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Iodine in PDB 4p4y: Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk

Protein crystallography data

The structure of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk, PDB code: 4p4y was solved by R.K.Spencer, H.Li, J.S.Nowick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.13 / 1.51
Space group H 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 66.260, 66.260, 154.630, 90.00, 90.00, 120.00
R / Rfree (%) 15.7 / 17.5

Other elements in 4p4y:

The structure of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk (pdb code 4p4y). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk, PDB code: 4p4y:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 4p4y

Go back to Iodine Binding Sites List in 4p4y
Iodine binding site 1 out of 7 in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I5

b:23.4
occ:1.00
 I A:PHI5 0.0 23.4 1.0
CZ A:PHI5 2.1 17.8 1.0
CE1 A:PHI5 3.0 19.2 1.0
CE2 A:PHI5 3.0 20.1 1.0
HE1 A:PHI5 3.1 23.1 1.0
HE2 A:PHI5 3.1 24.1 1.0
H C:PHI5 3.6 18.8 1.0
HB2 C:LEU3 3.6 23.5 1.0
O C:LEU3 3.7 19.0 1.0
HA C:LEU4 3.9 22.1 0.5
HD2 C:PHI5 3.9 26.0 1.0
CD2 C:PHI5 3.9 21.7 1.0
HA C:LEU4 3.9 22.2 0.6
C C:LEU3 4.0 16.5 1.0
N C:PHI5 4.1 15.7 1.0
HB2 C:PHI5 4.2 20.1 1.0
CG C:PHI5 4.2 17.5 1.0
N C:LEU4 4.3 17.0 0.5
HB3 C:LEU3 4.3 23.5 1.0
CD1 A:PHI5 4.3 27.2 1.0
CE2 C:PHI5 4.3 18.9 1.0
N C:LEU4 4.3 15.9 0.6
C C:LEU4 4.3 15.3 0.6
CD2 A:PHI5 4.3 20.6 1.0
CB C:LEU3 4.3 19.6 1.0
CA C:LEU4 4.4 18.4 0.5
CA C:LEU4 4.4 18.5 0.6
C C:LEU4 4.5 15.7 0.5
HE2 C:PHI5 4.6 22.6 1.0
CB C:PHI5 4.6 16.7 1.0
H C:LEU4 4.7 20.4 0.5
H C:LEU4 4.8 19.1 0.6
CD1 C:PHI5 4.8 28.4 1.0
CA C:LEU3 4.8 20.6 1.0
CG A:PHI5 4.9 17.4 1.0
HB3 A:MAA13 4.9 26.2 1.0
CZ C:PHI5 4.9 17.0 1.0
CA C:PHI5 5.0 16.7 1.0
O C:LEU4 5.0 16.4 0.6
HD13 C:LEU3 5.0 39.8 1.0

Iodine binding site 2 out of 7 in 4p4y

Go back to Iodine Binding Sites List in 4p4y
Iodine binding site 2 out of 7 in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I5

b:24.3
occ:1.00
 I B:PHI5 0.0 24.3 1.0
CZ B:PHI5 2.1 18.8 1.0
CE1 B:PHI5 3.0 25.0 1.0
CE2 B:PHI5 3.1 24.9 1.0
HE1 B:PHI5 3.1 30.0 1.0
HE2 B:PHI5 3.1 29.9 1.0
CD1 B:PHI5 4.3 25.4 1.0
CD2 B:PHI5 4.4 29.4 1.0
HB2 B:MAA13 4.5 29.1 1.0
HB3 B:MAA13 4.5 29.1 1.0
CG B:PHI5 4.9 20.9 1.0
CB B:MAA13 4.9 24.2 1.0

Iodine binding site 3 out of 7 in 4p4y

Go back to Iodine Binding Sites List in 4p4y
Iodine binding site 3 out of 7 in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I5

