Chlorine in PDB 6vlw: Crystal Structure of 426COD in Complex with VRC01 Fab

The structure of Crystal Structure of 426COD in Complex with VRC01 Fab, PDB code: 6vlw was solved by C.Weidle, M.Pancera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.57 / 3.42
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	137.367, 137.367, 66.188, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 26.1

The structure of Crystal Structure of 426COD in Complex with VRC01 Fab also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of 426COD in Complex with VRC01 Fab (pdb code 6vlw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of 426COD in Complex with VRC01 Fab, PDB code: 6vlw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in the Crystal Structure of 426COD in Complex with VRC01 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 426COD in Complex with VRC01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl302 b:51.7 occ:1.00 HG12 H:ILE110 3.7 83.4 1.0 HG22 H:THR87 3.7 72.3 1.0 HG23 H:THR87 4.0 72.3 1.0 HG22 H:VAL89 4.1 51.1 1.0 HB2 H:PRO108 4.2 46.1 1.0 CG2 H:THR87 4.2 60.3 1.0 HG23 H:VAL89 4.2 51.1 1.0 HG21 H:THR87 4.4 72.3 1.0 CG1 H:ILE110 4.5 69.5 1.0 HB3 H:PRO108 4.5 46.1 1.0 HG13 H:ILE110 4.5 83.4 1.0 HD11 H:ILE110 4.6 87.0 1.0 CG2 H:VAL89 4.6 42.6 1.0 HA H:ALA88 4.7 46.7 1.0 O H:ALA88 4.8 42.9 1.0 CB H:PRO108 4.8 38.4 1.0 H H:ALA88 4.9 51.0 1.0 HG21 H:VAL89 4.9 51.1 1.0 C H:ALA88 4.9 40.8 1.0 N H:ALA88 5.0 42.5 1.0 CD1 H:ILE110 5.0 72.5 1.0

Chlorine binding site 2 out of 8 in the Crystal Structure of 426COD in Complex with VRC01 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 426COD in Complex with VRC01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl303 b:38.2 occ:1.00 HG H:SER179 3.0 50.9 1.0 HG23 H:VAL169 3.2 45.5 1.0 HG1 L:THR180 3.2 47.9 1.0 H H:SER179 3.4 51.0 1.0 HB3 L:SER164 3.4 65.7 1.0 HA H:LEU178 3.5 55.5 1.0 HG L:SER164 3.6 73.6 1.0 HB2 H:SER179 3.6 48.3 1.0 HG H:SER177 3.7 51.7 1.0 HG21 H:VAL169 3.7 45.5 1.0 OG H:SER179 3.7 42.5 1.0 OG1 L:THR180 3.8 39.9 1.0 N H:SER179 3.8 42.5 1.0 HB2 L:SER164 3.8 65.7 1.0 CG2 H:VAL169 3.9 38.0 1.0 OG L:SER178 3.9 52.3 1.0 HG L:SER178 3.9 62.8 1.0 CB L:SER164 3.9 54.8 1.0 O H:SER177 4.1 47.9 1.0 O H:PRO167 4.1 54.9 1.0 CB H:SER179 4.1 40.2 1.0 OG L:SER164 4.2 61.4 1.0 CA H:LEU178 4.2 46.3 1.0 HB2 H:PHE166 4.2 77.7 1.0 HB H:VAL169 4.3 45.1 1.0 C H:LEU178 4.3 41.7 1.0 O L:SER178 4.3 37.9 1.0 C H:SER177 4.5 49.7 1.0 HA H:ALA168 4.5 59.7 1.0 N H:LEU178 4.5 56.0 1.0 OG H:SER177 4.5 43.1 1.0 H H:VAL169 4.5 54.7 1.0 HB L:THR180 4.5 50.5 1.0 CA H:SER179 4.6 43.2 1.0 HG22 H:VAL169 4.6 45.5 1.0 CB H:VAL169 4.7 37.6 1.0 HD11 H:LEU178 4.7 81.4 1.0 HB3 H:PHE166 4.8 77.7 1.0 CB L:THR180 4.8 42.0 1.0 N H:VAL169 4.9 45.6 1.0 HB3 H:SER177 4.9 58.0 1.0 CB H:PHE166 5.0 64.8 1.0

