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Magnesium in PDB 6b06: Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)

Protein crystallography data

The structure of Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B), PDB code: 6b06 was solved by M.-E.Picard, M.Cusson, R.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 101.17 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 187.219, 122.646, 68.145, 90.00, 107.05, 90.00
R / Rfree (%) 18.4 / 23.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) (pdb code 6b06). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B), PDB code: 6b06:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6b06

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Magnesium binding site 1 out of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)


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 CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:49.9
occ:1.00
 O A:HOH509 2.1 64.0 1.0
O A:HOH501 2.2 55.7 1.0
OD2 A:ASP151 2.2 53.7 1.0
OAN A:C6J400 2.4 43.2 1.0
OD1 A:ASP147 2.5 69.7 1.0
OAM A:C6J400 3.0 54.5 1.0
PAK A:C6J400 3.2 52.3 1.0
OD2 A:ASP147 3.2 73.9 1.0
CG A:ASP147 3.2 65.2 1.0
CG A:ASP151 3.2 63.6 1.0
MG A:MG402 3.5 49.9 1.0
OD1 A:ASP151 3.6 76.5 1.0
OAL A:C6J400 4.0 53.5 1.0
CE A:LYS310 4.2 85.9 1.0
OE1 A:GLN215 4.2 82.5 1.0
OD2 A:ASP218 4.3 90.2 1.0
OD1 A:ASP218 4.3 95.2 1.0
CG A:ASP218 4.5 92.6 1.0
NE2 A:GLN215 4.6 69.5 1.0
NZ A:LYS244 4.6 67.4 1.0
CAH A:C6J400 4.6 55.1 1.0
OAQ A:C6J400 4.6 52.0 1.0
CB A:ASP151 4.6 61.4 1.0
CAG A:C6J400 4.6 57.9 1.0
O A:HOH511 4.6 45.5 1.0
CB A:ASP147 4.7 54.8 1.0
NZ A:LYS310 4.7 89.8 1.0
CAE A:C6J400 4.8 65.2 1.0
CD A:GLN215 4.8 69.4 1.0
O A:HOH505 4.9 60.9 1.0
O A:HOH513 5.0 50.7 1.0

Magnesium binding site 2 out of 9 in 6b06

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Magnesium binding site 2 out of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)


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 CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:49.9
occ:1.00
 OAN A:C6J400 2.0 43.2 1.0
O A:HOH505 2.0 60.9 1.0
OAQ A:C6J400 2.1 52.0 1.0
OD2 A:ASP151 2.6 53.7 1.0
O A:HOH513 2.6 50.7 1.0
OD2 A:ASP147 2.7 73.9 1.0
O A:HOH511 3.3 45.5 1.0
O A:HOH504 3.3 54.7 1.0
PAI A:C6J400 3.5 58.5 1.0
MG A:MG401 3.5 49.9 1.0
CG A:ASP151 3.5 63.6 1.0
PAK A:C6J400 3.6 52.3 1.0
CB A:ASP151 3.7 61.4 1.0
CG A:ASP147 3.8 65.2 1.0
OAP A:C6J400 3.9 61.3 1.0
OAL A:C6J400 4.1 53.5 1.0
CAH A:C6J400 4.1 55.1 1.0
OD1 A:ASP147 4.3 69.7 1.0
OG A:SER153 4.3 78.8 1.0
MG A:MG403 4.4 63.5 1.0
NH2 A:ARG156 4.4 82.7 1.0
CAG A:C6J400 4.4 57.9 1.0
OAM A:C6J400 4.6 54.5 1.0
OD1 A:ASP151 4.7 76.5 1.0
OAO A:C6J400 4.8 57.2 1.0
OG1 A:THR304 4.9 88.2 1.0

Magnesium binding site 3 out of 9 in 6b06

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Magnesium binding site 3 out of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)


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 CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:63.5
occ:1.00
 O A:HOH503 1.8 56.1 1.0
OAP A:C6J400 2.1 61.3 1.0
O A:HOH506 2.3 90.1 1.0
O A:HOH513 2.3 50.7 1.0
OAL A:C6J400 2.4 53.5 1.0
OD2 A:ASP287 2.8 63.3 1.0
PAI A:C6J400 3.4 58.5 1.0
OD1 A:ASP305 3.5 68.8 1.0
OD1 A:ASP291 3.5 0.3 1.0
PAK A:C6J400 3.6 52.3 1.0
OD2 A:ASP305 3.8 68.0 1.0
CG A:ASP287 3.8 75.5 1.0
OAN A:C6J400 4.0 43.2 1.0
CAH A:C6J400 4.0 55.1 1.0
CG A:ASP305 4.1 69.8 1.0
CG A:ASP291 4.1 84.3 1.0
OAQ A:C6J400 4.1 52.0 1.0
CB A:ASP291 4.3 80.0 1.0
OD1 A:ASP287 4.3 79.3 1.0
MG A:MG402 4.4 49.9 1.0
O A:HOH504 4.4 54.7 1.0
O A:ASP287 4.5 55.1 1.0
OD1 A:ASP288 4.6 64.6 1.0
NZ A:LYS301 4.7 82.8 1.0
OAO A:C6J400 4.7 57.2 1.0
OAM A:C6J400 4.7 54.5 1.0
O A:HOH511 4.9 45.5 1.0
OD2 A:ASP291 5.0 72.7 1.0

Magnesium binding site 4 out of 9 in 6b06

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Magnesium binding site 4 out of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)


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 CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:44.4
occ:1.00
 O B:HOH503 1.9 55.3 1.0
OD1 B:ASP147 2.1 52.5 1.0
O B:HOH501 2.1 49.1 1.0
OAL B:C6J400 2.2 37.6 1.0
O B:HOH511 2.3 42.5 1.0
OD2 B:ASP151 2.3 43.5 1.0
CG B:ASP151 3.1 53.8 1.0
OAM B:C6J400 3.1 41.4 1.0
CG B:ASP147 3.1 52.2 1.0
OD1 B:ASP151 3.1 52.3 1.0
PAK B:C6J400 3.3 41.0 1.0
OD2 B:ASP147 3.4 46.0 1.0
OE1 B:GLN215 3.7 78.8 1.0
MG B:MG402 3.8 45.9 1.0
OD1 B:ASP218 4.0 99.2 1.0
OAN B:C6J400 4.2 40.8 1.0
NZ B:LYS310 4.3 75.8 1.0
NZ B:LYS244 4.3 52.2 1.0
NE2 B:GLN215 4.3 75.4 1.0
CG B:ASP218 4.4 86.0 1.0
CD B:GLN215 4.5 67.6 1.0
CB B:ASP147 4.5 48.6 1.0
OD2 B:ASP218 4.5 82.5 1.0
O B:HOH520 4.5 48.9 1.0
CE B:LYS310 4.5 71.8 1.0
CB B:ASP151 4.6 59.6 1.0
CAG B:C6J400 4.7 47.6 1.0
CAH B:C6J400 4.7 44.0 1.0
CAE B:C6J400 4.8 53.1 1.0

Magnesium binding site 5 out of 9 in 6b06

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Magnesium binding site 5 out of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)


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 CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:45.9
occ:1.00
 O B:HOH520 1.9 48.9 1.0
OAP B:C6J400 2.0 39.0 1.0
O B:HOH515 2.1 49.8 1.0
OD2 B:ASP151 2.2 43.5 1.0
OD2 B:ASP147 2.2 46.0 1.0
OAL B:C6J400 2.3 37.6 1.0
CG B:ASP151 3.1 53.8 1.0
PAI B:C6J400 3.3 48.8 1.0
CG B:ASP147 3.4 52.2 1.0
CB B:ASP151 3.4 59.6 1.0
PAK B:C6J400 3.5 41.0 1.0
O B:HOH518 3.7 58.8 1.0
MG B:MG401 3.8 44.4 1.0
OD1 B:ASP147 3.8 52.5 1.0
CAH B:C6J400 3.9 44.0 1.0
OAQ B:C6J400 3.9 42.6 1.0
OAN B:C6J400 3.9 40.8 1.0
O B:HOH505 4.1 48.0 1.0
O B:HOH506 4.1 49.6 1.0
O B:HOH511 4.1 42.5 1.0
CAG B:C6J400 4.1 47.6 1.0
NH2 B:ARG156 4.2 62.0 1.0
OD1 B:ASP151 4.3 52.3 1.0
OG B:SER153 4.3 73.7 1.0
OAO B:C6J400 4.5 37.6 1.0
OD1 B:ASP148 4.6 57.2 1.0
O B:ASP147 4.6 42.6 1.0
CB B:ASP147 4.6 48.6 1.0
OAM B:C6J400 4.7 41.4 1.0
C B:ASP147 4.9 50.2 1.0
OG1 B:THR304 4.9 67.4 1.0
CA B:ASP151 4.9 59.2 1.0
MG B:MG403 4.9 39.6 1.0

