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Bromine in PDB 6mei: Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain

Protein crystallography data

The structure of Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain, PDB code: 6mei was solved by A.I.Flyak, P.J.Bjorkman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.810, 75.790, 173.999, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 27.7

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain (pdb code 6mei). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 7 binding sites of Bromine where determined in the Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain, PDB code: 6mei:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7;

Bromine binding site 1 out of 7 in 6mei

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Bromine binding site 1 out of 7 in the Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br714

b:51.1
occ:1.00
 N C:CYS620 3.4 21.9 1.0
CB C:TYR485 3.5 48.8 1.0
CB C:CYS620 3.6 35.5 1.0
CA C:TYR618 3.7 28.6 1.0
CD C:PRO619 3.7 23.7 1.0
C C:TYR618 3.8 28.3 1.0
N C:PRO619 3.8 24.9 1.0
NH1 C:ARG455 3.9 70.7 1.0
CA C:CYS620 4.0 28.3 1.0
CE C:MET456 4.0 37.1 1.0
CB C:TYR618 4.2 25.0 1.0
O C:TYR618 4.3 28.9 1.0
CG C:TYR485 4.4 48.4 1.0
C C:CYS620 4.4 30.6 1.0
CG C:PRO619 4.5 22.4 1.0
C C:PRO619 4.5 26.4 1.0
CA C:TYR485 4.6 48.4 1.0
SG C:CYS620 4.6 31.5 1.0
CA C:PRO619 4.7 21.1 1.0
CD1 C:TYR618 4.8 25.0 1.0
CG2 C:THR621 4.8 24.9 1.0
SD C:MET456 4.8 53.5 1.0
N C:THR621 4.8 29.9 1.0
O C:HIS617 4.8 23.2 1.0
CG C:TYR618 4.9 23.4 1.0
O C:CYS620 4.9 30.8 1.0
CD1 C:TYR485 4.9 52.5 1.0
N C:TYR618 5.0 22.4 1.0

Bromine binding site 2 out of 7 in 6mei

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Bromine binding site 2 out of 7 in the Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br715

b:66.7
occ:1.00
 C4 C:NAG703 3.5 40.6 1.0
O3 C:NAG703 3.9 53.2 1.0
O6 C:NAG703 3.9 44.2 1.0
O4 C:NAG703 3.9 45.9 1.0
C3 C:NAG703 4.3 41.0 1.0
C5 C:NAG703 4.5 41.4 1.0
C6 C:NAG703 4.6 41.1 1.0
C2 C:NAG703 4.8 42.1 1.0
O5 C:NAG703 4.9 38.8 1.0

Bromine binding site 3 out of 7 in 6mei

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Bromine binding site 3 out of 7 in the Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br716

b:57.9
occ:1.00
 N C:HIS445 3.7 32.3 1.0
C C:TYR443 3.7 27.9 1.0
CA C:TYR443 3.7 28.9 1.0
CB C:HIS445 3.9 30.9 1.0
N C:THR444 3.9 27.6 1.0
O C:TYR443 4.0 28.9 1.0
CA C:HIS445 4.2 28.3 1.0
CG2 H:ILE54 4.2 34.7 1.0
CB C:TYR443 4.2 27.4 1.0
N C:LYS446 4.3 36.0 1.0
CD2 C:HIS445 4.3 40.8 1.0
CG C:LYS446 4.4 29.4 1.0
C C:HIS445 4.4 27.4 1.0
CG C:HIS445 4.4 46.4 1.0
CD1 C:TYR443 4.5 24.7 1.0
C C:THR444 4.7 34.4 1.0
CG C:TYR443 4.9 21.3 1.0
N C:TYR443 4.9 27.4 1.0
O C:PHE442 4.9 23.7 1.0
CA C:THR444 4.9 29.5 1.0

Bromine binding site 4 out of 7 in 6mei

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Bromine binding site 4 out of 7 in the Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br301

b:53.6
occ:1.00
 NH2 H:ARG98 3.0 27.3 1.0
CG2 H:VAL2 3.5 25.2 1.0
N H:GLN1 3.7 38.4 1.0
NH1 H:ARG98 3.8 29.6 1.0
CZ H:ARG98 3.8 27.0 1.0
N H:VAL2 3.8 29.2 1.0
CB C:HIS434 3.8 35.6 1.0
CG1 H:VAL2 3.9 29.7 1.0
O C:HIS434 4.0 37.9 1.0
CB H:VAL2 4.1 30.3 1.0
CD2 C:HIS434 4.2 26.8 1.0
CA C:HIS434 4.3 34.8 1.0
C C:HIS434 4.3 34.1 1.0
NE H:ARG94 4.4 37.0 1.0
CG C:HIS434 4.4 35.5 1.0
CD H:PRO102 4.4 22.1 1.0
CG H:PRO102 4.5 20.4 1.0
CA H:VAL2 4.5 33.0 1.0
C H:GLN1 4.8 35.4 1.0
NH2 H:ARG94 4.8 35.2 1.0
CA H:GLN1 4.8 35.5 1.0

