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Iodine in PDB 5vf1: X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22

Protein crystallography data

The structure of X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22, PDB code: 5vf1 was solved by K.H.Chen, K.A.Corro, S.P.Le, J.S.Nowick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.84 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 121.220, 121.220, 29.958, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 27.3

Iodine Binding Sites:

The binding sites of Iodine atom in the X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22 (pdb code 5vf1). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22, PDB code: 5vf1:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 5vf1

Go back to Iodine Binding Sites List in 5vf1
Iodine binding site 1 out of 6 in the X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I5

b:34.9
occ:1.00
I A:PHI5 0.0 34.9 1.0
CZ A:PHI5 2.1 31.5 1.0
HD23 F:LEU3 3.0 64.7 1.0
CE1 A:PHI5 3.0 35.0 1.0
CE2 A:PHI5 3.0 31.7 1.0
HE2 A:PHI5 3.1 38.1 1.0
HE1 A:PHI5 3.1 42.0 1.0
HB2 A:ALA11 3.3 41.1 1.0
HB1 A:ALA11 3.4 41.1 1.0
CB A:ALA11 3.7 34.2 1.0
HB3 A:ALA11 3.7 41.1 1.0
HB2 A:ALA7 3.8 41.7 1.0
HD1 F:PHI5 3.8 42.2 1.0
CD2 F:LEU3 3.9 53.9 1.0
HD21 F:LEU3 3.9 64.7 1.0
HB2 F:PHI5 3.9 40.8 1.0
HD22 F:LEU3 4.3 64.7 1.0
CD1 A:PHI5 4.3 29.7 1.0
CD2 A:PHI5 4.3 36.5 1.0
CB A:ALA7 4.5 34.8 1.0
HB1 A:ALA7 4.5 41.7 1.0
CD1 F:PHI5 4.7 35.1 1.0
HB3 A:ALA7 4.7 41.7 1.0
CB F:PHI5 4.8 34.0 1.0
CG A:PHI5 4.9 31.2 1.0
HB3 F:PHI5 4.9 40.8 1.0
HB3 F:LEU3 4.9 51.7 1.0
HG F:LEU3 4.9 59.6 1.0
CG F:LEU3 5.0 49.7 1.0

Iodine binding site 2 out of 6 in 5vf1

Go back to Iodine Binding Sites List in 5vf1
Iodine binding site 2 out of 6 in the X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I5

b:72.2
occ:1.00
I B:PHI5 0.0 72.2 1.0
CZ B:PHI5 2.1 65.6 1.0
O B:HOH108 2.8 28.4 0.5
CE1 B:PHI5 3.1 63.0 1.0
CE2 B:PHI5 3.1 64.2 1.0
HE1 B:PHI5 3.1 75.7 1.0
HE2 B:PHI5 3.1 77.0 1.0
HB2 B:ALA11 3.3 74.7 1.0
HB1 B:ALA11 3.7 74.7 1.0
CB B:ALA11 3.8 62.2 1.0
HB3 B:ALA11 3.9 74.7 1.0
HB2 B:ALA7 4.2 77.6 1.0
CD1 B:PHI5 4.3 59.0 1.0
CD2 B:PHI5 4.4 60.2 1.0
CG B:PHI5 4.9 57.4 1.0

Iodine binding site 3 out of 6 in 5vf1

Go back to Iodine Binding Sites List in 5vf1
Iodine binding site 3 out of 6 in the X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I5

b:44.7
occ:1.00
I C:PHI5 0.0 44.7 1.0
CZ C:PHI5 2.1 39.8 1.0
HE2 C:PHI5 3.0 51.8 1.0
CE2 C:PHI5 3.0 43.1 1.0
CE1 C:PHI5 3.1 46.5 1.0
HE1 C:PHI5 3.2 55.7 1.0
HB2 C:ALA11 3.3 45.0 1.0
HB2 C:ALA7 3.5 41.2 1.0
HB1 C:ALA11 3.6 45.0 1.0
HD23 E:LEU3 3.7 48.9 1.0
HD2 E:PHI5 3.8 52.8 1.0
CB C:ALA11 3.8 37.5 1.0
HB2 E:PHI5 4.0 48.0 1.0
HB3 C:ALA11 4.1 45.0 1.0
HD21 E:LEU3 4.2 48.9 1.0
CB C:ALA7 4.2 34.4 1.0
HB1 C:ALA7 4.3 41.2 1.0
CD2 C:PHI5 4.3 43.6 1.0
CD1 C:PHI5 4.4 44.6 1.0
CD2 E:LEU3 4.4 40.7 1.0
HB3 C:ALA7 4.5 41.2 1.0
CD2 E:PHI5 4.6 44.0 1.0
CB E:PHI5 4.8 40.0 1.0
HB3 E:PHI5 4.8 48.0 1.0
CG C:PHI5 4.9 36.6 1.0
HG E:LEU3 4.9 50.0 1.0

