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Chlorine in PDB 4rfe: Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab

Protein crystallography data

The structure of Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab, PDB code: 4rfe was solved by X.Wu, N.Gohain, W.D.Tolbert, M.Pazgier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.20 / 1.91
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.418, 79.585, 82.042, 78.79, 82.89, 65.17
R / Rfree (%) 19.2 / 24.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab (pdb code 4rfe). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab, PDB code: 4rfe:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 4rfe

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Chlorine binding site 1 out of 9 in the Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl301

b:52.7
occ:1.00
 O L:HOH535 4.6 26.8 1.0

Chlorine binding site 2 out of 9 in 4rfe

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Chlorine binding site 2 out of 9 in the Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl302

b:48.5
occ:1.00
 CB L:SER59 3.7 27.4 1.0
NE L:ARG61 3.7 17.5 1.0
NH2 L:ARG61 3.7 17.2 1.0
OG L:SER59 3.9 30.2 1.0
CZ L:ARG61 4.2 16.3 1.0
OE1 L:GLN79 4.3 23.0 1.0
O L:HOH585 4.6 36.9 1.0
CD L:ARG61 4.9 18.9 1.0
NE2 L:GLN79 4.9 16.4 1.0
CD L:GLN79 5.0 16.4 1.0

Chlorine binding site 3 out of 9 in 4rfe

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Chlorine binding site 3 out of 9 in the Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl303

b:55.0
occ:1.00
 OG1 L:THR157 3.5 29.8 1.0
N L:ASN156 3.5 26.9 1.0
CB L:THR157 3.6 26.6 1.0
O L:HOH504 3.9 33.3 1.0
N L:THR157 3.9 26.2 1.0
CA L:ASN156 4.2 27.9 1.0
C L:ASN156 4.2 27.4 1.0
CA L:THR157 4.4 26.4 1.0
CB L:ASN156 4.5 29.4 1.0
C L:VAL155 4.5 25.0 1.0
O L:HOH459 4.6 25.2 1.0
CA L:VAL155 4.6 23.8 1.0
CG2 L:THR157 4.8 28.6 1.0
CG1 L:VAL155 4.9 22.4 1.0
O L:SER154 4.9 23.2 1.0

Chlorine binding site 4 out of 9 in 4rfe

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Chlorine binding site 4 out of 9 in the Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:55.0
occ:1.00
 N B:ASN156 3.6 27.0 1.0
O B:HOH491 3.6 33.9 1.0
N B:THR157 3.9 26.2 1.0
OG1 B:THR157 3.9 29.3 1.0
CB B:THR157 4.1 26.0 1.0
CA B:ASN156 4.3 28.2 1.0
C B:ASN156 4.3 27.7 1.0
CA B:VAL155 4.5 25.2 1.0
C B:VAL155 4.5 26.2 1.0
CB B:ASN156 4.5 29.6 1.0
O B:SER154 4.6 25.8 1.0
CA B:THR157 4.7 25.9 1.0
CG1 B:VAL155 5.0 23.3 1.0

Chlorine binding site 5 out of 9 in 4rfe

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Chlorine binding site 5 out of 9 in the Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:57.2
occ:1.00
 NE2 B:GLN184 3.6 25.0 1.0
CG B:GLN184 3.8 20.9 1.0
CE1 B:HIS188 3.8 20.3 1.0
O B:HOH467 4.0 30.6 1.0
CD B:GLN184 4.2 24.6 1.0
NE2 B:HIS188 4.3 18.7 1.0
CB B:GLN184 4.5 19.5 1.0
O B:HOH491 4.9 33.9 1.0
ND1 B:HIS188 5.0 18.2 1.0

Chlorine binding site 6 out of 9 in 4rfe

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Chlorine binding site 6 out of 9 in the Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:47.0
occ:1.00
 CB B:SER59 3.7 26.6 1.0
NH2 B:ARG61 3.8 18.5 1.0
OG B:SER59 3.9 27.0 1.0
NE B:ARG61 3.9 14.1 1.0
OE1 B:GLN79 4.3 22.7 1.0
CZ B:ARG61 4.4 19.1 1.0
NE2 B:GLN79 4.5 18.9 1.0
CD B:GLN79 4.7 19.2 1.0

Chlorine binding site 7 out of 9 in 4rfe

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Chlorine binding site 7 out of 9 in the Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:51.4
occ:1.00
 N D:ASN156 3.3 30.5 1.0
N D:THR157 4.0 29.4 1.0
CA D:ASN156 4.0 31.2 1.0
OG1 D:THR157 4.1 30.3 1.0
O D:HOH446 4.1 27.1 1.0
CB D:ASN156 4.2 32.0 1.0
C D:VAL155 4.2 28.6 1.0
CA D:VAL155 4.2 27.3 1.0
C D:ASN156 4.3 31.5 1.0
O D:SER154 4.4 25.6 1.0
CB D:THR157 4.5 28.7 1.0
CG1 D:VAL155 4.6 25.2 1.0
ND2 D:ASN156 4.8 34.8 1.0
CA D:THR157 4.8 28.0 1.0
CG D:ASN156 4.9 34.0 1.0

Chlorine binding site 8 out of 9 in 4rfe

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Chlorine binding site 8 out of 9 in the Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl301

b:51.5
occ:1.00
 OG1 F:THR157 3.7 29.3 1.0
N F:ASN156 3.7 26.4 1.0
N F:THR157 3.9 26.6 1.0
CB F:THR157 4.0 26.2 1.0
O F:HOH554 4.2 36.1 1.0
C F:ASN156 4.3 28.0 1.0
CA F:ASN156 4.4 28.1 1.0
CB F:ASN156 4.5 28.9 1.0
O F:HOH542 4.6 29.3 1.0
CA F:THR157 4.6 25.2 1.0
CA F:VAL155 4.7 23.8 1.0
C F:VAL155 4.7 25.4 1.0
CG1 F:VAL155 4.9 21.8 1.0
O F:SER154 4.9 24.6 1.0
O F:ASN156 5.0 29.0 1.0

Chlorine binding site 9 out of 9 in 4rfe

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Chlorine binding site 9 out of 9 in the Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Adcc-Potent Anti-Hiv-1 Rhesus Macaque Antibody JR4 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl302

b:49.7
occ:1.00
 O L:HOH508 3.9 25.7 1.0
O F:HOH422 4.1 11.3 1.0
CB F:SER63 4.3 17.5 1.0
NH2 F:ARG54 4.4 30.3 1.0
O F:HOH579 4.7 37.6 1.0

Reference:

N.Gohain, W.D.Tolbert, P.Acharya, L.Yu, T.Liu, P.Zhao, C.Orlandi, M.L.Visciano, R.Kamin-Lewis, M.M.Sajadi, L.Martin, J.E.Robinson, P.D.Kwong, A.L.Devico, K.Ray, G.K.Lewis, M.Pazgier. Cocrystal Structures of Antibody N60-I3 and Antibody JR4 in Complex with GP120 Define More Cluster A Epitopes Involved in Effective Antibody-Dependent Effector Function Against Hiv-1. J.Virol. V. 89 8840 2015.
ISSN: ISSN 0022-538X
PubMed: 26085162
DOI: 10.1128/JVI.01232-15
Page generated: Fri Jul 26 01:13:57 2024

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