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Manganese in PDB 5er8: Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate

Enzymatic activity of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate

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

Protein crystallography data

The structure of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate, PDB code: 5er8 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) 43.39 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.601, 142.601, 117.632, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 23.9

Other elements in 5er8:

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

Chlorine (Cl) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate (pdb code 5er8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate, PDB code: 5er8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 5er8

Go back to Manganese Binding Sites List in 5er8
Manganese binding site 1 out of 9 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:69.3
occ:0.90
 OAK A:NRD704 1.7 63.5 0.9
OAN A:NRD704 1.8 68.2 0.9
O A:HOH803 1.8 83.2 1.0
OD1 A:ASP92 2.1 70.6 1.0
O A:HOH806 2.2 84.0 1.0
OD2 A:ASP96 2.7 76.3 1.0
NZ A:LYS239 2.9 74.4 1.0
MN A:MN702 2.9 68.8 0.9
CG A:ASP92 3.0 73.7 1.0
PAI A:NRD704 3.1 59.1 0.9
PAM A:NRD704 3.2 62.3 0.9
OD2 A:ASP92 3.2 88.2 1.0
OE2 A:GLU240 3.5 74.6 1.0
CAG A:NRD704 3.6 64.1 0.9
O A:HOH813 3.7 75.8 1.0
OAH A:NRD704 3.7 63.0 0.9
CG A:ASP96 3.8 81.2 1.0
OAL A:NRD704 3.9 59.9 0.9
OAP A:NRD704 4.0 72.0 0.9
CB A:ASP96 4.1 87.5 1.0
OAO A:NRD704 4.2 70.3 0.9
NH2 A:ARG325 4.2 63.2 1.0
OAJ A:NRD704 4.2 58.2 0.9
CE A:LYS239 4.3 70.9 1.0
O A:HOH828 4.4 73.9 1.0
CB A:ASP92 4.4 74.7 1.0
O A:HOH801 4.4 77.6 1.0
O A:ASP92 4.4 82.5 1.0
O A:HOH807 4.5 94.5 1.0
CD A:GLU240 4.6 64.7 1.0
MN A:MN703 4.7 55.1 0.9
O A:HOH804 4.7 78.2 1.0
C A:ASP92 4.8 78.9 1.0
OD1 A:ASP96 4.9 92.5 1.0
OD1 A:ASP93 4.9 73.2 1.0
CG A:GLU240 5.0 66.6 1.0

Manganese binding site 2 out of 9 in 5er8

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Manganese binding site 2 out of 9 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:68.8
occ:0.90
 O A:HOH807 1.8 94.5 1.0
O A:HOH813 1.8 75.8 1.0
OD2 A:ASP96 1.9 76.3 1.0
OD2 A:ASP92 1.9 88.2 1.0
O A:HOH801 2.0 77.6 1.0
O A:HOH804 2.4 78.2 1.0
OAN A:NRD704 2.6 68.2 0.9
CG A:ASP92 2.9 73.7 1.0
CG A:ASP96 2.9 81.2 1.0
MN A:MN701 2.9 69.3 0.9
OAP A:NRD704 3.1 72.0 0.9
OD1 A:ASP92 3.2 70.6 1.0
PAM A:NRD704 3.4 62.3 0.9
OD1 A:ASP96 3.4 92.5 1.0
O A:HOH803 3.6 83.2 1.0
OD2 A:ASP191 3.8 89.0 1.0
CB A:ASP92 4.2 74.7 1.0
O A:ASP92 4.2 82.5 1.0
CB A:ASP96 4.2 87.5 1.0
OAK A:NRD704 4.3 63.5 0.9
O A:ASP191 4.3 1.0 1.0
NH1 A:ARG188 4.4 87.3 1.0
OAH A:NRD704 4.5 63.0 0.9
OAO A:NRD704 4.5 70.3 0.9
CG A:ASP191 4.6 85.4 1.0
CAG A:NRD704 4.6 64.1 0.9
OD1 A:ASP191 4.6 84.6 1.0
CA A:ASP92 4.7 78.2 1.0
O A:HOH806 4.7 84.0 1.0
C A:ASP92 4.7 78.9 1.0
OE2 A:GLU240 4.9 74.6 1.0

Manganese binding site 3 out of 9 in 5er8

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Manganese binding site 3 out of 9 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn703