Iodine binding site 4 out of 6 in 5vf1

Go back to Iodine Binding Sites List in 5vf1
Iodine binding site 4 out of 6 in the X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I5

b:77.7
occ:1.00
I D:PHI5 0.0 77.7 1.0
CZ D:PHI5 2.1 56.9 1.0
CE1 D:PHI5 3.1 53.7 1.0
HE1 D:PHI5 3.1 64.4 1.0
CE2 D:PHI5 3.1 48.5 1.0
HE2 D:PHI5 3.2 58.2 1.0
HB1 D:MEA13 4.2 57.8 1.0
HD13 D:LEU3 4.2 63.4 1.0
HD2 D:MEA13 4.3 61.9 1.0
CD2 D:MEA13 4.3 51.6 1.0
CD1 D:PHI5 4.4 52.1 1.0
CD2 D:PHI5 4.4 47.0 1.0
CG D:MEA13 4.6 48.8 1.0
CE2 D:MEA13 4.7 54.7 1.0
CB D:MEA13 4.8 48.2 1.0
O A:HOH104 4.8 43.8 1.0
HD23 A:LEU15 4.8 47.4 1.0
CG D:PHI5 4.9 45.8 1.0
HE2 D:MEA13 5.0 65.6 1.0
HD22 D:LEU3 5.0 58.8 1.0
O C:HOH106 5.0 44.5 1.0

Iodine binding site 5 out of 6 in 5vf1

Go back to Iodine Binding Sites List in 5vf1
Iodine binding site 5 out of 6 in the X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I5

b:40.0
occ:1.00
I E:PHI5 0.0 40.0 1.0
CZ E:PHI5 2.1 34.0 1.0
CE1 E:PHI5 3.0 33.2 1.0
HE1 E:PHI5 3.1 39.8 1.0
CE2 E:PHI5 3.1 35.0 1.0
HD2 E:MEA13 3.1 50.0 1.0
HE2 E:PHI5 3.2 42.0 1.0
CD2 E:MEA13 3.9 41.6 1.0
HZ C:MEA13 4.0 75.8 1.0
HE2 E:MEA13 4.1 57.6 1.0
HB3 C:PHI5 4.3 41.1 1.0
CD1 E:PHI5 4.3 38.3 1.0
CD2 E:PHI5 4.4 44.0 1.0
HB1 E:MEA13 4.4 53.3 1.0
CE2 E:MEA13 4.4 48.0 1.0
HB2 C:PHI5 4.5 41.1 1.0
HE2 C:MEA13 4.5 77.8 1.0
CZ C:MEA13 4.8 63.2 1.0
CB C:PHI5 4.8 34.3 1.0
HB1 E:ALA11 4.9 48.8 1.0
O D:HOH107 4.9 54.6 1.0
CG E:PHI5 4.9 40.9 1.0
HB3 E:ALA11 4.9 48.8 1.0
CG E:MEA13 5.0 43.6 1.0

Iodine binding site 6 out of 6 in 5vf1

Go back to Iodine Binding Sites List in 5vf1
Iodine binding site 6 out of 6 in the X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing ABETA16-22 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I5

b:39.1
occ:1.00
I F:PHI5 0.0 39.1 1.0
CZ F:PHI5 2.1 41.3 1.0
HD1 F:MEA13 2.9 44.5 1.0
CE1 F:PHI5 3.1 38.3 1.0
CE2 F:PHI5 3.1 34.8 1.0
HE1 F:PHI5 3.1 46.0 1.0
HE2 F:PHI5 3.1 41.8 1.0
CD1 F:MEA13 3.8 37.1 1.0
O B:HOH103 3.8 25.7 1.0
HE1 F:MEA13 3.8 47.9 1.0
HB3 A:PHI5 4.1 37.2 1.0
HE2 A:MEA13 4.1 45.5 1.0
HB2 A:PHI5 4.2 37.2 1.0
CE1 F:MEA13 4.2 40.0 1.0
CD1 F:PHI5 4.3 35.1 1.0
CD2 F:PHI5 4.4 33.9 1.0
HB1 F:MEA13 4.4 47.0 1.0
CB A:PHI5 4.6 31.0 1.0
CG F:PHI5 4.9 33.5 1.0
HB3 F:ALA11 4.9 45.9 1.0
CG F:MEA13 4.9 39.7 1.0

Reference:

K.H.Chen, K.A.Corro, S.P.Le, J.S.Nowick. X-Ray Crystallographic Structure of A Giant Double-Walled Peptide Nanotube Formed By A Macrocyclic Beta-Sheet Containing A Beta 16-22. J. Am. Chem. Soc. V. 139 8102 2017.
ISSN: ESSN 1520-5126
PubMed: 28598147
DOI: 10.1021/JACS.7B03890
Page generated: Sun Dec 13 19:41:37 2020

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