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Chlorine in PDB 3oaz: A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity

Protein crystallography data

The structure of A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity, PDB code: 3oaz was solved by K.J.Doores, Z.Fulton, V.Hong, M.K.Patel, C.N.Scanlan, M.R.Wormald, M.G.Finn, D.R.Burton, I.A.Wilson, B.G.Davis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.65 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.623, 72.092, 84.074, 90.00, 95.78, 90.00
R / Rfree (%) 17.6 / 21.8

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Chlorine atom in the A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity (pdb code 3oaz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 28 binding sites of Chlorine where determined in the A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity, PDB code: 3oaz:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 28 in 3oaz

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Chlorine binding site 1 out of 28 in the A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl232

b:15.1
occ:1.00
 O H:HOH555 3.4 16.1 1.0
O H:HOH296 3.5 17.8 1.0
OD1 H:ASP98 3.8 34.8 0.5
CE1 L:TYR49 3.9 17.7 1.0
CG L:LYS55 3.9 22.8 1.0
CA H:SER97 3.9 27.3 0.3
CA H:SER97 3.9 27.7 0.7
OG H:SER97 3.9 31.2 0.7
N H:ASP98 4.0 31.0 1.0
CE L:LYS55 4.2 31.0 1.0
CZ L:TYR49 4.3 21.9 1.0
CD2 L:LEU46 4.3 15.5 1.0
CB H:SER97 4.3 27.6 0.3
CG H:ASP98 4.3 33.3 0.5
CB H:SER97 4.3 28.0 0.7
CB H:ASP101 4.4 20.4 1.0
CD L:LYS55 4.4 25.0 1.0
OH L:TYR49 4.4 24.9 1.0
C H:SER97 4.4 29.2 1.0
CD1 L:TYR49 4.5 19.6 1.0
OD2 H:ASP98 4.6 34.5 0.5
CB L:LYS55 4.8 19.3 1.0
O H:GLY96 4.8 22.5 1.0
OD2 H:ASP101 4.9 22.7 1.0
O L:HOH561 5.0 25.7 1.0

Chlorine binding site 2 out of 28 in 3oaz

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Chlorine binding site 2 out of 28 in the A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl233

b:18.5
occ:1.00
 O H:ASP101 2.8 22.6 1.0
O L:HOH283 2.9 26.9 1.0
O L:HOH645 3.0 30.1 1.0
N L:LEU46 3.4 14.6 1.0
C H:ASP101 3.6 20.2 1.0
O H:HOH292 3.9 16.7 1.0
CA L:LYS45 4.0 17.1 1.0
CB L:LEU46 4.1 14.5 1.0
CD1 H:TRP103 4.2 14.9 1.0
CE L:LYS55 4.2 31.0 1.0
C L:LYS45 4.2 15.1 1.0
N H:ALA102 4.3 18.7 1.0
CA L:LEU46 4.4 14.4 1.0
CA H:ALA102 4.4 18.6 1.0
O L:PRO44 4.4 17.1 1.0
CA H:ASP101 4.4 19.4 1.0
NZ L:LYS55 4.6 31.5 1.0
CB L:LYS45 4.7 18.5 1.0
O H:PHE100F 4.7 16.5 1.0
CD L:LYS55 4.7 25.0 1.0
NE1 H:TRP103 4.8 16.2 1.0
O L:LEU46 4.9 14.5 1.0
CG L:LYS45 4.9 25.0 1.0

Chlorine binding site 3 out of 28 in 3oaz

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Chlorine binding site 3 out of 28 in the A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl234

b:31.0
occ:1.00
 O H:HOH1101 2.7 19.5 1.0
O H:HOH1091 2.9 25.5 1.0
O H:HOH1028 3.4 28.4 1.0
C H:ALA88 3.9 15.5 1.0
CA H:ALA88 3.9 15.8 1.0
N H:ILE89 4.2 14.8 1.0
N H:ALA88 4.2 15.9 1.0
O H:HOH580 4.2 35.6 1.0
CG H:PRO41 4.2 21.7 1.0
CG1 H:VAL108 4.2 20.9 1.0
CG2 H:THR87 4.3 20.0 1.0
CG1 H:ILE89 4.3 19.5 1.0
O H:ALA88 4.4 15.9 1.0
C H:THR87 4.7 17.0 1.0
O H:ARG39 4.7 18.0 1.0
CD H:PRO41 4.8 19.6 1.0
O H:VAL109 4.9 18.3 1.0
N H:PRO41 4.9 20.6 1.0
O H:THR87 4.9 17.0 1.0
CB H:PRO41 5.0 22.7 1.0
CA H:PRO41 5.0 22.1 1.0

Chlorine binding site 4 out of 28 in 3oaz

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Chlorine binding site 4 out of 28 in the A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl235

b:30.9
occ:1.00
 OD1 H:ASN211 2.1 34.7 1.0
CG H:ASN211 3.0 29.1 1.0
ND2 H:ASN211 3.2 33.6 1.0
O H:HOH1025 3.7 25.4 1.0
CG H:LYS218 3.8 29.7 1.0
CA H:LYS213 3.8 23.1 1.0
CE H:LYS218 3.9 36.2 1.0
N H:LYS213 3.9 22.1 1.0
O H:THR217 4.0 25.7 1.0
O H:HIS212 4.0 21.9 1.0
C H:HIS212 4.0 21.6 1.0
CA H:ASN216 4.1 26.5 0.5
CA H:ASN216 4.1 27.0 0.5
N H:THR217 4.1 25.7 1.0
C H:ASN216 4.2 26.9 1.0
CD H:LYS213 4.2 34.3 1.0
N H:HIS212 4.3 21.8 1.0
CB H:ASN211 4.4 24.7 1.0
C H:THR217 4.4 25.6 1.0
CD H:LYS218 4.4 34.3 1.0
ND2 H:ASN216 4.6 33.3 0.5
CB H:LYS213 4.7 23.8 1.0
CA H:ASN211 4.7 23.0 1.0
NZ H:LYS213 4.8 37.8 1.0
C H:ASN211 4.8 22.3 1.0
CG H:ASN216 4.8 31.4 0.5
C H:LYS213 4.8 22.8 1.0
N H:ASN216 4.8 25.6 1.0
O H:LYS213 4.9 23.1 1.0
CA H:HIS212 4.9 21.0 1.0
CA H:THR217 4.9 26.6 1.0
CG H:LYS213 4.9 28.9 1.0
N H:LYS218 4.9 26.3 1.0
O H:ASN216 4.9 28.6 1.0
ND2 H:ASN216 4.9 25.3 0.5

Chlorine binding site 5 out of 28 in 3oaz

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Chlorine binding site 5 out of 28 in the A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl236

b:34.4
occ:1.00
 CB H:SER112 3.7 30.6 0.5
O H:HOH267 3.8 22.8 1.0
CA H:SER112 3.8 29.7 0.5
CA H:SER112 3.8 30.0 0.5
CB H:SER112 3.9 30.9 0.5
CD H:PRO113 4.0 23.6 1.0
O M:LEU178 4.1 36.1 1.0
CA M:SER180 4.1 44.5 1.0
OG H:SER112 4.1 32.4 0.5
N M:SER180 4.2 41.4 1.0
CG2 H:THR110 4.3 26.4 1.0
C M:GLN179 4.5 39.4 1.0
CB M:SER180 4.5 46.1 1.0
N H:SER112 4.5 27.2 1.0
O H:VAL111 4.7 24.4 1.0
CD1 H:LEU11 4.7 26.7 0.7
O M:GLN179 4.8 39.9 1.0
O M:HOH889 4.8 26.3 1.0
N H:PRO113 4.9 21.8 1.0
C H:SER112 4.9 31.6 1.0
C H:VAL111 4.9 25.1 1.0
NE2 L:GLN160 5.0 45.8 1.0

Chlorine binding site 6 out of 28 in 3oaz

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Chlorine binding site 6 out of 28 in the A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl217

b:2.5
occ:1.00
 OD1 K:ASN137 3.6 20.0 1.0
OG K:SER114 3.6 20.8 1.0
CB K:SER114 3.8 16.4 1.0
O K:HOH602 4.1 38.8 1.0
O K:HOH705 4.1 35.0 1.0
CB K:ASN137 4.1 14.3 1.0
ND2 K:ASN138 4.2 20.6 1.0
CZ K:PHE116 4.3 19.1 1.0
CG K:ASN137 4.3 17.1 1.0
O K:HOH454 4.3 14.6 1.0
CG2 H:THR137 4.4 20.1 1.0
CE2 K:PHE116 4.5 17.8 1.0
CG2 H:THR192 4.5 17.1 1.0
CG K:ASN138 4.7 14.9 1.0
O K:ASN137 4.7 16.5 1.0
CB K:ASN138 4.8 16.0 1.0
OG1 H:THR192 4.9 18.0 1.0
CB H:THR137 4.9 19.1 1.0
CB H:THR192 4.9 14.8 1.0
C K:ASN137 5.0 14.4 1.0

Chlorine binding site 7 out of 28 in 3oaz

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Chlorine binding site 7 out of 28 in the A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl218

b:17.5
occ:1.00
 OG H:SER134 3.1 32.0 1.0
CE K:LYS207 3.4 33.5 1.0
NZ K:LYS207 3.5 38.7 1.0
N K:VAL115 3.6 16.6 1.0
O K:HOH722 3.8 24.8 1.0
CB H:SER134 4.1 28.4 1.0
O K:VAL115 4.1 15.7 1.0
CA K:SER114 4.2 17.0 1.0
O K:HOH436 4.2 29.9 1.0
CG1 K:VAL205 4.4 24.5 1.0
CB K:VAL115 4.4 16.4 1.0
C K:SER114 4.4 16.1 1.0
CA K:VAL115 4.4 15.4 1.0
O H:HOH727 4.5 44.1 1.0
CG2 K:VAL115 4.6 15.3 1.0
O K:PRO113 4.7 17.4 1.0
C K:VAL115 4.8 15.7 1.0
CB K:SER114 4.8 16.4 1.0
CD K:LYS207 4.9 31.6 1.0
CA H:SER134 4.9 28.6 1.0

Chlorine binding site 8 out of 28 in 3oaz

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Chlorine binding site 8 out of 28 in the A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl219

b:17.1
occ:1.00
 NZ K:LYS169 3.3 35.4 1.0
O H:HOH844 3.3 26.7 1.0
CB H:SER168 3.9 23.7 1.0
CA H:SER168 4.0 22.4 1.0
CD K:LYS169 4.1 29.2 1.0
OG H:SER168 4.2 28.0 1.0
CE K:LYS169 4.2 31.2 1.0
N H:SER168 4.7 21.4 1.0

Chlorine binding site 9 out of 28 in 3oaz

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Chlorine binding site 9 out of 28 in the A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl220

b:24.7
occ:1.00
 O K:HOH622 3.3 26.7 1.0
O K:HOH232 3.4 15.3 1.0
OG1 K:THR85 3.6 16.0 1.0
O K:HOH263 3.8 15.2 1.0
CG K:ARG103 3.9 17.6 1.0
CG K:PRO40 3.9 20.5 1.0
N K:THR85 3.9 14.0 1.0
C K:ALA84 3.9 14.5 1.0
O K:HOH373 4.0 23.9 1.0
CA K:ALA84 4.0 15.4 1.0
CD K:PRO40 4.2 20.2 1.0
CD K:ARG103 4.3 23.3 1.0
O K:ALA84 4.5 13.7 1.0
O K:HOH299 4.5 20.9 1.0
CB K:THR85 4.5 15.5 1.0
N K:ALA84 4.6 15.9 1.0
O K:GLN38 4.7 15.7 1.0
CA K:THR85 4.7 13.8 1.0
OE1 K:GLU165 4.8 25.8 0.5
O K:HOH268 4.9 16.7 1.0
N K:PRO40 4.9 20.0 1.0

Chlorine binding site 10 out of 28 in 3oaz

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Chlorine binding site 10 out of 28 in the A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of A Non-Self Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl222

b:23.6
occ:1.00
 O H:HOH868 2.4 26.1 1.0
OE1 K:GLN160 3.1 28.7 1.0
O K:HOH635 3.1 28.0 1.0
O K:HOH251 3.4 14.3 1.0
CG2 H:VAL177 3.6 19.2 0.3
CB K:GLN160 3.8 20.4 1.0
CD K:GLN160 3.9 28.7 1.0
CG K:GLN160 4.2 25.2 1.0
CB K:THR178 4.2 18.3 1.0
CG2 K:THR178 4.3 20.0 1.0
CG H:GLN179 4.3 22.5 1.0
O K:HOH253 4.4 20.5 1.0
OE1 H:GLN179 4.4 26.3 1.0
O H:HOH545 4.4 27.8 1.0
OG1 K:THR180 4.6 27.1 1.0
CB H:SER186 4.7 17.0 1.0
CB H:VAL177 4.7 22.2 0.7
CD H:GLN179 4.7 23.9 1.0
OG1 K:THR178 4.8 19.0 1.0
O K:THR178 4.8 16.7 1.0
CG1 H:VAL177 4.8 22.8 0.7
CB H:VAL177 4.8 21.2 0.3
OG H:SER186 4.9 21.0 1.0
CA K:GLN160 4.9 20.1 1.0
O K:HOH539 4.9 28.9 1.0
N K:GLN160 5.0 19.0 1.0

Reference:

K.J.Doores, Z.Fulton, V.Hong, M.K.Patel, C.N.Scanlan, M.R.Wormald, M.G.Finn, D.R.Burton, I.A.Wilson, B.G.Davis. A Nonself Sugar Mimic of the Hiv Glycan Shield Shows Enhanced Antigenicity. Proc.Natl.Acad.Sci.Usa V. 107 17107 2010.
ISSN: ISSN 0027-8424
PubMed: 20852065
DOI: 10.1073/PNAS.1002717107
Page generated: Sun Jul 21 01:31:31 2024

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