b:22.1
occ:1.00
 I C:PHI5 0.0 22.1 1.0
CZ C:PHI5 2.1 17.0 1.0
CE1 C:PHI5 3.0 22.7 1.0
HE1 C:PHI5 3.0 27.2 1.0
CE2 C:PHI5 3.0 18.9 1.0
HE2 C:PHI5 3.1 22.6 1.0
O B:PHI5 3.3 19.0 1.0
HA B:TYR6 3.3 22.4 0.4
HB3 B:PHI5 3.4 29.4 1.0
HG22 B:THR7 3.4 22.7 1.0
H A:PHI5 3.5 19.7 1.0
HG13 B:VAL11 3.7 23.2 1.0
O A:LEU3 3.8 19.1 1.0
C B:PHI5 3.8 14.9 1.0
HB3 A:LEU3 3.8 22.7 1.0
HA A:LEU4 3.9 18.7 1.0
HB2 B:PHI5 3.9 29.4 1.0
CD2 A:PHI5 3.9 20.6 1.0
HA B:TYR6 3.9 22.1 0.6
HD2 A:PHI5 3.9 24.7 1.0
HB2 A:PHI5 4.0 18.1 1.0
N A:PHI5 4.0 16.4 1.0
CA B:TYR6 4.0 18.6 0.4
HB2 A:LEU3 4.1 22.7 1.0
CB B:PHI5 4.1 24.5 1.0
CG A:PHI5 4.1 17.4 1.0
N B:TYR6 4.1 20.4 0.6
C A:LEU3 4.1 17.1 1.0
N B:TYR6 4.1 19.9 0.4
HG22 B:VAL11 4.2 24.7 1.0
CG2 B:THR7 4.2 18.9 1.0
CD1 C:PHI5 4.3 28.4 1.0
HG23 B:THR7 4.3 22.7 1.0
CE2 A:PHI5 4.3 20.1 1.0
CD2 C:PHI5 4.3 21.7 1.0
CA B:TYR6 4.3 18.4 0.6
C B:TYR6 4.3 20.3 0.4
C B:TYR6 4.4 20.9 0.6
H B:THR7 4.4 24.7 1.0
CB A:LEU3 4.4 18.9 1.0
HB B:THR7 4.4 29.3 1.0
N A:LEU4 4.4 18.8 1.0
HG12 B:VAL11 4.4 23.2 1.0
CA A:LEU4 4.4 15.6 1.0
CB A:PHI5 4.5 15.1 1.0
N B:THR7 4.5 20.6 1.0
C A:LEU4 4.5 15.0 1.0
CG1 B:VAL11 4.5 19.3 1.0
CA B:PHI5 4.6 19.8 1.0
H B:TYR6 4.6 24.4 0.6
HE2 A:PHI5 4.6 24.1 1.0
CD1 A:PHI5 4.7 27.2 1.0
H B:TYR6 4.8 23.9 0.4
CB B:THR7 4.8 24.4 1.0
HG21 B:VAL11 4.8 24.7 1.0
HB3 C:MAA13 4.8 32.4 1.0
CZ A:PHI5 4.9 17.8 1.0
CG C:PHI5 4.9 17.5 1.0
O B:TYR6 4.9 19.6 0.6
HD1 B:PHI5 4.9 30.5 1.0
HB2 C:MAA13 4.9 32.4 1.0
CA A:PHI5 4.9 18.0 1.0
CG2 B:VAL11 4.9 20.6 1.0
CA A:LEU3 4.9 16.0 1.0
H A:LEU4 4.9 22.6 1.0
HD21 A:LEU3 4.9 42.2 1.0
HG21 B:THR7 5.0 22.7 1.0
O B:TYR6 5.0 19.0 0.4

Iodine binding site 4 out of 7 in 4p4y

Go back to Iodine Binding Sites List in 4p4y
Iodine binding site 4 out of 7 in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I5

b:24.5
occ:1.00
 I D:PHI5 0.0 24.5 1.0
CZ D:PHI5 2.1 21.8 1.0
CE1 D:PHI5 3.0 18.6 1.0
HE1 D:PHI5 3.0 22.3 1.0
CE2 D:PHI5 3.1 23.0 1.0
HE2 D:PHI5 3.2 27.6 1.0
H E:PHI5 3.5 26.2 1.0
HB2 E:LEU3 3.6 23.2 1.0
O E:LEU3 3.6 19.9 1.0
HA E:LEU4 3.9 21.5 1.0
C E:LEU3 3.9 16.6 1.0
N E:PHI5 4.0 21.8 1.0
HD2 E:PHI5 4.0 34.0 1.0
CD2 E:PHI5 4.0 28.4 1.0
HB2 E:PHI5 4.0 25.1 1.0
N E:LEU4 4.2 19.1 1.0
CG E:PHI5 4.2 18.9 1.0
C E:LEU4 4.3 21.8 1.0
HB3 E:LEU3 4.3 23.2 1.0
CA E:LEU4 4.3 17.9 1.0
CD1 D:PHI5 4.3 21.4 1.0
CB E:LEU3 4.3 19.3 1.0
CD2 D:PHI5 4.4 21.6 1.0
CE2 E:PHI5 4.4 21.8 1.0
CB E:PHI5 4.5 20.9 1.0
HB3 D:MAA13 4.6 29.4 1.0
H E:LEU4 4.7 22.9 1.0
HE2 E:PHI5 4.7 26.2 1.0
CA E:LEU3 4.8 18.5 1.0
CD1 E:PHI5 4.8 23.4 1.0
HB2 D:MAA13 4.9 29.4 1.0
CA E:PHI5 4.9 18.0 1.0
CG D:PHI5 4.9 19.5 1.0

