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Magnesium in PDB 5erm: Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate

Enzymatic activity of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate

All present enzymatic activity of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate:
4.2.3.43;

Protein crystallography data

The structure of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate, PDB code: 5erm 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) 46.90 / 2.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.295, 143.295, 118.261, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 20.6

Other elements in 5erm:

The structure of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate (pdb code 5erm). 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 Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate, PDB code: 5erm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5erm

Go back to Magnesium Binding Sites List in 5erm
Magnesium binding site 1 out of 6 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate


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 Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:70.0
occ:1.00
 O A:HOH534 1.9 73.1 1.0
OD2 A:ASP92 2.1 65.5 1.0
O A:HOH501 2.3 48.2 1.0
O A:HOH532 2.4 60.4 1.0
OD2 A:ASP96 2.4 65.2 1.0
O3 A:210401 2.6 65.1 1.0
MG A:MG404 2.7 52.9 1.0
OD1 A:ASP96 2.9 68.3 1.0
CG A:ASP92 3.0 60.0 1.0
CG A:ASP96 3.0 71.6 1.0
OD1 A:ASP92 3.2 56.3 1.0
O2 A:210401 3.2 56.8 1.0
O A:HOH505 3.4 58.3 1.0
P1 A:210401 3.5 55.3 1.0
O A:ASP92 4.0 77.7 1.0
O A:HOH533 4.1 68.6 1.0
O A:HOH508 4.3 55.7 1.0
CB A:ASP92 4.3 49.9 1.0
CB A:ASP96 4.5 77.5 1.0
O14 A:210401 4.6 65.2 1.0
O5 A:210401 4.6 53.4 1.0
C A:ASP92 4.7 65.4 1.0
OD2 A:ASP191 4.7 66.6 1.0
C7 A:210401 4.7 57.0 1.0
O10 A:210401 4.7 53.6 1.0
CA A:ASP92 4.8 57.9 1.0
OD1 A:ASP191 4.8 58.2 1.0

Magnesium binding site 2 out of 6 in 5erm

Go back to Magnesium Binding Sites List in 5erm
Magnesium binding site 2 out of 6 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate


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 Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:52.9
occ:1.00
 O3 A:210401 1.7 65.1 1.0
OD1 A:ASP92 2.0 56.3 1.0
O10 A:210401 2.1 53.6 1.0
O A:HOH505 2.2 58.3 1.0
O A:HOH508 2.3 55.7 1.0
OD2 A:ASP96 2.6 65.2 1.0
MG A:MG403 2.7 70.0 1.0
CG A:ASP92 2.9 60.0 1.0
P1 A:210401 3.0 55.3 1.0
OD2 A:ASP92 3.1 65.5 1.0
P8 A:210401 3.3 51.9 1.0
C7 A:210401 3.4 57.0 1.0
NZ A:LYS239 3.5 64.3 1.0
O14 A:210401 3.5 65.2 1.0
OE2 A:GLU240 3.7 55.9 1.0
O2 A:210401 3.8 56.8 1.0
CG A:ASP96 3.8 71.6 1.0
O5 A:210401 4.1 53.4 1.0
O12 A:210401 4.2 59.3 1.0
O A:HOH571 4.2 49.4 1.0
CB A:ASP92 4.3 49.9 1.0
O9 A:210401 4.3 53.5 1.0
MG A:MG405 4.3 49.7 1.0
O A:HOH501 4.4 48.2 1.0
O A:ASP92 4.4 77.7 1.0
O A:HOH532 4.4 60.4 1.0
OD1 A:ASP96 4.5 68.3 1.0
O A:HOH534 4.5 73.1 1.0
CE A:LYS239 4.6 55.6 1.0
CD A:GLU240 4.6 57.9 1.0
C A:ASP92 4.7 65.4 1.0
NH2 A:ARG325 4.7 55.5 1.0
CB A:ASP96 4.8 77.5 1.0
CG A:GLU240 4.8 60.2 1.0
C16 A:210401 4.9 50.4 1.0
OD1 A:ASP93 4.9 54.1 1.0

Magnesium binding site 3 out of 6 in 5erm

Go back to Magnesium Binding Sites List in 5erm
Magnesium binding site 3 out of 6 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate


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 Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:49.7
occ:1.00
 OE2 A:GLU240 1.9 55.9 1.0
O A:HOH513 1.9 52.0 1.0
OD1 A:ASN232 2.2 50.2 1.0
O9 A:210401 2.3 53.5 1.0
OG A:SER236 2.3 52.7 1.0
O5 A:210401 2.4 53.4 1.0
CB A:SER236 2.9 46.4 1.0
CD A:GLU240 2.9 57.9 1.0
P1 A:210401 3.2 55.3 1.0
P8 A:210401 3.2 51.9 1.0
CG A:ASN232 3.3 51.0 1.0
O3 A:210401 3.3 65.1 1.0
O10 A:210401 3.4 53.6 1.0
OE1 A:GLU240 3.4 59.4 1.0
C7 A:210401 3.6 57.0 1.0
NH2 A:ARG188 3.7 55.9 1.0
ND2 A:ASN232 3.8 51.5 1.0
C16 A:210401 3.9 50.4 1.0
CG A:GLU240 4.1 60.2 1.0
O A:ASN232 4.1 53.4 1.0
MG A:MG404 4.3 52.9 1.0
CA A:SER236 4.4 41.1 1.0
C A:ASN232 4.5 46.9 1.0
OH A:TYR326 4.5 58.2 1.0
CB A:ASN232 4.5 48.0 1.0
O A:HOH505 4.6 58.3 1.0
OD1 A:ASP233 4.6 54.0 1.0
CZ A:ARG188 4.6 54.0 1.0
O12 A:210401 4.6 59.3 1.0
O2 A:210401 4.6 56.8 1.0
NH1 A:ARG188 4.8 61.8 1.0
NZ A:LYS239 4.8 64.3 1.0
C A:SER236 4.8 45.1 1.0
CE A:LYS239 4.9 55.6 1.0
N A:ASP233 4.9 50.6 1.0
O A:SER236 5.0 52.6 1.0
O14 A:210401 5.0 65.2 1.0

Magnesium binding site 4 out of 6 in 5erm

Go back to Magnesium Binding Sites List in 5erm
Magnesium binding site 4 out of 6 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate


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 Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:56.6
occ:1.00
 O B:HOH801 1.8 61.6 1.0
O5 B:210704 2.4 66.4 1.0
OD1 B:ASP92 2.4 57.8 1.0
O B:HOH821 2.4 56.5 1.0
O9 B:210704 2.5 71.3 1.0
OD2 B:ASP96 2.7 75.8 1.0
MG B:MG702 2.8 73.8 1.0
CG B:ASP92 3.2 53.2 1.0
OD2 B:ASP92 3.4 61.5 1.0
CG B:ASP96 3.6 83.4 1.0
P1 B:210704 3.7 56.7 1.0
P8 B:210704 3.8 59.5 1.0
O14 B:210704 4.0 67.9 1.0
CG2 B:VAL98 4.0 74.6 1.0
O B:HOH875 4.0 75.0 1.0
OE2 B:GLU240 4.0 62.0 1.0
CB B:ASP96 4.0 78.8 1.0
C7 B:210704 4.1 52.9 1.0
NZ B:LYS239 4.1 56.8 1.0
O B:ASP92 4.2 61.7 1.0
O B:HOH862 4.2 64.4 1.0
O B:HOH811 4.3 70.0 1.0
O B:HOH870 4.3 66.3 1.0
OD1 B:ASP96 4.5 94.7 1.0
O2 B:210704 4.6 61.5 1.0
CB B:ASP92 4.6 52.0 1.0
O12 B:210704 4.6 55.2 1.0
C B:ASP92 4.7 50.9 1.0
O3 B:210704 4.8 57.8 1.0
NH2 B:ARG325 4.8 53.6 1.0
O10 B:210704 4.9 56.0 1.0
CB B:VAL98 4.9 88.6 1.0
CD B:GLU240 4.9 58.8 1.0
CG B:GLU240 5.0 52.0 1.0

Magnesium binding site 5 out of 6 in 5erm

Go back to Magnesium Binding Sites List in 5erm
Magnesium binding site 5 out of 6 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate


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 Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:73.8
occ:1.00
 O B:HOH862 1.8 64.4 1.0
OD2 B:ASP96 2.1 75.8 1.0
O B:HOH870 2.2 66.3 1.0
O B:HOH811 2.3 70.0 1.0
O5 B:210704 2.6 66.4 1.0
CG B:ASP96 2.6 83.4 1.0
OD2 B:ASP92 2.7 61.5 1.0
MG B:MG701 2.8 56.6 1.0
OD1 B:ASP96 2.8 94.7 1.0
CG B:ASP92 3.6 53.2 1.0
OD1 B:ASP92 3.7 57.8 1.0
O B:HOH815 3.9 66.1 1.0
O B:HOH801 3.9 61.6 1.0
P1 B:210704 3.9 56.7 1.0
CB B:ASP96 3.9 78.8 1.0
O B:HOH875 3.9 75.0 1.0
O B:HOH820 4.1 49.3 1.0
O3 B:210704 4.1 57.8 1.0
OD2 B:ASP191 4.4 78.7 1.0
O B:ASP92 4.5 61.7 1.0
O9 B:210704 4.7 71.3 1.0
NH1 B:ARG188 4.8 77.8 1.0
O14 B:210704 4.8 67.9 1.0
O B:HOH821 4.9 56.5 1.0
CB B:ASP92 4.9 52.0 1.0
O2 B:210704 5.0 61.5 1.0
O B:HOH810 5.0 66.3 1.0
C7 B:210704 5.0 52.9 1.0

Magnesium binding site 6 out of 6 in 5erm

Go back to Magnesium Binding Sites List in 5erm
Magnesium binding site 6 out of 6 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate


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 Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Magnesium Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:53.0
occ:1.00
 O2 B:210704 1.7 61.5 1.0
O B:HOH832 2.2 53.9 1.0
OG B:SER236 2.2 48.5 1.0
O10 B:210704 2.2 56.0 1.0
OE2 B:GLU240 2.3 62.0 1.0
OD1 B:ASN232 2.3 43.6 1.0
CB B:SER236 3.0 39.3 1.0
P1 B:210704 3.0 56.7 1.0
CD B:GLU240 3.2 58.8 1.0
P8 B:210704 3.2 59.5 1.0
CG B:ASN232 3.3 43.6 1.0
NH2 B:ARG188 3.4 61.5 1.0
O9 B:210704 3.5 71.3 1.0
C7 B:210704 3.5 52.9 1.0
O5 B:210704 3.6 66.4 1.0
OE1 B:GLU240 3.7 55.3 1.0
ND2 B:ASN232 3.7 51.2 1.0
O B:HOH801 3.7 61.6 1.0
C16 B:210704 3.9 49.0 1.0
O B:ASN232 4.0 42.9 1.0
O3 B:210704 4.2 57.8 1.0
CG B:GLU240 4.3 52.0 1.0
O B:HOH820 4.4 49.3 1.0
CA B:SER236 4.4 37.1 1.0
C B:ASN232 4.4 39.2 1.0
OD1 B:ASP233 4.5 46.9 1.0
O B:SER236 4.5 53.6 1.0
CZ B:ARG188 4.5 65.7 1.0
CB B:ASN232 4.6 35.9 1.0
O12 B:210704 4.6 55.2 1.0
OH B:TYR326 4.6 45.7 1.0
ND2 B:ASN254 4.7 45.6 1.0
C B:SER236 4.7 41.3 1.0
N B:ASP233 4.8 36.4 1.0
CE B:LYS239 4.8 57.4 1.0
CA B:ASP233 4.8 40.9 1.0
NH1 B:ARG188 4.9 77.8 1.0
O14 B:210704 4.9 67.9 1.0
NZ B:LYS239 5.0 56.8 1.0

Reference:

M.Chen, W.K.Chou, T.Toyomasu, D.E.Cane, D.W.Christianson. Structure and Function of Fusicoccadiene Synthase, A Hexameric Bifunctional Diterpene Synthase. Acs Chem.Biol. V. 11 889 2016.
ISSN: ESSN 1554-8937
PubMed: 26734760
DOI: 10.1021/ACSCHEMBIO.5B00960
Page generated: Sun Sep 29 03:53:31 2024

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