Atomistry » Iodine » PDB 4p0d-4s2v » 4p4y
Atomistry »
  Iodine »
    PDB 4p0d-4s2v »
      4p4y »

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 Dec 13 19:36:09 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy