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Chlorine in PDB 4wc8: Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69).

Protein crystallography data

The structure of Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69)., PDB code: 4wc8 was solved by R.K.Spencer, J.S.Nowick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.59 / 1.91
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.048, 58.048, 112.954, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 21.9

Other elements in 4wc8:

The structure of Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69). also contains other interesting chemical elements:

Iodine (I) 12 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69). (pdb code 4wc8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69)., PDB code: 4wc8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 4wc8

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Chlorine binding site 1 out of 9 in the Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl101

b:62.2
occ:1.00
 H B:LYS10 3.1 48.0 1.0
HG2 B:LYS10 3.2 69.5 1.0
HB2 B:ORN9 3.3 35.2 1.0
O B:HOH202 3.3 48.7 1.0
HA B:ORN9 3.3 42.7 1.0
HB3 B:ORN9 3.7 35.2 1.0
HB2 B:GLU8 3.8 50.0 1.0
CB B:ORN9 3.8 29.3 1.0
N B:LYS10 3.9 40.0 1.0
CA B:ORN9 4.0 35.6 1.0
HE2 B:LYS10 4.1 87.6 1.0
CG B:LYS10 4.1 57.9 1.0
HG3 B:LYS10 4.4 69.5 1.0
C B:ORN9 4.5 32.4 1.0
H B:GLU8 4.6 35.3 1.0
HE3 B:LYS10 4.7 87.6 1.0
CE B:LYS10 4.7 73.0 1.0
CB B:GLU8 4.7 41.6 1.0
HB3 B:LYS10 4.9 64.2 1.0
CB B:LYS10 4.9 53.5 1.0
CD B:LYS10 4.9 67.1 1.0
CA B:LYS10 4.9 40.6 1.0

Chlorine binding site 2 out of 9 in 4wc8

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Chlorine binding site 2 out of 9 in the Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl102

b:72.8
occ:1.00
 H2 E:ORN1 3.1 36.6 1.0
H1 E:ORN1 3.1 36.6 1.0
O B:HOH206 3.2 52.1 1.0
HZ1 B:LYS16 3.3 63.7 1.0
HE2 B:LYS16 3.5 61.5 1.0
HG2 E:ORN1 3.5 41.0 1.0
N E:ORN1 3.6 30.5 1.0
HA B:LYS16 3.9 37.3 1.0
NZ B:LYS16 3.9 53.1 1.0
HZ2 B:LYS16 4.0 63.7 1.0
H3 E:ORN1 4.0 36.6 1.0
HD3 B:LYS16 4.1 59.5 1.0
CE B:LYS16 4.1 51.2 1.0
O B:VAL15 4.1 34.0 1.0
HE1 B:ORN1 4.3 37.1 1.0
HB3 E:ORN1 4.5 31.8 1.0
CG E:ORN1 4.5 34.2 1.0
CD B:LYS16 4.6 49.6 1.0
O E:HOH203 4.7 46.5 1.0
HZ3 B:LYS16 4.7 63.7 1.0
CA E:ORN1 4.8 26.3 1.0
CA B:LYS16 4.8 31.1 1.0
CB E:ORN1 4.8 26.5 1.0
HG3 E:ORN1 5.0 41.0 1.0
HE3 B:LYS16 5.0 61.5 1.0

Chlorine binding site 3 out of 9 in 4wc8

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Chlorine binding site 3 out of 9 in the Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl103

b:70.6
occ:1.00
 H3 D:ORN1 2.1 36.4 1.0
HG2 D:ORN1 2.9 31.9 1.0
N D:ORN1 3.1 30.3 1.0
OE2 B:GLU8 3.2 60.3 1.0
HA D:ORN1 3.3 31.4 1.0
H2 D:ORN1 3.4 36.4 1.0
HD2 D:ORN1 3.7 27.7 1.0
H1 D:ORN1 3.7 36.4 1.0
CA D:ORN1 3.7 26.2 1.0
CG D:ORN1 3.8 26.6 1.0
OE1 B:GLU8 3.9 65.7 1.0
CD B:GLU8 4.0 55.2 1.0
CD D:ORN1 4.1 23.1 1.0
HD3 D:ORN1 4.3 27.7 1.0
CB D:ORN1 4.3 32.4 1.0
HG3 D:ORN1 4.6 31.9 1.0
HA B:GLU8 4.7 43.1 1.0
HB2 D:ORN1 4.7 38.9 1.0

Chlorine binding site 4 out of 9 in 4wc8

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Chlorine binding site 4 out of 9 in the Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69). within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl101

b:60.4
occ:1.00
 H2 F:ORN1 2.7 36.7 1.0
HA F:ORN1 2.7 32.0 1.0
HD2 F:ORN1 3.1 44.2 1.0
O F:HOH206 3.1 54.6 1.0
HH G:TYR6 3.2 60.3 1.0
N F:ORN1 3.3 30.6 1.0
H1 F:ORN1 3.4 36.7 1.0
CA F:ORN1 3.5 26.6 1.0
HG2 F:ORN1 3.5 41.1 1.0
HE1 G:TYR6 3.5 45.9 1.0
OH G:TYR6 4.0 50.2 1.0
CD F:ORN1 4.0 36.8 1.0
O F:HOH205 4.0 48.1 1.0
CG F:ORN1 4.1 34.3 1.0
H3 F:ORN1 4.2 36.7 1.0
CE1 G:TYR6 4.3 38.2 1.0
HD3 F:ORN1 4.3 44.2 1.0
CB F:ORN1 4.4 33.9 1.0
CZ G:TYR6 4.6 41.1 1.0
C F:ORN1 4.7 27.6 1.0
O F:LYS16 4.7 27.8 1.0
H F:TYR2 4.9 29.0 1.0

Chlorine binding site 5 out of 9 in 4wc8

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Chlorine binding site 5 out of 9 in the Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69). within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl102

b:70.0
occ:1.00
 H3 G:ORN1 2.8 38.3 1.0
HA G:ORN1 3.5 32.6 1.0
H2 G:ORN1 3.6 38.3 1.0
N G:ORN1 3.6 31.9 1.0
OH H:TYR6 3.7 56.7 1.0
HE1 H:TYR6 3.8 58.9 1.0
HG2 G:ORN1 3.8 46.0 1.0
HD2 G:ORN1 3.8 47.5 1.0
CA G:ORN1 4.1 27.1 1.0
HH H:TYR6 4.2 68.1 1.0
H1 G:ORN1 4.4 38.3 1.0
CE1 H:TYR6 4.5 49.0 1.0
CZ H:TYR6 4.5 51.5 1.0
CG G:ORN1 4.6 38.3 1.0
CD G:ORN1 4.6 39.6 1.0
HD3 G:ORN1 4.8 47.5 1.0
CB G:ORN1 5.0 28.0 1.0

Chlorine binding site 6 out of 9 in 4wc8

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Chlorine binding site 6 out of 9 in the Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69). within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl102

b:71.9
occ:1.00
 H2 L:ORN1 2.5 39.4 1.0
HZ2 H:LYS16 2.7 72.8 1.0
N L:ORN1 3.4 32.9 1.0
NZ H:LYS16 3.5 60.6 1.0
H3 L:ORN1 3.5 39.4 1.0
HZ3 H:LYS16 3.6 72.8 1.0
HG2 L:ORN1 3.6 39.9 1.0
H1 L:ORN1 3.6 39.4 1.0
HE2 H:LYS16 3.8 65.2 1.0
HD3 H:LYS16 4.1 62.5 1.0
HZ1 H:LYS16 4.1 72.8 1.0
CE H:LYS16 4.1 54.4 1.0
O L:HOH105 4.3 35.1 1.0
CA L:ORN1 4.6 31.6 1.0
CG L:ORN1 4.6 33.2 1.0
CD H:LYS16 4.6 52.1 1.0
HA L:ORN1 4.7 38.0 1.0

Chlorine binding site 7 out of 9 in 4wc8

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Chlorine binding site 7 out of 9 in the Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69). within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl103

b:61.8
occ:1.00
 H3 I:ORN1 2.9 45.1 1.0
HZ3 D:LYS16 2.9 74.3 1.0
H2 I:ORN1 3.1 45.1 1.0
N I:ORN1 3.5 37.6 1.0
HD3 D:LYS16 3.5 67.9 1.0
HG3 I:ORN1 3.7 42.8 1.0
H1 I:ORN1 3.8 45.1 1.0
NZ D:LYS16 3.8 61.9 1.0
HZ2 D:LYS16 4.2 74.3 1.0
HA D:LYS16 4.3 32.3 1.0
HZ1 D:LYS16 4.3 74.3 1.0
CD D:LYS16 4.3 56.6 1.0
HE2 D:LYS16 4.4 73.5 1.0
O D:VAL15 4.4 30.3 1.0
CE D:LYS16 4.4 61.2 1.0
HD2 D:LYS16 4.7 67.9 1.0
HB3 I:ORN1 4.7 41.6 1.0
CG I:ORN1 4.7 35.6 1.0
CA I:ORN1 4.8 29.1 1.0
HE1 D:ORN1 4.8 33.6 1.0
CB I:ORN1 5.0 34.7 1.0

Chlorine binding site 8 out of 9 in 4wc8

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Chlorine binding site 8 out of 9 in the Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69). within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl104

b:73.3
occ:1.00
 H1 I:ORN9 2.3 81.5 1.0
N I:ORN9 3.2 67.9 1.0
H3 I:ORN9 3.3 81.5 1.0
H2 I:ORN9 3.4 81.5 1.0
O I:ORN9 4.3 57.0 1.0
CA I:ORN9 4.4 64.8 1.0
HA I:ORN9 4.6 77.7 1.0
C I:ORN9 4.7 57.2 1.0

Chlorine binding site 9 out of 9 in 4wc8

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Chlorine binding site 9 out of 9 in the Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Heterogeneous Dodecamer Formed From Macrocycles Containing A Sequence From Beta-2-Microglobulin(63-69). within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl102

b:39.3
occ:0.50
 HE1 L:ORN1 2.3 37.5 1.0
HZ1 K:LYS10 2.7 63.8 1.0
HZ2 K:LYS10 2.8 63.8 1.0
NZ K:LYS10 3.2 53.1 1.0
NE L:ORN1 3.3 31.3 1.0
HD2 K:LYS10 3.3 58.5 1.0
HD3 K:LYS10 3.4 58.5 1.0
HA L:LYS16 3.4 36.1 1.0
O L:VAL15 3.6 37.4 1.0
CD K:LYS10 3.7 48.8 1.0
HD3 L:ORN1 3.7 47.5 1.0
HG12 L:VAL15 3.8 42.8 1.0
HG3 L:ORN1 3.8 39.9 1.0
HZ3 K:LYS10 3.8 63.8 1.0
CD L:ORN1 4.0 39.6 1.0
CE K:LYS10 4.1 52.2 1.0
CA L:LYS16 4.2 30.1 1.0
C L:LYS16 4.3 30.8 1.0
C L:VAL15 4.3 35.6 1.0
CG L:ORN1 4.5 33.2 1.0
N L:LYS16 4.6 25.8 1.0
HE3 K:LYS10 4.6 62.6 1.0
HE2 K:LYS10 4.7 62.6 1.0
CG1 L:VAL15 4.7 35.7 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: Fri Jul 26 02:48:35 2024

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