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Chlorine in PDB 4p4w: Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk

Protein crystallography data

The structure of Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk, PDB code: 4p4w was solved by R.K.Spencer, A.Kreutzer, J.S.Nowick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.53 / 1.50
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 58.193, 58.193, 121.279, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 20.9

Other elements in 4p4w:

The structure of Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk also contains other interesting chemical elements:

Iodine (I) 14 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk (pdb code 4p4w). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk, PDB code: 4p4w:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4p4w

Go back to Chlorine Binding Sites List in 4p4w
Chlorine binding site 1 out of 6 in the Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl101

b:30.8
occ:1.00
HZ1 C:LYS16 2.1 18.8 1.0
HE2 C:LYS16 2.7 30.3 1.0
NZ C:LYS16 2.8 15.6 1.0
HZ2 C:LYS16 3.1 18.8 1.0
CE C:LYS16 3.1 25.3 1.0
HE2 A:TYR2 3.3 15.8 1.0
HE3 C:LYS16 3.3 30.3 1.0
HD13 C:LEU4 3.5 18.8 1.0
HZ3 C:LYS16 3.6 18.8 1.0
HD11 C:LEU4 3.6 18.8 1.0
CE2 A:TYR2 3.6 13.1 1.0
CD1 C:LEU4 3.9 15.7 1.0
HD12 C:LEU4 4.1 18.8 1.0
CD2 A:TYR2 4.2 11.9 1.0
CZ A:TYR2 4.2 13.2 1.0
HD2 A:TYR2 4.2 14.3 1.0
OH A:TYR2 4.4 17.5 1.0
CD C:LYS16 4.6 37.7 1.0
HD3 C:LYS16 4.7 45.2 1.0

Chlorine binding site 2 out of 6 in 4p4w

Go back to Chlorine Binding Sites List in 4p4w
Chlorine binding site 2 out of 6 in the Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl103

b:30.1
occ:1.00
H F:ORN1 2.0 24.9 1.0
N F:ORN1 2.8 20.8 1.0
HA F:ORN1 2.8 19.4 1.0
O D:HOH207 3.0 32.2 1.0
HB2 D:TYR6 3.2 15.4 1.0
CA F:ORN1 3.2 16.1 1.0
HD2 D:TYR6 3.3 23.4 1.0
O F:HOH202 3.4 29.2 1.0
C F:ORN1 3.5 13.4 1.0
H2 F:ORN1 3.6 24.9 1.0
O F:HOH212 3.6 46.4 1.0
O F:ORN1 3.8 15.4 1.0
CD2 D:TYR6 3.9 19.5 1.0
CB D:TYR6 4.0 12.8 1.0
N F:TYR2 4.1 14.9 1.0
O D:THR7 4.1 18.8 1.0
H F:TYR2 4.2 17.8 1.0
CG D:TYR6 4.2 13.0 1.0
HB3 D:TYR6 4.3 15.4 1.0
HG2 D:GLU8 4.3 24.6 1.0
H D:THR7 4.5 16.9 1.0
HG3 D:GLU8 4.5 24.6 1.0
CE2 F:TYR2 4.7 15.2 1.0
CB F:ORN1 4.7 20.7 1.0
CE2 D:TYR6 4.7 20.1 1.0
CD2 F:TYR2 4.8 12.4 1.0
HA F:TYR2 4.8 14.1 1.0
CZ F:TYR2 4.8 14.1 1.0
HG3 F:ORN1 4.8 37.7 1.0
HD2 F:ORN1 4.8 26.3 1.0
HE2 D:TYR6 4.9 24.2 1.0
HE2 F:TYR2 4.9 18.2 1.0
CG D:GLU8 4.9 20.5 1.0
C D:THR7 4.9 20.1 1.0
CG F:TYR2 5.0 14.6 1.0
CE1 F:TYR2 5.0 13.9 1.0
N D:THR7 5.0 14.1 1.0
CA F:TYR2 5.0 11.7 1.0

Chlorine binding site 3 out of 6 in 4p4w

Go back to Chlorine Binding Sites List in 4p4w
Chlorine binding site 3 out of 6 in the Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl101

b:30.1
occ:1.00
H G:THR7 2.7 33.6 1.0
O G:HOH215 2.7 56.1 1.0
HG2 D:ORN9 2.8 26.3 1.0
O D:HOH213 2.9 48.5 1.0
HA G:TYR6 3.0 25.2 1.0
HB2 G:TYR6 3.2 27.0 1.0
HD2 D:ORN9 3.5 26.0 1.0
N G:THR7 3.5 28.0 1.0
CG D:ORN9 3.7 21.9 1.0
CA G:TYR6 3.7 21.0 1.0
CB G:TYR6 3.8 22.5 1.0
HG3 D:ORN9 3.8 26.3 1.0
HB3 G:TYR6 3.9 27.0 1.0
OG1 G:THR7 3.9 42.2 1.0
CD D:ORN9 4.0 21.7 1.0
HG21 G:THR7 4.1 53.8 1.0
C G:TYR6 4.1 27.4 1.0
HG1 G:THR7 4.2 50.7 1.0
HD3 D:ORN9 4.3 26.0 1.0
H2 D:ORN9 4.5 30.9 1.0
CA G:THR7 4.5 26.6 1.0
O G:THR7 4.6 32.0 1.0
N D:ORN9 4.6 25.8 1.0
CB G:THR7 4.6 31.8 1.0
O G:PHI5 4.7 22.4 1.0
CG2 G:THR7 4.8 44.8 1.0
O G:HOH210 4.9 43.2 1.0
N G:TYR6 4.9 18.9 1.0
CB D:ORN9 5.0 19.3 1.0

