 out of 12 in 4okz

Go back to Magnesium Binding Sites List in 4okz
Magnesium binding site 7 out of 12 in the Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate


Mono view


Stereo pair view

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

b:22.6
occ:1.00
OE2 C:GLU87 1.8 19.9 1.0
O2A C:3E9904 2.1 19.3 1.0
O C:HOH1293 2.1 19.6 1.0
O3B C:3E9904 2.2 23.1 1.0
O C:HOH1288 2.2 16.1 1.0
O C:HOH1014 2.3 22.9 1.0
CD C:GLU87 2.9 18.4 1.0
PA C:3E9904 2.9 20.1 1.0
PB C:3E9904 3.0 21.2 1.0
O3A C:3E9904 3.1 19.0 1.0
MG C:MG902 3.2 18.3 1.0
OE1 C:GLU87 3.4 19.1 1.0
OD2 C:ASP82 3.6 16.0 1.0
O1A C:3E9904 3.7 19.3 1.0
OD2 C:ASP83 3.9 22.2 1.0
NZ C:LYS231 3.9 20.6 1.0
NH1 C:ARG310 4.0 20.1 1.0
O2B C:3E9904 4.0 18.6 1.0
CG C:GLU87 4.1 17.8 1.0
O C:HOH1298 4.1 21.8 1.0
OE1 C:GLU232 4.3 21.8 1.0
O1 C:3E9904 4.3 19.7 1.0
O1B C:3E9904 4.3 22.0 1.0
O C:HOH1042 4.6 21.5 1.0
MG C:MG903 4.7 21.2 1.0
CB C:GLU87 4.8 17.7 1.0
CG C:ASP82 4.8 16.0 1.0
C2 C:3E9904 4.9 27.9 1.0
O C:HOH1289 4.9 20.8 1.0
O C:HOH1015 4.9 27.7 1.0
CE C:LYS231 4.9 22.4 1.0
O C:HOH1273 5.0 16.1 1.0

Magnesium binding site 8 out of 12 in 4okz

Go back to Magnesium Binding Sites List in 4okz
Magnesium binding site 8 out of 12 in the Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate


Mono view


Stereo pair view

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

b:18.3
occ:1.00
O2A C:3E9904 1.9 19.3 1.0
O C:HOH1298 2.0 21.8 1.0
O C:HOH1289 2.2 20.8 1.0
O C:HOH1273 2.2 16.1 1.0
OE2 C:GLU87 2.2 19.9 1.0
OD2 C:ASP82 2.2 16.0 1.0
CD C:GLU87 3.0 18.4 1.0
CG C:ASP82 3.1 16.0 1.0
MG C:MG901 3.2 22.6 1.0
PA C:3E9904 3.3 20.1 1.0
OD1 C:ASP82 3.4 15.9 1.0
CG C:GLU87 3.6 17.8 1.0
O C:HOH1288 3.7 16.1 1.0
OE1 C:GLU87 3.8 19.1 1.0
O1 C:3E9904 3.8 19.7 1.0
C2 C:3E9904 3.9 27.9 1.0
O1A C:3E9904 4.2 19.3 1.0
O C:HOH1293 4.2 19.6 1.0
O C:HOH1042 4.2 21.5 1.0
OE2 C:GLU159 4.3 21.2 1.0
OE1 C:GLU159 4.4 21.1 1.0
CB C:ASP82 4.5 14.8 1.0
O3A C:3E9904 4.5 19.0 1.0
C1 C:3E9904 4.6 23.9 1.0
O C:ASP181 4.7 20.0 1.0
CD C:GLU159 4.8 20.8 1.0
NH2 C:ARG178 4.8 19.5 1.0
OD2 C:ASP181 4.9 23.2 1.0
O C:ASP82 4.9 17.3 1.0

Magnesium binding site 9 out of 12 in 4okz

Go back to Magnesium Binding Sites List in 4okz
Magnesium binding site 9 out of 12 in the Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate


Mono view


Stereo pair view

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

b:21.2
occ:1.00
OG C:SER228 1.9 21.0 1.0
OD1 C:ASN224 2.1 21.1 1.0
OE1 C:GLU232 2.1 21.8 1.0
O1A C:3E9904 2.2 19.3 1.0
O1B C:3E9904 2.2 22.0 1.0
O C:HOH1294 2.3 22.5 1.0
PB C:3E9904 2.8 21.2 1.0
CB C:SER228 3.0 21.1 1.0
CG C:ASN224 3.0 20.3 1.0
CD C:GLU232 3.1 20.7 1.0
O3A C:3E9904 3.2 19.0 1.0
ND2 C:ASN224 3.4 18.6 1.0
PA C:3E9904 3.4 20.1 1.0
OE2 C:GLU232 3.7 21.2 1.0
O3B C:3E9904 3.7 23.1 1.0
O2B C:3E9904 3.8 18.6 1.0
O C:HOH1042 3.9 21.5 1.0
O C:ASN224 3.9 21.4 1.0
O C:HOH1293 4.0 19.6 1.0
NH1 C:ARG178 4.0 20.8 1.0
CG C:GLU232 4.2 20.5 1.0
C C:ASN224 4.3 21.0 1.0
O1 C:3E9904 4.4 19.7 1.0
CA C:SER228 4.4 20.9 1.0
CB C:ASN224 4.4 19.6 1.0
O2A C:3E9904 4.4 19.3 1.0
OD2 C:ASP225 4.6 20.6 1.0
MG C:MG901 4.7 22.6 1.0
N C:ASP225 4.8 20.3 1.0
CE C:LYS231 4.8 22.4 1.0
C C:SER228 4.9 21.8 1.0
CA C:ASP225 4.9 21.1 1.0
O C:SER228 4.9 21.9 1.0
CA C:ASN224 5.0 20.8 1.0

Magnesium binding site 10 out of 12 in 4okz

Go back to Magnesium Binding Sites List in 4okz
Magnesium binding site 10 out of 12 in the Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Selinadiene Synthase in Complex with Dihydrofarnesyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg901

b:30.9
occ:1.00
OE2 D:GLU87 1.8 27.1 1.0
O3B D:3E9904 1.9 30.7 1.0
O D:HOH1263 2.0 24.1 1.0
O D:HOH1213 2.0 31.7 1.0
O D:HOH1254 2.3 28.4 1.0
O2A D:3E9904 2.5 27.7 1.0
CD D:GLU87 2.9 26.8 1.0
PB D:3E9904 2.9 25.6 1.0
PA D:3E9904 3.2 26.4 1.0
O3A D:3E9904 3.2 24.6 1.0
MG D:MG902 3.3 26.2 1.0
OE1 D:GLU87 3.3 29.6 1.0
NZ D:LYS231 3.7 26.7 1.0
O1A D:3E9904 3.8 24.5 1.0
OD2 D:ASP82 3.8 23.5 1.0
O2B D:3E9904 3.9 21.5 1.0
NH1 D:ARG310 3.9 28.8 1.0
OD2 D:ASP83 4.0 28.6 1.0
CG D:GLU87 4.1 26.4 1.0
OE1 D:GLU232 4.2 25.1 1.0
O D:HOH1264 4.3 26.2 1.0
O1B D:3E9904 4.3 27.1 1.0
O D:HOH1268 4.6 29.3 1.0
O D:HOH1082 4.6 30.1 1.0
O1 D:3E9904 4.7 26.0 1.0
MG D:MG903 4.7 26.2 1.0
O D:HOH1023 4.7 34.6 1.0
CB D:GLU87 4.7 28.3 1.0
CE D:LYS231 4.8 28.3 1.0
O D:HOH1227 4.9 26.2 1.0
CG D:ASP82 5.0 23.5 1.0
O D:HOH1251 5.0 29.5 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: Mon Dec 14 19:18:10 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy