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Calcium in PDB 5nes: Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa

Protein crystallography data

The structure of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa, PDB code: 5nes was solved by J.-L.Reymond, T.Darbre, A.Stocker, W.Hong, C.Van Delden, T.Koehler, A.Luscher, R.Visini, Y.Fu, I.Di Bonaventura, R.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.78 / 1.61
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.201, 48.527, 52.562, 84.92, 79.98, 80.61
R / Rfree (%) 14.3 / 16.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa (pdb code 5nes). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa, PDB code: 5nes:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5nes

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Calcium binding site 1 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:5.4
occ:1.00
 OD1 A:ASP99 2.4 8.5 1.0
OD2 A:ASP104 2.4 6.1 1.0
OE2 A:GLU95 2.4 6.5 1.0
OD1 A:ASP101 2.4 5.6 1.0
O4 A:ZDC305 2.5 5.0 1.0
O3 A:ZDC305 2.5 7.1 1.0
OE1 A:GLU95 2.5 6.5 1.0
OD1 A:ASP104 2.6 4.5 1.0
CD A:GLU95 2.8 7.2 1.0
CG A:ASP104 2.9 4.6 1.0
C4 A:ZDC305 3.3 5.5 1.0
C3 A:ZDC305 3.4 6.0 1.0
CG A:ASP99 3.4 9.3 1.0
CG A:ASP101 3.5 6.5 1.0
OD2 A:ASP99 3.7 9.2 1.0
CA A:CA302 3.7 4.3 1.0
OD2 A:ASP101 4.0 5.5 1.0
O A:HOH504 4.0 20.1 1.0
N A:ASP101 4.2 8.7 1.0
OD1 A:ASP96 4.2 7.6 1.0
CG A:GLU95 4.3 5.8 1.0
CB A:ASP104 4.4 3.4 1.0
N A:TYR102 4.5 6.9 1.0
N A:ASP96 4.5 3.9 1.0
N A:ASN100 4.6 7.0 1.0
CB A:ASP101 4.6 6.9 1.0
N A:GLY97 4.7 5.8 1.0
CA A:GLU95 4.7 4.1 1.0
C2 A:ZDC305 4.7 7.4 1.0
CB A:ASP99 4.7 10.4 1.0
C5 A:ZDC305 4.7 7.7 1.0
OD1 A:ASN103 4.8 5.5 1.0
CA A:ASP101 4.8 6.6 1.0
O2 A:ZDC305 4.8 5.3 1.0
N A:ASP99 4.9 11.4 1.0
CG A:ASP96 4.9 7.2 1.0
CB A:GLU95 4.9 3.0 1.0
C A:ASP99 5.0 11.1 1.0

Calcium binding site 2 out of 8 in 5nes

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Calcium binding site 2 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:4.3
occ:1.00
 OD1 A:ASN103 2.4 5.5 1.0
O A:ASN21 2.4 4.4 1.0
OD1 A:ASP104 2.4 4.5 1.0
OD2 A:ASP101 2.4 5.5 1.0
O2 A:ZDC305 2.5 5.3 1.0
O3 A:ZDC305 2.5 7.1 1.0
O C:GLY114 2.5 4.8 1.0
OD1 A:ASP101 3.1 5.6 1.0
CG A:ASP101 3.1 6.5 1.0
C3 A:ZDC305 3.4 6.0 1.0
C2 A:ZDC305 3.4 7.4 1.0
CG A:ASN103 3.4 6.4 1.0
C C:GLY114 3.5 6.5 1.0
C A:ASN21 3.6 5.3 1.0
CG A:ASP104 3.6 4.6 1.0
OXT C:GLY114 3.6 8.8 1.0
CA A:CA301 3.7 5.4 1.0
C4 A:ZDC305 3.8 5.5 1.0
ND2 A:ASN103 3.8 4.2 1.0
CB A:ASN21 4.2 4.2 1.0
CA A:ASP104 4.2 2.9 1.0
N A:ASP104 4.3 1.9 1.0
CA A:SER22 4.4 5.8 1.0
N A:SER22 4.4 4.2 1.0
O4 A:ZDC305 4.4 5.0 1.0
OD2 A:ASP104 4.4 6.1 1.0
C A:ASN103 4.5 3.5 1.0
CB A:ASP104 4.5 3.4 1.0
CA A:ASN21 4.5 4.9 1.0
CB A:SER22 4.6 5.2 1.0
O A:HOH464 4.6 16.0 1.0
CB A:ASP101 4.6 6.9 1.0
OD2 A:ASP99 4.6 9.2 1.0
CB A:ASN103 4.8 6.3 1.0
O A:ASN103 4.8 3.2 1.0
C1 A:ZDC305 4.8 7.5 1.0
CA C:GLY114 4.8 5.9 1.0
N A:ASN103 4.9 3.3 1.0
CA A:ASN103 5.0 4.9 1.0

Calcium binding site 3 out of 8 in 5nes

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Calcium binding site 3 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:5.9
occ:1.00
 OD1 C:ASN103 2.3 6.3 1.0
O C:ASN21 2.4 5.6 1.0
OD1 C:ASP104 2.4 5.2 1.0
OD2 C:ASP101 2.4 8.7 1.0
O3 A:ZDC304 2.5 7.4 1.0
O2 A:ZDC304 2.5 8.3 1.0
O A:GLY114 2.5 7.0 1.0
OD1 C:ASP101 3.1 7.1 1.0
CG C:ASP101 3.1 8.8 1.0
CG C:ASN103 3.4 5.7 1.0
C3 A:ZDC304 3.4 7.4 1.0
C2 A:ZDC304 3.4 8.6 1.0
C A:GLY114 3.5 9.3 1.0
C C:ASN21 3.6 5.4 1.0
CG C:ASP104 3.6 4.7 1.0
OXT A:GLY114 3.7 10.3 1.0
CA C:CA201 3.7 6.3 1.0
ND2 C:ASN103 3.8 6.3 1.0
C4 A:ZDC304 3.8 6.3 1.0
CB C:ASN21 4.2 3.7 1.0
CA C:ASP104 4.2 2.7 1.0
N C:ASP104 4.3 3.7 1.0
CA C:SER22 4.4 7.7 1.0
N C:SER22 4.4 6.8 1.0
O4 A:ZDC304 4.4 6.5 1.0
C C:ASN103 4.5 3.6 1.0
OD2 C:ASP104 4.5 6.9 1.0
CB C:ASP104 4.5 3.7 1.0
O C:HOH348 4.5 17.1 1.0
OD2 C:ASP99 4.5 8.3 1.0
CA C:ASN21 4.6 3.2 1.0
CB C:ASP101 4.6 7.3 1.0
CB C:SER22 4.6 7.2 1.0
CB C:ASN103 4.7 5.3 1.0
C1 A:ZDC304 4.8 8.0 1.0
O C:ASN103 4.8 4.2 1.0
CA A:GLY114 4.8 7.6 1.0
N C:ASN103 4.9 4.2 1.0
CA C:ASN103 4.9 3.6 1.0

Calcium binding site 4 out of 8 in 5nes

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Calcium binding site 4 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:5.3
occ:1.00
 OD2 B:ASP104 2.4 5.3 1.0
OE2 B:GLU95 2.4 6.8 1.0
OD1 B:ASP99 2.4 8.0 1.0
OD1 B:ASP101 2.4 4.9 1.0
OE1 B:GLU95 2.4 7.2 1.0
O4 B:ZDC201 2.5 6.8 1.0
O3 B:ZDC201 2.5 6.5 1.0
OD1 B:ASP104 2.6 4.5 1.0
CD B:GLU95 2.7 6.8 1.0
CG B:ASP104 2.9 4.7 1.0
C4 B:ZDC201 3.3 5.7 1.0
C3 B:ZDC201 3.4 6.7 1.0
CG B:ASP99 3.4 9.0 1.0
CG B:ASP101 3.5 6.7 1.0
OD2 B:ASP99 3.7 9.1 1.0
CA B:CA203 3.8 4.7 1.0
OD2 B:ASP101 4.0 4.3 1.0
O B:HOH379 4.1 16.3 1.0
N B:ASP101 4.1 6.8 1.0
OD1 B:ASP96 4.1 9.0 1.0
CG B:GLU95 4.2 5.0 1.0
CB B:ASP104 4.4 3.1 1.0
N B:TYR102 4.4 3.5 1.0
N B:ASP96 4.5 3.4 1.0
N B:ASN100 4.5 7.3 1.0
CB B:ASP101 4.6 8.1 1.0
N B:GLY97 4.6 6.6 1.0
CA B:GLU95 4.7 4.7 1.0
C2 B:ZDC201 4.7 7.0 1.0
OD1 B:ASN103 4.7 5.0 1.0
C5 B:ZDC201 4.7 10.6 1.0
CA B:ASP101 4.7 6.9 1.0
CB B:ASP99 4.8 9.1 1.0
N B:ASP99 4.8 8.9 1.0
CB B:GLU95 4.8 6.0 1.0
O2 B:ZDC201 4.9 5.9 1.0
CG B:ASP96 4.9 8.7 1.0
C B:ASP101 5.0 6.8 1.0
C B:ASP99 5.0 8.8 1.0

Calcium binding site 5 out of 8 in 5nes

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Calcium binding site 5 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:4.7
occ:1.00
 OD1 B:ASN103 2.3 5.0 1.0
O B:ASN21 2.4 4.8 1.0
OD1 B:ASP104 2.4 4.5 1.0
OD2 B:ASP101 2.4 4.3 1.0
O3 B:ZDC201 2.5 6.5 1.0
O D:GLY114 2.5 4.8 1.0
O2 B:ZDC201 2.5 5.9 1.0
OD1 B:ASP101 3.1 4.9 1.0
CG B:ASP101 3.1 6.7 1.0
C3 B:ZDC201 3.4 6.7 1.0
CG B:ASN103 3.4 3.9 1.0
C2 B:ZDC201 3.4 7.0 1.0
C D:GLY114 3.5 9.6 1.0
C B:ASN21 3.6 4.5 1.0
CG B:ASP104 3.6 4.7 1.0
OXT D:GLY114 3.7 9.4 1.0
CA B:CA202 3.8 5.3 1.0
ND2 B:ASN103 3.8 4.1 1.0
C4 B:ZDC201 3.8 5.7 1.0
CA B:ASP104 4.2 2.5 1.0
CB B:ASN21 4.2 2.7 1.0
N B:ASP104 4.2 3.1 1.0
CA B:SER22 4.4 7.3 1.0
N B:SER22 4.4 4.3 1.0
OD2 B:ASP104 4.4 5.3 1.0
O4 B:ZDC201 4.5 6.8 1.0
CB B:ASP104 4.5 3.1 1.0
O B:HOH342 4.5 13.6 1.0
C B:ASN103 4.5 2.8 1.0
OD2 B:ASP99 4.5 9.1 1.0
CA B:ASN21 4.5 4.0 1.0
CB B:ASP101 4.6 8.1 1.0
CB B:SER22 4.6 7.6 1.0
CB B:ASN103 4.7 4.2 1.0
C1 B:ZDC201 4.8 9.6 1.0
O B:ASN103 4.8 3.4 1.0
CA D:GLY114 4.8 5.0 1.0
N B:ASN103 4.9 4.5 1.0
CA B:ASN103 5.0 3.1 1.0

Calcium binding site 6 out of 8 in 5nes

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Calcium binding site 6 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:5.2
occ:1.00
 OD1 D:ASN103 2.4 6.2 1.0
OD1 D:ASP104 2.4 4.4 1.0
O D:ASN21 2.4 4.9 1.0
OD2 D:ASP101 2.4 7.8 1.0
O3 B:ZDC205 2.5 5.9 1.0
O B:GLY114 2.5 6.2 1.0
O2 B:ZDC205 2.5 6.9 1.0
OD1 D:ASP101 3.1 6.6 1.0
CG D:ASP101 3.1 7.5 1.0
C3 B:ZDC205 3.4 5.8 1.0
CG D:ASN103 3.4 7.8 1.0
C2 B:ZDC205 3.4 6.4 1.0
C B:GLY114 3.5 11.6 1.0
C D:ASN21 3.6 5.4 1.0
CG D:ASP104 3.6 4.8 1.0
OXT B:GLY114 3.7 8.2 1.0
CA D:CA201 3.7 5.4 1.0
C4 B:ZDC205 3.8 7.5 1.0
ND2 D:ASN103 3.8 6.3 1.0
CB D:ASN21 4.1 4.7 1.0
CA D:ASP104 4.2 3.9 1.0
N D:ASP104 4.2 3.4 1.0
O D:HOH321 4.4 13.4 1.0
O4 B:ZDC205 4.4 7.5 1.0
OD2 D:ASP104 4.4 4.8 1.0
CA D:SER22 4.4 5.7 1.0
C D:ASN103 4.5 2.5 1.0
CB D:ASP104 4.5 3.0 1.0
N D:SER22 4.5 4.7 1.0
CA D:ASN21 4.5 4.6 1.0
OD2 D:ASP99 4.5 10.0 1.0
CB D:ASP101 4.6 8.2 1.0
CB D:SER22 4.6 6.0 1.0
CB D:ASN103 4.7 4.2 1.0
O D:ASN103 4.8 4.2 1.0
C1 B:ZDC205 4.8 13.2 1.0
CA B:GLY114 4.8 7.1 1.0
N D:ASN103 4.9 4.8 1.0
CA D:ASN103 4.9 5.0 1.0

