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Iodine in PDB 6cg4: Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V

Protein crystallography data

The structure of Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V, PDB code: 6cg4 was solved by P.J.Salveson, J.S.Nowick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.78 / 2.08
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 39.317, 39.317, 59.384, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 26.3

Iodine Binding Sites:

The binding sites of Iodine atom in the Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V (pdb code 6cg4). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V, PDB code: 6cg4:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 6cg4

Go back to Iodine Binding Sites List in 6cg4
Iodine binding site 1 out of 10 in the Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I101

b:30.7
occ:1.00
 I A:IOD102 2.9 56.5 0.5
HB2 C:GLU7 3.2 16.9 1.0
O C:HOH202 3.3 16.3 1.0
HG23 A:VAL3 3.3 18.4 1.0
HN3 A:ORN15 3.3 19.6 1.0
O A:ORN1 3.5 12.5 1.0
HG12 C:ILE11 3.6 19.7 1.0
HD11 C:ILE11 3.7 17.9 1.0
H C:GLU7 3.8 13.3 1.0
HG22 A:VAL3 3.8 18.4 1.0
HD13 C:ILE11 3.9 17.9 1.0
CG2 A:VAL3 4.0 15.2 1.0
HA A:CYS2 4.0 13.7 1.0
C A:ORN1 4.1 13.8 1.0
CD1 C:ILE11 4.1 14.9 1.0
CB C:GLU7 4.2 14.0 1.0
HG3 A:ORN15 4.2 19.2 1.0
NE A:ORN15 4.2 16.2 1.0
CG1 C:ILE11 4.3 16.3 1.0
HE2 A:ORN15 4.3 19.6 1.0
N C:GLU7 4.3 11.6 1.0
HB3 C:GLU7 4.4 16.9 1.0
HG21 A:VAL3 4.4 18.4 1.0
C A:CYS2 4.4 12.5 1.0
CA A:CYS2 4.5 11.3 1.0
HB2 A:ORN15 4.5 20.8 1.0
OE1 C:GLU7 4.5 20.7 1.0
N A:CYS2 4.5 12.6 1.0
H2 A:ORN1 4.6 16.7 1.0
N A:VAL3 4.6 13.9 1.0
HA C:CYS6 4.7 13.9 1.0
HB2 A:ORN1 4.7 15.7 1.0
O A:CYS2 4.7 9.4 1.0
HE1 A:ORN15 4.7 19.6 1.0
HG23 C:ILE11 4.7 21.8 1.0
H A:VAL3 4.7 16.8 1.0
CA C:GLU7 4.8 11.6 1.0
HG13 C:ILE11 4.8 19.7 1.0
HA C:GLU7 4.9 13.5 1.0
CG A:ORN15 4.9 15.9 1.0

Iodine binding site 2 out of 10 in 6cg4

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Iodine binding site 2 out of 10 in the Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I102

b:56.5
occ:0.50
 HN3 A:ORN15 2.4 19.6 1.0
I A:IOD101 2.9 30.7 1.0
NE A:ORN15 3.2 16.2 1.0
HE1 A:ORN15 3.3 19.6 1.0
HD11 C:ILE11 3.3 17.9 1.0
HD3 A:ORN15 3.5 20.9 1.0
O A:HOH202 3.5 25.1 1.0
HG3 A:ORN15 3.8 19.2 1.0
CD A:ORN15 3.8 17.3 1.0
HE2 A:ORN15 3.9 19.6 1.0
CD1 C:ILE11 4.2 14.9 1.0
HD13 C:ILE11 4.2 17.9 1.0
HG22 A:VAL3 4.3 18.4 1.0
CG A:ORN15 4.4 15.9 1.0
HD2 A:ORN15 4.7 20.9 1.0
HG23 A:VAL3 4.7 18.4 1.0
HD12 C:ILE11 4.7 17.9 1.0
HG12 C:ILE11 4.8 19.7 1.0
CG2 A:VAL3 4.8 15.2 1.0
HG21 A:VAL3 4.8 18.4 1.0
HB2 A:ORN15 5.0 20.8 1.0