Iodine binding site 5 out of 7 in 4p4y

Go back to Iodine Binding Sites List in 4p4y
Iodine binding site 5 out of 7 in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I5

b:21.4
occ:1.00
 I E:PHI5 0.0 21.4 1.0
CZ E:PHI5 2.1 23.6 1.0
CE1 E:PHI5 3.1 21.2 1.0
CE2 E:PHI5 3.1 21.8 1.0
HE1 E:PHI5 3.1 25.4 1.0
HE2 E:PHI5 3.2 26.2 1.0
H D:PHI5 3.5 20.6 1.0
HD2 D:PHI5 3.7 26.0 1.0
HB3 D:LEU3 3.7 28.4 1.0
O D:LEU3 3.8 21.4 1.0
HB2 D:PHI5 3.8 25.7 1.0
CD2 D:PHI5 3.8 21.6 1.0
HA D:LEU4 3.8 29.5 0.6
N D:PHI5 4.0 17.2 1.0
HB2 D:LEU3 4.0 28.4 1.0
HA D:LEU4 4.0 28.0 0.4
CG D:PHI5 4.1 19.5 1.0
C D:LEU3 4.1 25.5 1.0
CE2 D:PHI5 4.3 23.0 1.0
CB D:LEU3 4.3 23.7 1.0
CB D:PHI5 4.3 21.4 1.0
CD1 E:PHI5 4.4 23.4 1.0
C D:LEU4 4.4 18.8 0.4
CD2 E:PHI5 4.4 28.4 1.0
N D:LEU4 4.4 26.7 0.6
CA D:LEU4 4.4 24.6 0.6
N D:LEU4 4.4 25.3 0.4
C D:LEU4 4.5 19.8 0.6
CA D:LEU4 4.5 23.4 0.4
HE2 D:PHI5 4.5 27.6 1.0
HD23 D:LEU3 4.7 55.5 1.0
CD1 D:PHI5 4.8 21.4 1.0
CA D:PHI5 4.8 20.8 1.0
CA D:LEU3 4.9 20.8 1.0
HB3 E:MAA13 4.9 43.0 1.0
CG E:PHI5 4.9 18.9 1.0
H D:LEU4 4.9 32.0 0.6
H D:LEU4 4.9 30.3 0.4
CZ D:PHI5 5.0 21.8 1.0
HB2 E:MAA13 5.0 43.0 1.0

Iodine binding site 6 out of 7 in 4p4y

Go back to Iodine Binding Sites List in 4p4y
Iodine binding site 6 out of 7 in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I5

b:23.7
occ:1.00
 I F:PHI5 0.0 23.7 1.0
CZ F:PHI5 2.1 18.5 1.0
CE1 F:PHI5 3.0 20.0 1.0
HE1 F:PHI5 3.1 24.0 1.0
CE2 F:PHI5 3.1 19.9 1.0
HE2 F:PHI5 3.2 23.8 1.0
HA E:TYR6 3.3 36.9 1.0
HB3 E:PHI5 3.3 25.1 1.0
HG23 E:THR7 3.4 28.3 1.0
O E:PHI5 3.4 24.7 1.0
HG13 E:VAL11 3.6 24.5 1.0
C E:PHI5 3.7 19.1 1.0
HB2 E:PHI5 3.8 25.1 1.0
HB E:THR7 3.9 29.1 1.0
CA E:TYR6 3.9 30.8 1.0
CB E:PHI5 3.9 20.9 1.0
N E:TYR6 4.0 21.1 1.0
CG2 E:THR7 4.1 23.6 1.0
C E:TYR6 4.1 25.6 1.0
HG21 E:THR7 4.1 28.3 1.0
HG22 E:VAL11 4.1 26.0 1.0
CD1 F:PHI5 4.3 20.8 1.0
N E:THR7 4.3 22.4 1.0
H E:THR7 4.4 26.9 1.0
CD2 F:PHI5 4.4 22.8 1.0
CB E:THR7 4.5 24.2 1.0
CG1 E:VAL11 4.5 20.4 1.0
CA E:PHI5 4.5 18.0 1.0
H E:TYR6 4.5 25.3 1.0
HG11 E:VAL11 4.5 24.5 1.0
O E:TYR6 4.7 25.2 1.0
HD1 E:PHI5 4.7 28.0 1.0
CG F:PHI5 4.9 20.0 1.0
CG2 E:VAL11 4.9 21.6 1.0
HG22 E:THR7 4.9 28.3 1.0
HG21 E:VAL11 4.9 26.0 1.0

Iodine binding site 7 out of 7 in 4p4y

Go back to Iodine Binding Sites List in 4p4y
Iodine binding site 7 out of 7 in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Maa)Tvk within 5.0Å range:
probe atom residue distance (Å) B Occ
G:I5

b:23.4
occ:1.00
 I G:PHI5 0.0 23.4 1.0
CZ G:PHI5 2.1 17.6 1.0
CE1 G:PHI5 3.0 27.6 1.0
HE1 G:PHI5 3.0 33.1 1.0
CE2 G:PHI5 3.1 27.8 1.0
HE2 G:PHI5 3.1 33.4 1.0
CD1 G:PHI5 4.3 23.2 1.0
CD2 G:PHI5 4.4 30.0 1.0
HB3 G:MAA13 4.7 28.1 1.0
HB2 G:MAA13 4.8 28.1 1.0
CG G:PHI5 4.9 23.2 1.0

Reference:

R.K.Spencer, A.G.Kreutzer, P.J.Salveson, H.Li, J.S.Nowick. X-Ray Crystallographic Structures of Oligomers of Peptides Derived From Beta 2-Microglobulin. J.Am.Chem.Soc. 2015.
ISSN: ESSN 1520-5126
PubMed: 25915729
DOI: 10.1021/JACS.5B01673
Page generated: Sun Aug 11 19:20:41 2024

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