Chlorine binding site 3 out of 8 in the Crystal Structure of 426COD in Complex with VRC01 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 426COD in Complex with VRC01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl304 b:54.9 occ:1.00 H H:VAL121 2.8 55.2 1.0 HA H:SER120 3.3 55.9 1.0 N H:VAL121 3.6 46.0 1.0 HG11 H:VAL207 3.8 78.1 1.0 HB H:VAL121 4.0 61.2 1.0 O H:VAL121 4.0 46.8 1.0 CA H:SER120 4.1 46.5 1.0 HG23 H:VAL121 4.1 59.6 1.0 HB3 H:SER120 4.2 52.9 1.0 HG21 H:VAL207 4.3 87.3 1.0 OE1 L:GLU125 4.3 70.6 1.0 C H:SER120 4.4 44.4 1.0 CA H:VAL121 4.5 47.2 1.0 CB H:VAL121 4.6 51.0 1.0 CB H:SER120 4.6 44.1 1.0 CG1 H:VAL207 4.7 65.1 1.0 C H:VAL121 4.7 47.8 1.0 O H:PRO119 4.8 67.9 1.0 HG13 H:VAL207 4.9 78.1 1.0 CG2 H:VAL121 4.9 49.7 1.0 HZ2 H:LYS209 4.9 68.8 1.0 OG H:SER120 5.0 47.0 1.0

Chlorine binding site 4 out of 8 in the Crystal Structure of 426COD in Complex with VRC01 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 426COD in Complex with VRC01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl305 b:69.2 occ:1.00 HG1 L:THR166 2.8 86.1 1.0 ND1 H:HIS164 3.4 68.6 1.0 OG1 L:THR166 3.5 71.8 1.0 HE1 H:HIS164 3.6 87.9 1.0 CE1 H:HIS164 3.8 73.2 1.0 HG21 L:THR166 3.9 64.6 1.0 HA L:ASP169 3.9 99.2 1.0 HA H:HIS164 4.0 78.4 1.0 HB2 L:ASP169 4.1 99.3 1.0 O H:VAL163 4.3 75.0 1.0 CG L:ASP169 4.4 84.1 1.0 OD1 L:ASP169 4.4 84.8 1.0 CB L:ASP169 4.6 82.8 1.0 CB L:THR166 4.6 63.7 1.0 CG2 L:THR166 4.6 53.8 1.0 CG H:HIS164 4.6 68.0 1.0 CA L:ASP169 4.7 82.7 1.0 O L:GLU167 4.7 70.6 1.0 OD2 L:ASP169 4.7 85.1 1.0 HB L:THR166 4.9 76.4 1.0 CA H:HIS164 4.9 65.3 1.0 H L:GLU167 5.0 80.9 1.0 H H:THR165 5.0 79.0 1.0 HG23 L:THR166 5.0 64.6 1.0

Chlorine binding site 5 out of 8 in the Crystal Structure of 426COD in Complex with VRC01 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 426COD in Complex with VRC01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl306 b:47.9 occ:1.00 H H:ARG44 2.9 56.0 1.0 HE H:ARG44 3.1 93.8 1.0 HA H:LYS43 3.3 62.8 1.0 HH21 H:ARG44 3.7 0.0 1.0 N H:ARG44 3.7 46.7 1.0 HG2 H:ARG44 3.7 49.7 1.0 HB3 H:LYS43 3.8 72.2 1.0 HB3 H:ARG44 3.8 56.8 1.0 NE H:ARG44 3.9 78.2 1.0 O H:HOH409 4.0 24.4 1.0 CA H:LYS43 4.1 52.4 1.0 NH2 H:ARG44 4.3 94.2 1.0 CB H:LYS43 4.4 60.1 1.0 CG H:ARG44 4.4 41.4 1.0 CB H:ARG44 4.4 47.3 1.0 C H:LYS43 4.4 51.6 1.0 HG2 H:LYS43 4.5 82.8 1.0 CZ H:ARG44 4.6 83.7 1.0 CA H:ARG44 4.7 39.5 1.0 CD H:ARG44 4.8 54.8 1.0 HA L:GLN100 4.8 60.3 1.0 O H:GLY42 4.8 64.0 1.0 HE3 H:LYS43 5.0 0.5 1.0