b:55.1
occ:0.90
 OAL A:NRD704 1.9 59.9 0.9
OD1 A:ASN232 2.0 62.0 1.0
O A:HOH802 2.0 71.5 1.0
OAO A:NRD704 2.1 70.3 0.9
OE2 A:GLU240 2.2 74.6 1.0
OE1 A:GLU240 2.3 65.9 1.0
OG A:SER236 2.3 54.9 1.0
CD A:GLU240 2.5 64.7 1.0
NH2 A:ARG188 2.6 89.0 1.0
CG A:ASN232 2.8 59.5 1.0
ND2 A:ASN232 3.0 59.1 1.0
CB A:SER236 3.1 55.7 1.0
PAI A:NRD704 3.2 59.1 0.9
PAM A:NRD704 3.2 62.3 0.9
OAN A:NRD704 3.6 68.2 0.9
CAG A:NRD704 3.7 64.1 0.9
O A:HOH803 3.7 83.2 1.0
CZ A:ARG188 3.7 90.5 1.0
OAK A:NRD704 3.8 63.5 0.9
CG A:GLU240 3.9 66.6 1.0
CAF A:NRD704 4.0 65.7 0.9
CB A:ASN232 4.2 56.0 1.0
O A:ASN232 4.3 59.5 1.0
NH1 A:ARG188 4.3 87.3 1.0
OD1 A:ASP233 4.3 66.2 1.0
OAJ A:NRD704 4.4 58.2 0.9
C A:ASN232 4.4 57.0 1.0
CA A:SER236 4.5 57.3 1.0
OAP A:NRD704 4.6 72.0 0.9
MN A:MN701 4.7 69.3 0.9
NE A:ARG188 4.7 85.8 1.0
CE A:LYS239 4.7 70.9 1.0
N A:ASP233 4.7 54.8 1.0
NZ A:LYS239 4.7 74.4 1.0
CA A:ASP233 4.8 54.9 1.0
CA A:ASN232 4.9 54.8 1.0
C A:SER236 5.0 55.3 1.0
OH A:TYR326 5.0 58.4 1.0
O A:SER236 5.0 66.6 1.0

Manganese binding site 4 out of 9 in 5er8

Go back to Manganese Binding Sites List in 5er8
Manganese binding site 4 out of 9 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn706

b:0.1
occ:1.00
 O A:HOH830 2.2 79.8 1.0
O A:HOH822 2.2 70.6 1.0
O A:HOH821 2.3 78.5 1.0
O A:HOH808 3.1 73.1 1.0
O A:HOH832 3.9 75.4 1.0
O A:TYR14 4.2 62.6 1.0
O A:PRO11 4.2 76.6 1.0
CL A:CL705 4.3 74.5 1.0
O A:HOH823 4.3 73.9 1.0
CB A:THR16 4.6 59.0 1.0
N A:THR16 4.8 62.4 1.0
C A:PRO11 5.0 68.3 1.0

Manganese binding site 5 out of 9 in 5er8

Go back to Manganese Binding Sites List in 5er8
Manganese binding site 5 out of 9 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:66.8
occ:0.90
 OAO B:NRD704 1.8 69.7 0.9
O B:HOH803 2.0 75.6 1.0
OD1 B:ASP92 2.1 66.7 1.0
OAL B:NRD704 2.2 63.9 0.9
O B:HOH821 2.2 79.7 1.0
OD2 B:ASP96 2.5 72.9 1.0
MN B:MN702 3.0 63.7 0.9
CG B:ASP92 3.0 68.3 1.0
NZ B:LYS239 3.2 69.6 1.0
PAM B:NRD704 3.2 58.8 0.9
OD2 B:ASP92 3.2 68.8 1.0
PAI B:NRD704 3.5 62.5 0.9
CG B:ASP96 3.6 81.2 1.0
CAG B:NRD704 3.8 62.0 0.9
OAP B:NRD704 3.8 68.9 0.9
CB B:ASP96 3.9 77.0 1.0
OAH B:NRD704 3.9 60.9 0.9
O B:HOH823 4.1 72.2 1.0
OAK B:NRD704 4.2 57.4 0.9
OE2 B:GLU240 4.3 63.7 1.0
OAN B:NRD704 4.3 68.0 0.9
O B:ASP92 4.3 73.7 1.0
CE B:LYS239 4.3 63.9 1.0
O B:HOH836 4.4 60.6 1.0
CB B:ASP92 4.4 70.6 1.0
NH2 B:ARG325 4.5 65.0 1.0
O B:HOH818 4.6 74.5 1.0
OAJ B:NRD704 4.7 59.1 0.9
OD1 B:ASP96 4.7 92.5 1.0
C B:ASP92 4.7 71.7 1.0
OD1 B:ASP93 4.8 64.9 1.0
MN B:MN703 4.8 66.6 0.9
O B:HOH809 5.0 88.6 1.0

Manganese binding site 6 out of 9 in 5er8

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Manganese binding site 6 out of 9 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn702

b:63.7
occ:0.90
 OD2 B:ASP92 1.9 68.8 1.0
OD2 B:ASP96 2.1 72.9 1.0
O B:HOH809 2.1 88.6 1.0
O B:HOH818 2.1 74.5 1.0
O B:HOH823 2.1 72.2 1.0
OAO B:NRD704 2.3 69.7 0.9
CG B:ASP92 2.9 68.3 1.0
MN B:MN701 3.0 66.8 0.9
CG B:ASP96 3.1 81.2 1.0
OAN B:NRD704 3.2 68.0 0.9
PAM B:NRD704 3.2 58.8 0.9
OD1 B:ASP92 3.3 66.7 1.0
OD1 B:ASP96 3.5 92.5 1.0
O B:HOH821 3.8 79.7 1.0
OD2 B:ASP191 4.1 0.6 1.0
NH1 B:ARG188 4.1 99.4 1.0
CB B:ASP92 4.3 70.6 1.0
OAP B:NRD704 4.3 68.9 0.9
OAH B:NRD704 4.3 60.9 0.9
O B:ASP92 4.4 73.7 1.0
CB B:ASP96 4.5 77.0 1.0
CAG B:NRD704 4.5 62.0 0.9
OAL B:NRD704 4.5 63.9 0.9
O B:HOH803 4.5 75.6 1.0
O B:ASP191 4.5 0.4 1.0
CA B:ASP92 4.8 72.1 1.0
O B:HOH810 4.8 66.4 1.0
CG B:ASP191 4.8 0.0 1.0
OD1 B:ASP191 4.9 0.6 1.0
C B:ASP92 4.9 71.7 1.0

Manganese binding site 7 out of 9 in 5er8

Go back to Manganese Binding Sites List in 5er8
Manganese binding site 7 out of 9 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn703

b:66.6
occ:0.90
 OAP B:NRD704 1.8 68.9 0.9
OE2 B:GLU240 1.8 63.7 1.0
OAK B:NRD704 1.9 57.4 0.9
OG B:SER236 2.0 55.3 1.0
O B:HOH802 2.1 62.7 1.0
OD1 B:ASN232 2.2 67.9 1.0
ND2 B:ASN232 2.3 57.3 1.0
CG B:ASN232 2.5 56.5 1.0
NH2 B:ARG188 2.8 78.2 1.0
CB B:SER236 2.9 58.1 1.0
CD B:GLU240 2.9 63.8 1.0
PAM B:NRD704 3.2 58.8 0.9
PAI B:NRD704 3.2 62.5 0.9
OE1 B:GLU240 3.4 55.5 1.0
CAG B:NRD704 3.7 62.0 0.9
O B:HOH821 3.8 79.7 1.0
CAF B:NRD704 3.8 65.0 0.9
OAL B:NRD704 3.9 63.9 0.9
CZ B:ARG188 3.9 88.7 1.0
O B:ASN232 4.0 63.3 1.0
OAO B:NRD704 4.0 69.7 0.9
CB B:ASN232 4.1 53.0 1.0
OD1 B:ASP233 4.1 59.8 1.0
C B:ASN232 4.2 51.6 1.0
CG B:GLU240 4.2 61.4 1.0
OAN B:NRD704 4.3 68.0 0.9
CA B:SER236 4.3 52.9 1.0
OAJ B:NRD704 4.4 59.1 0.9
NH1 B:ARG188 4.4 99.4 1.0
N B:ASP233 4.6 50.3 1.0
CE B:LYS239 4.6 63.9 1.0
OH B:TYR326 4.7 67.9 1.0
CA B:ASP233 4.7 52.2 1.0
CA B:ASN232 4.8 49.9 1.0
MN B:MN701 4.8 66.8 0.9
NZ B:LYS239 4.8 69.6 1.0
C B:SER236 4.8 52.9 1.0
O B:SER236 4.9 65.8 1.0
ND2 B:ASN254 4.9 63.4 1.0
N B:SER236 4.9 51.4 1.0
NE B:ARG188 4.9 84.0 1.0

Manganese binding site 8 out of 9 in 5er8

Go back to Manganese Binding Sites List in 5er8
Manganese binding site 8 out of 9 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn706

b:94.6
occ:1.00
 O B:HOH814 2.1 75.1 1.0
O B:HOH842 2.2 90.9 1.0
O B:HOH812 2.2 70.3 1.0
O B:HOH833 2.2 63.4 1.0
O B:TYR14 3.8 58.1 1.0
CL B:CL705 4.0 70.4 1.0
OG1 B:THR16 4.2 55.1 1.0
O B:PRO11 4.3 69.0 1.0
CG2 B:THR16 4.4 52.6 1.0
N B:THR16 4.4 54.2 1.0
CA B:TYR15 4.7 58.6 1.0
CB B:THR16 4.8 49.0 1.0
C B:TYR14 4.9 56.6 1.0
C B:TYR15 4.9 54.8 1.0

Manganese binding site 9 out of 9 in 5er8

Go back to Manganese Binding Sites List in 5er8
Manganese binding site 9 out of 9 in the Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Cyclization Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Manganese Ions and Neridronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn707

b:0.3
occ:1.00
 O B:SER297 2.1 78.0 1.0
O B:HOH824 3.0 76.0 1.0
C B:SER297 3.3 74.6 1.0
NE2 B:HIS212 3.5 89.4 1.0
OE1 B:GLU213 3.5 74.8 1.0
CA B:SER297 4.1 75.3 1.0
CE1 B:HIS212 4.2 85.6 1.0
CB B:SER297 4.2 72.1 1.0
N B:ILE298 4.3 72.7 1.0
CD B:GLU213 4.4 70.9 1.0
CA B:ILE298 4.5 68.7 1.0
CD2 B:HIS212 4.6 85.4 1.0
CG B:GLU213 4.6 71.4 1.0
N B:SER299 4.7 64.3 1.0
C B:ILE298 5.0 65.0 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 Oct 6 00:09:18 2024

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