Magnesium binding site 6 out of 9 in 6b06

Go back to Magnesium Binding Sites List in 6b06
Magnesium binding site 6 out of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)


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 CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:39.6
occ:1.00
 OAQ B:C6J400 2.0 42.6 1.0
O B:HOH514 2.0 46.6 1.0
OD2 B:ASP287 2.0 53.1 1.0
O B:HOH506 2.1 49.6 1.0
OAN B:C6J400 2.2 40.8 1.0
O B:HOH513 2.2 48.6 1.0
CG B:ASP287 3.1 55.3 1.0
PAI B:C6J400 3.2 48.8 1.0
PAK B:C6J400 3.5 41.0 1.0
OD1 B:ASP287 3.6 52.3 1.0
CAH B:C6J400 3.7 44.0 1.0
O B:HOH520 3.8 48.9 1.0
OD1 B:ASP291 4.0 93.8 1.0
O B:ASP287 4.1 49.3 1.0
OD1 B:ASP305 4.2 60.1 1.0
OD1 B:ASP288 4.2 49.5 1.0
OAP B:C6J400 4.3 39.0 1.0
CB B:ASP287 4.3 49.2 1.0
OAL B:C6J400 4.4 37.6 1.0
OAO B:C6J400 4.4 37.6 1.0
OE1 B:GLN284 4.4 51.8 1.0
OD2 B:ASP305 4.5 59.0 1.0
C B:ASP287 4.5 46.4 1.0
NZ B:LYS301 4.5 71.9 1.0
OAM B:C6J400 4.5 41.4 1.0
CB B:ASP291 4.6 74.9 1.0
CG B:ASP291 4.6 82.0 1.0
CG B:ASP305 4.8 58.5 1.0
O B:HOH518 4.8 58.8 1.0
N B:ASP288 4.9 47.8 1.0
MG B:MG402 4.9 45.9 1.0
CA B:ASP287 5.0 48.0 1.0

Magnesium binding site 7 out of 9 in 6b06

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Magnesium binding site 7 out of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)


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 CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:63.6
occ:1.00
 O C:HOH504 1.8 67.0 1.0
O C:HOH510 1.9 66.8 1.0
O C:HOH506 2.1 58.8 1.0
OD1 C:ASP147 2.2 51.1 1.0
OAM C:C6J400 2.2 56.8 1.0
OD2 C:ASP151 2.3 50.8 1.0
OD1 C:ASP151 2.9 51.9 1.0
CG C:ASP151 2.9 59.9 1.0
CG C:ASP147 3.2 59.8 1.0
OAN C:C6J400 3.3 59.9 1.0
PAK C:C6J400 3.4 63.9 1.0
MG C:MG402 3.4 56.9 1.0
OD2 C:ASP147 3.6 51.1 1.0
OD2 C:ASP218 4.0 86.3 1.0
OE1 C:GLN215 4.0 91.1 1.0
NE2 C:GLN215 4.1 87.6 1.0
O C:HOH509 4.1 62.9 1.0
OAL C:C6J400 4.4 67.1 1.0
CB C:ASP151 4.4 59.4 1.0
CB C:ASP147 4.5 64.0 1.0
CD C:GLN215 4.5 81.3 1.0
CE C:LYS310 4.5 85.8 1.0
CG C:ASP218 4.6 83.0 1.0
CAG C:C6J400 4.6 74.5 1.0
OD1 C:ASP218 4.6 83.7 1.0
CAH C:C6J400 4.6 59.4 1.0
O C:HOH501 4.7 61.2 1.0
OAP C:C6J400 4.8 46.1 1.0
CAE C:C6J400 4.8 81.9 1.0
O C:ASP147 4.9 54.2 1.0

Magnesium binding site 8 out of 9 in 6b06

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Magnesium binding site 8 out of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)


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 CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:56.9
occ:1.00
 OAP C:C6J400 1.8 46.1 1.0
O C:HOH501 1.9 61.2 1.0
OAM C:C6J400 1.9 56.8 1.0
O C:HOH509 2.0 62.9 1.0
OD2 C:ASP151 2.1 50.8 1.0
OD2 C:ASP147 2.3 51.1 1.0
PAI C:C6J400 3.1 63.5 1.0
PAK C:C6J400 3.2 63.9 1.0
CG C:ASP147 3.2 59.8 1.0
CG C:ASP151 3.3 59.9 1.0
MG C:MG401 3.4 63.6 1.0
OD1 C:ASP147 3.5 51.1 1.0
CAH C:C6J400 3.6 59.4 1.0
O C:HOH502 3.7 48.1 1.0
OAL C:C6J400 3.8 67.1 1.0
CB C:ASP151 3.8 59.4 1.0
OAQ C:C6J400 3.8 69.4 1.0
CAG C:C6J400 3.8 74.5 1.0
NH2 C:ARG156 3.8 69.5 1.0
O C:HOH510 4.2 66.8 1.0
OG C:SER153 4.2 84.3 1.0
OAO C:C6J400 4.3 36.5 1.0
OD1 C:ASP151 4.3 51.9 1.0
OAN C:C6J400 4.4 59.9 1.0
OD1 C:ASP148 4.4 77.6 1.0
CB C:ASP147 4.6 64.0 1.0
O C:HOH504 4.7 67.0 1.0
O C:ASP147 5.0 54.2 1.0
CAE C:C6J400 5.0 81.9 1.0

Magnesium binding site 9 out of 9 in 6b06

Go back to Magnesium Binding Sites List in 6b06
Magnesium binding site 9 out of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)


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 CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with Ipp and [2-(1-Methylpyridin-2- Yl)-1-Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:71.8
occ:1.00
 OD2 C:ASP287 1.7 58.9 1.0
O C:HOH505 1.9 63.3 1.0
O C:HOH503 2.0 73.4 1.0
OAQ C:C6J400 2.2 69.4 1.0
O C:HOH502 2.2 48.1 1.0
OAL C:C6J400 2.5 67.1 1.0
CG C:ASP287 2.7 73.3 1.0
OD1 C:ASP287 3.2 67.3 1.0
O C:ASP287 3.5 63.1 1.0
PAI C:C6J400 3.5 63.5 1.0
OD1 C:ASP291 3.8 91.0 1.0
PAK C:C6J400 3.9 63.9 1.0
C C:ASP287 4.0 59.9 1.0
CB C:ASP287 4.0 74.4 1.0
CAH C:C6J400 4.0 59.4 1.0
OD2 C:ASP305 4.1 91.6 1.0
OD1 C:ASP305 4.1 95.5 1.0
NZ C:LYS301 4.1 83.4 1.0
CB C:ASP291 4.2 97.1 1.0
OAP C:C6J400 4.4 46.1 1.0
CG C:ASP291 4.4 95.4 1.0
CG C:ASP305 4.5 93.3 1.0
CA C:ASP287 4.5 66.3 1.0
N C:ASP288 4.6 58.2 1.0
OAO C:C6J400 4.6 36.5 1.0
O C:HOH509 4.7 62.9 1.0
OD1 C:ASP288 4.7 77.2 1.0
OAM C:C6J400 4.8 56.8 1.0
CA C:ASP288 4.8 65.4 1.0
OE1 C:GLN284 4.8 55.8 1.0
OAN C:C6J400 4.9 59.9 1.0

Reference:

M.E.Picard, A.Nisole, C.Beliveau, S.Sen, A.Barbar, R.Shi, M.Cusson. Structural Characterization of A Lepidopteran Type-II Farnesyl Diphosphate Synthase From the Spruce Budworm, Choristoneura Fumiferana: Implications For Inhibitor Design. Insect Biochem. Mol. Biol. V. 92 84 2017.
ISSN: ISSN 1879-0240
PubMed: 29183817
DOI: 10.1016/J.IBMB.2017.11.011
Page generated: Mon Sep 30 19:26:11 2024

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