Chlorine binding site 6 out of 8 in the Crystal Structure of 426COD in Complex with VRC01 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 426COD in Complex with VRC01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl202 b:36.1 occ:1.00 HB2 G:ASN166 2.8 78.9 1.0 CB G:ASN166 3.7 65.7 1.0 O G:PRO10 3.7 57.4 1.0 HB2 G:ARG12 3.8 95.2 1.0 HB3 G:ASN166 3.8 78.9 1.0 O7 G:NAG206 4.1 73.6 1.0 H G:ASN166 4.1 65.5 1.0 ND2 G:ASN166 4.2 77.5 1.0 HG2 G:PRO10 4.2 72.9 1.0 HG21 G:THR153 4.3 65.8 1.0 HE G:ARG12 4.3 0.8 1.0 HH21 G:ARG12 4.4 76.4 1.0 HB2 G:PRO10 4.4 82.5 1.0 CG G:ASN166 4.5 68.7 1.0 N G:ASN166 4.7 54.5 1.0 NE G:ARG12 4.7 92.3 1.0 CB G:ARG12 4.7 79.3 1.0 CA G:ASN166 4.7 60.0 1.0 HD12 G:LEU149 4.7 59.9 1.0 NH2 G:ARG12 4.7 63.7 1.0 HA G:ASN166 4.9 72.0 1.0 HG22 G:THR153 4.9 65.8 1.0 HA G:ARG12 4.9 90.5 1.0 C G:PRO10 4.9 54.2 1.0 CZ G:ARG12 5.0 84.1 1.0 H2 G:NAG206 5.0 0.3 1.0 HB3 G:ARG12 5.0 95.2 1.0

Chlorine binding site 7 out of 8 in the Crystal Structure of 426COD in Complex with VRC01 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 426COD in Complex with VRC01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl203 b:71.1 occ:1.00 O G:GLY73 3.4 78.6 1.0 HD21 G:LEU75 3.4 0.1 1.0 HD23 G:LEU75 3.6 0.1 1.0 C8 G:NAG205 3.6 0.5 1.0 O7 G:NAG205 3.9 0.2 1.0 CD2 G:LEU75 3.9 0.2 1.0 HB2 G:ASN22 3.9 0.7 1.0 C7 G:NAG205 4.0 0.1 1.0 HA G:ASN72 4.1 80.1 1.0 HD22 G:LEU75 4.2 0.1 1.0 HB3 G:ASN22 4.5 0.7 1.0 HA G:SER74 4.5 71.3 1.0 C G:GLY73 4.6 66.4 1.0 OG1 G:THR24 4.6 55.4 1.0 CB G:ASN22 4.6 90.6 1.0 HG1 G:THR24 4.7 66.5 1.0 C G:ASN72 4.8 68.0 1.0 ND2 G:ASN22 4.8 0.4 1.0 CA G:ASN72 4.9 66.7 1.0 O G:ASN72 5.0 71.0 1.0

Chlorine binding site 8 out of 8 in the Crystal Structure of 426COD in Complex with VRC01 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 426COD in Complex with VRC01 Fab within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl204 b:35.8 occ:1.00 H G:GLY147 3.3 40.6 1.0 O G:GLY147 3.6 29.8 1.0 HA2 G:GLY146 3.9 43.4 1.0 N G:GLY147 4.1 33.9 1.0 C G:GLY147 4.6 37.2 1.0 CA G:GLY146 4.7 36.2 1.0 HA3 G:GLY146 4.8 43.4 1.0 HG22 H:THR70 4.8 56.8 1.0 CA G:GLY147 4.9 35.1 1.0 C G:GLY146 4.9 40.2 1.0

Y.R.Lin, K.R.Parks, C.Weidle, A.S.Naidu, A.Khechaduri, A.O.Riker, B.Takushi, J.H.Chun, A.J.Borst, D.Veesler, A.Stuart, P.Agrawal, M.Gray, M.Pancera, P.S.Huang, L.Stamatatos. Hiv-1 VRC01 Germline-Targeting Immunogens Select Distinct Epitope-Specific B Cell Receptors. Immunity V. 53 840 2020.
ISSN: ISSN 1074-7613
PubMed: 33053332
DOI: 10.1016/J.IMMUNI.2020.09.007