Calcium binding site 7 out of 8 in 5nes

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Calcium binding site 7 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:6.3
occ:1.00
 OD1 C:ASP99 2.4 8.8 1.0
OD1 C:ASP101 2.4 7.1 1.0
OE2 C:GLU95 2.4 8.7 1.0
OD2 C:ASP104 2.4 6.9 1.0
OE1 C:GLU95 2.5 7.6 1.0
O4 A:ZDC304 2.5 6.5 1.0
O3 A:ZDC304 2.5 7.4 1.0
OD1 C:ASP104 2.7 5.2 1.0
CD C:GLU95 2.8 8.3 1.0
CG C:ASP104 2.9 4.7 1.0
C4 A:ZDC304 3.3 6.3 1.0
C3 A:ZDC304 3.4 7.4 1.0
CG C:ASP99 3.4 9.4 1.0
CG C:ASP101 3.5 8.8 1.0
OD2 C:ASP99 3.7 8.3 1.0
CA A:CA303 3.7 5.9 1.0
OD2 C:ASP101 4.0 8.7 1.0
OD1 C:ASP96 4.1 7.8 1.0
O C:HOH350 4.1 18.3 1.0
N C:ASP101 4.1 8.8 1.0
CG C:GLU95 4.3 5.5 1.0
CB C:ASP104 4.4 3.7 1.0
N C:TYR102 4.4 6.0 1.0
N C:ASN100 4.5 11.2 1.0
N C:ASP96 4.6 5.6 1.0
N C:GLY97 4.6 6.1 1.0
CB C:ASP101 4.6 7.3 1.0
OD1 C:ASN103 4.7 6.3 1.0
C2 A:ZDC304 4.7 8.6 1.0
CA C:GLU95 4.7 3.9 1.0
CB C:ASP99 4.7 9.4 1.0
C5 A:ZDC304 4.8 13.1 1.0
N C:ASP99 4.8 9.5 1.0
CA C:ASP101 4.8 6.6 1.0
O2 A:ZDC304 4.8 8.3 1.0
CB C:GLU95 4.9 5.7 1.0
CG C:ASP96 4.9 9.8 1.0
C C:ASP99 5.0 13.0 1.0
C C:ASP101 5.0 6.2 1.0

Calcium binding site 8 out of 8 in 5nes

Go back to Calcium Binding Sites List in 5nes
Calcium binding site 8 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:5.4
occ:1.00
 OD1 D:ASP101 2.3 6.6 1.0
OD1 D:ASP99 2.4 9.4 1.0
OE2 D:GLU95 2.4 6.8 1.0
OD2 D:ASP104 2.4 4.8 1.0
OE1 D:GLU95 2.4 7.1 1.0
O3 B:ZDC205 2.5 5.9 1.0
O4 B:ZDC205 2.5 7.5 1.0
OD1 D:ASP104 2.6 4.4 1.0
CD D:GLU95 2.8 8.0 1.0
CG D:ASP104 2.9 4.8 1.0
C4 B:ZDC205 3.3 7.5 1.0
C3 B:ZDC205 3.4 5.8 1.0
CG D:ASP99 3.4 11.7 1.0
CG D:ASP101 3.4 7.5 1.0
CA B:CA204 3.7 5.2 1.0
OD2 D:ASP99 3.7 10.0 1.0
OD2 D:ASP101 4.0 7.8 1.0
N D:ASP101 4.1 7.9 1.0
O D:HOH383 4.2 12.9 1.0
OD1 D:ASP96 4.2 9.9 1.0
CG D:GLU95 4.2 5.3 1.0
N D:TYR102 4.4 6.6 1.0
CB D:ASP104 4.4 3.0 1.0
N D:ASN100 4.4 7.4 1.0
N D:ASP96 4.5 5.0 1.0
CB D:ASP101 4.6 8.2 1.0
OD1 D:ASN103 4.7 6.2 1.0
CA D:GLU95 4.7 4.8 1.0
N D:GLY97 4.7 6.8 1.0
C2 B:ZDC205 4.7 6.4 1.0
CA D:ASP101 4.7 5.5 1.0
CB D:ASP99 4.7 10.4 1.0
N D:ASP99 4.8 10.8 1.0
C5 B:ZDC205 4.8 20.4 1.0
O2 B:ZDC205 4.8 6.9 1.0
CB D:GLU95 4.9 6.6 1.0
CG D:ASP96 4.9 7.3 1.0
C D:ASP99 5.0 8.4 1.0
C D:ASP101 5.0 7.5 1.0

Reference:

R.He, I.Di Bonaventura, R.Visini, B.H.Gan, Y.Fu, D.Probst, A.Luscher, T.Kohler, C.Van Delden, A.Stocker, W.Hong, T.Darbre, J.L.Reymond. Design, Crystal Structure and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa. Chem Sci V. 8 7464 2017.
ISSN: ISSN 2041-6520
PubMed: 29163899
DOI: 10.1039/C7SC01599B
Page generated: Mon Jul 15 08:56:29 2024

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