Chlorine binding site 4 out of 6 in 4p4w

Go back to Chlorine Binding Sites List in 4p4w
Chlorine binding site 4 out of 6 in the Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl102

b:30.1
occ:1.00
HH G:TYR2 2.9 68.5 1.0
HZ1 G:LYS16 3.3 73.5 1.0
OH G:TYR2 3.6 57.1 1.0
HE1 G:TYR2 3.8 67.5 1.0
NZ G:LYS16 4.2 61.3 1.0
HD3 G:LYS16 4.3 69.2 1.0
CE1 G:TYR2 4.3 56.3 1.0
CZ G:TYR2 4.4 54.9 1.0
HZ2 G:LYS16 4.4 73.5 1.0
HE2 G:LYS16 4.5 79.4 1.0
HZ3 G:LYS16 4.7 73.5 1.0
CE G:LYS16 4.8 66.1 1.0

Chlorine binding site 5 out of 6 in 4p4w

Go back to Chlorine Binding Sites List in 4p4w
Chlorine binding site 5 out of 6 in the Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl102

b:30.3
occ:1.00
HG3 J:ORN1 2.4 37.8 1.0
N J:ORN1 3.1 29.2 1.0
CG J:ORN1 3.4 31.5 1.0
H2 J:ORN1 3.5 35.0 1.0
HE2 I:LYS10 3.5 50.8 1.0
H J:ORN1 3.6 35.0 1.0
HD2 J:ORN1 3.6 33.7 1.0
HD3 J:ORN1 3.7 33.7 1.0
HA J:ORN1 3.7 32.9 1.0
HZ3 I:LYS10 3.8 59.1 1.0
CD J:ORN1 3.8 28.1 1.0
HZ1 I:LYS10 3.8 59.1 1.0
CA J:ORN1 3.9 27.4 1.0
NZ I:LYS10 4.1 49.2 1.0
CB J:ORN1 4.2 30.4 1.0
HG2 J:ORN1 4.2 37.8 1.0
CE I:LYS10 4.3 42.3 1.0
HB2 J:ORN1 4.6 36.5 1.0
O B:HOH113 4.8 29.1 1.0
HE3 I:LYS10 4.9 50.8 1.0
O J:HOH212 4.9 42.4 1.0
HD2 I:LYS10 4.9 62.9 1.0
HZ2 I:LYS10 5.0 59.1 1.0

Chlorine binding site 6 out of 6 in 4p4w

Go back to Chlorine Binding Sites List in 4p4w
Chlorine binding site 6 out of 6 in the Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl101

b:30.1
occ:1.00
O B:HOH106 2.5 39.1 1.0
O K:HOH205 2.6 33.4 1.0
HB3 K:TYR2 3.2 17.3 1.0
HD1 K:TYR2 3.7 26.4 1.0
O K:ORN1 3.8 21.1 1.0
H K:ORN1 4.0 36.5 1.0
HB2 A:ALA14 4.1 14.4 1.0
CB K:TYR2 4.1 14.4 1.0
HB1 A:ALA14 4.1 14.4 1.0
C K:ORN1 4.1 19.8 1.0
HE2 A:LYS16 4.3 44.4 1.0
HH A:TYR6 4.3 22.2 1.0
OH A:TYR6 4.3 18.5 1.0
HA K:ORN1 4.3 27.8 1.0
CD1 K:TYR2 4.4 22.0 1.0
CZ A:TYR6 4.4 14.9 1.0
HA A:ALA14 4.5 17.6 1.0
CB A:ALA14 4.5 12.0 1.0
O A:HOH202 4.6 33.9 1.0
N K:TYR2 4.6 16.9 1.0
HB2 K:TYR2 4.6 17.3 1.0
HZ1 A:LYS16 4.6 44.9 1.0
HE1 A:TYR6 4.6 16.6 1.0
CE1 A:TYR6 4.7 13.8 1.0
CA K:ORN1 4.7 23.2 1.0
HH B:TYR2 4.7 23.7 1.0
CG K:TYR2 4.7 16.4 1.0
N K:ORN1 4.7 30.4 1.0
CA K:TYR2 4.9 15.1 1.0
HZ3 A:LYS16 4.9 44.9 1.0
HA K:TYR2 5.0 18.2 1.0
CE2 A:TYR6 5.0 18.9 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: Sat Dec 12 11:02:38 2020

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