Iodine binding site 3 out of 10 in 6cg4

Go back to Iodine Binding Sites List in 6cg4
Iodine binding site 3 out of 10 in the Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I103

b:25.2
occ:0.58
 HE2 A:ORN15 3.6 19.6 1.0
O A:HOH206 3.7 32.3 1.0
O C:HOH202 3.7 16.3 1.0
HB2 A:ORN1 3.8 15.7 1.0
HE1 A:ORN15 3.9 19.6 1.0
O A:HOH202 4.0 25.1 1.0
NE A:ORN15 4.1 16.2 1.0
H2 A:ORN1 4.4 16.7 1.0
HN3 A:ORN15 4.4 19.6 1.0
HG3 A:ORN1 4.5 11.7 1.0
CB A:ORN1 4.8 13.0 1.0
OE1 C:GLU7 4.9 20.7 1.0
HB2 A:ORN15 4.9 20.8 1.0

Iodine binding site 4 out of 10 in 6cg4

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Iodine binding site 4 out of 10 in the Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I104

b:54.8
occ:0.75
 HG21 A:ILE12 5.0 22.4 1.0

Iodine binding site 5 out of 10 in 6cg4

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Iodine binding site 5 out of 10 in the Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I101

b:0.5
occ:1.00
 HD11 A:ILE11 3.0 15.8 1.0
HG2 B:ORN15 3.1 40.1 1.0
HB2 B:ORN1 3.3 20.7 1.0
O A:HOH203 3.4 9.6 1.0
HG12 A:ILE11 3.5 14.1 1.0
HD13 A:ILE11 3.6 15.8 1.0
HG22 B:VAL3 3.6 21.9 1.0
HG23 B:VAL3 3.6 21.9 1.0
CD1 A:ILE11 3.6 13.0 1.0
O B:HOH204 3.6 28.2 1.0
O B:ORN1 3.9 16.7 1.0
HB2 A:GLU7 3.9 18.4 1.0
H11 B:MPD106 3.9 85.0 1.0
CG2 B:VAL3 4.0 18.1 1.0
CG B:ORN15 4.0 33.4 1.0
CG1 A:ILE11 4.1 11.7 1.0
HD2 B:ORN15 4.1 43.4 1.0
H13 B:MPD106 4.1 85.0 1.0
H2 B:ORN1 4.2 23.9 1.0
HG3 B:ORN15 4.2 40.1 1.0
C B:ORN1 4.2 16.6 1.0
HG21 B:VAL3 4.2 21.9 1.0
CB B:ORN1 4.2 17.7 1.0
HB3 B:ORN1 4.4 20.7 1.0
HG13 A:ILE11 4.4 14.1 1.0
H A:GLU7 4.5 11.6 1.0
HD12 A:ILE11 4.5 15.8 1.0
C1 B:MPD106 4.6 70.8 1.0
CD B:ORN15 4.6 36.1 1.0
HE2 B:ORN15 4.6 45.2 1.0
CA B:ORN1 4.7 18.8 1.0
HA B:CYS2 4.8 17.6 1.0
N B:CYS2 4.8 15.9 1.0
CB A:GLU7 4.8 15.2 1.0
HB3 B:ORN15 4.9 36.2 1.0
N B:ORN1 4.9 19.8 1.0
H31 B:MPD106 5.0 82.8 1.0
HB3 A:GLU7 5.0 18.4 1.0

Iodine binding site 6 out of 10 in 6cg4

Go back to Iodine Binding Sites List in 6cg4
Iodine binding site 6 out of 10 in the Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I102

b:36.0
occ:0.47
 I B:IOD105 4.7 0.4 0.9

Iodine binding site 7 out of 10 in 6cg4

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Iodine binding site 7 out of 10 in the Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I103

b:31.0
occ:1.00
 HD13 B:ILE12 2.1 35.4 1.0
CD1 B:ILE12 2.8 29.4 1.0
HD11 B:ILE12 2.8 35.4 1.0
HD12 B:ILE12 3.1 35.4 1.0
H05 B:EZY13 3.2 39.0 1.0
HA B:ILE12 3.7 24.4 1.0
C01 B:EZY13 4.0 32.4 1.0
CG1 B:ILE12 4.1 26.8 1.0
C07 B:EZY13 4.2 35.3 1.0
HG12 B:ILE12 4.2 32.3 1.0
HG23 B:ILE12 4.3 27.5 1.0
H08 B:EZY13 4.3 39.0 1.0
H12 B:EZY13 4.4 42.5 1.0
O B:ILE11 4.4 19.5 1.0
C06 B:EZY13 4.5 35.3 1.0
CA B:ILE12 4.6 20.2 1.0
HG13 B:ILE12 4.8 32.3 1.0
CB B:ILE12 4.8 23.1 1.0
O01 B:EZY13 4.8 42.1 1.0
C02 B:EZY13 4.8 37.4 1.0

Iodine binding site 8 out of 10 in 6cg4

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Iodine binding site 8 out of 10 in the Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I104

b:48.8
occ:0.47
 HD3 B:ORN15 3.1 43.4 1.0
HN3 B:ORN15 3.2 45.2 1.0
HE1 B:ORN15 3.7 45.2 1.0
NE B:ORN15 3.7 37.6 1.0
HB2 B:ORN15 3.8 36.2 1.0
CD B:ORN15 3.9 36.1 1.0
O B:ORN15 4.2 25.3 1.0
O B:HOH202 4.5 32.6 1.0
HD2 B:ORN15 4.5 43.4 1.0
CB B:ORN15 4.6 30.1 1.0
HE2 B:ORN15 4.6 45.2 1.0
CG B:ORN15 4.8 33.4 1.0
H B:ORN15 4.8 29.4 1.0
CA B:ORN15 4.9 26.5 1.0
C B:ORN15 4.9 23.8 1.0

Iodine binding site 9 out of 10 in 6cg4

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Iodine binding site 9 out of 10 in the Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I105

b:0.4
occ:0.85
 I B:IOD102 4.7 36.0 0.5

Iodine binding site 10 out of 10 in 6cg4

Go back to Iodine Binding Sites List in 6cg4
Iodine binding site 10 out of 10 in the Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Covalently Crosslinked Trimer of A Macrocyclic Peptide Derived From Abeta(17-36) - (Orn)Lcvffced(Orn)Aii(2-Nitrobenzylglycine)L(Orn)V within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I101

b:28.9
occ:0.39
 HE1 C:ORN9 3.3 25.4 1.0
HB2 C:ORN9 3.4 19.4 1.0
HG2 C:GLU7 3.5 19.9 1.0
HD2 C:ORN9 3.7 25.7 1.0
HB3 C:ORN9 3.7 19.4 1.0
OE2 C:GLU7 3.8 19.5 1.0
CD C:GLU7 4.0 19.1 1.0
CB C:ORN9 4.1 16.1 1.0
NE C:ORN9 4.1 21.1 1.0
CG C:GLU7 4.2 16.5 1.0
O C:HOH208 4.2 0.2 1.0
CD C:ORN9 4.4 21.3 1.0
H2 C:ORN9 4.5 15.5 1.0
OE1 C:GLU7 4.5 20.7 1.0
HG3 C:GLU7 4.7 19.9 1.0
CG C:ORN9 4.9 19.1 1.0
H3 C:ORN9 4.9 15.5 1.0

Reference:

P.J.Salveson, S.Haerianardakani, A.Thuy-Boun, A.G.Kreutzer, J.S.Nowick. Controlling the Oligomerization State of A Beta-Derived Peptides with Light. J. Am. Chem. Soc. V. 140 5842 2018.
ISSN: ESSN 1520-5126
PubMed: 29627987
DOI: 10.1021/JACS.8B02658
Page generated: Sun Aug 11 22:48:02 2024

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