Bromine binding site 5 out of 7 in 6mei

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Bromine binding site 5 out of 7 in the Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br302

b:40.7
occ:1.00
 N L:PHE98 3.3 27.1 1.0
O L:HOH471 3.3 21.1 1.0
N H:TRP47 3.5 23.5 1.0
CA L:THR97 3.9 27.0 1.0
CB H:TRP47 4.0 28.1 1.0
O L:HOH453 4.1 24.9 1.0
C L:THR97 4.1 24.0 1.0
CB L:PHE98 4.1 21.6 1.0
CA H:GLU46 4.1 22.2 1.0
CA L:PHE98 4.2 25.6 1.0
O H:LEU45 4.3 28.7 1.0
C H:GLU46 4.3 24.6 1.0
CA H:TRP47 4.3 23.6 1.0
CD2 L:PHE98 4.4 22.5 1.0
CB L:THR97 4.4 27.3 1.0
O L:ARG96 4.4 29.1 1.0
O L:PHE98 4.5 28.2 1.0
O L:HOH416 4.5 24.7 1.0
O L:HOH467 4.6 34.3 1.0
CG2 L:THR97 4.7 19.9 1.0
O H:TRP47 4.7 27.7 1.0
CG H:GLU46 4.7 34.8 1.0
CG L:PHE98 4.7 23.1 1.0
C L:PHE98 4.8 25.2 1.0
N L:THR97 5.0 23.7 1.0
C H:LEU45 5.0 27.5 1.0
N H:GLU46 5.0 23.8 1.0

Bromine binding site 6 out of 7 in 6mei

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Bromine binding site 6 out of 7 in the Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br303

b:44.8
occ:1.00
 NH1 H:ARG94 2.1 27.5 1.0
N H:GLU33 3.1 28.0 1.0
CZ H:ARG94 3.3 31.9 1.0
CB H:GLU33 3.4 28.6 1.0
O H:HOH438 3.5 18.3 1.0
CA H:GLY96 3.7 23.9 1.0
CB C:ALA439 3.8 31.1 1.0
CA H:GLU33 3.8 28.8 1.0
CA H:TYR32 4.0 26.2 1.0
C H:TYR32 4.0 29.5 1.0
NH2 H:ARG94 4.1 35.2 1.0
NE H:ARG94 4.2 37.0 1.0
CB H:TYR32 4.2 21.9 1.0
CD H:ARG94 4.3 32.5 1.0
CD1 H:TYR32 4.3 24.9 1.0
N H:GLY96 4.3 21.6 1.0
CG H:PRO53 4.4 24.9 1.0
CG H:ARG94 4.5 26.5 1.0
CG H:GLU33 4.8 30.8 1.0
CG H:TYR32 4.8 22.9 1.0
C H:GLU33 4.8 27.9 1.0
O H:GLU33 4.8 28.2 1.0
C H:GLY96 5.0 24.1 1.0

Bromine binding site 7 out of 7 in 6mei

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Bromine binding site 7 out of 7 in the Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of Broadly Neutralizing Antibody HEPC3 in Complex with Hepatitis C Virus Envelope Glycoprotein E2 Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Br301

b:77.3
occ:1.00
 NE2 L:GLN27 3.1 27.2 1.0
CA L:GLY26 3.2 40.6 1.0
O L:HOH406 3.5 37.2 1.0
N L:GLN3 3.5 33.9 1.0
C L:GLY26 3.7 41.8 1.0
CA L:ILE2 3.9 26.2 1.0
O L:ASP1 4.0 34.1 1.0
N L:GLN27 4.2 41.1 1.0
CD L:GLN27 4.2 42.4 1.0
N L:GLY26 4.2 34.6 1.0
O L:GLY26 4.2 45.2 1.0
C L:ILE2 4.2 28.2 1.0
CB L:GLN3 4.3 27.9 1.0
CG L:GLN27 4.4 43.2 1.0
CA L:GLN3 4.5 30.6 1.0
CG2 L:ILE2 4.6 37.1 1.0
CB L:ILE2 4.7 26.5 1.0
O L:GLN3 4.7 41.3 1.0
C L:ASP1 4.8 30.9 1.0
N L:ILE2 4.8 31.7 1.0
CB L:GLN27 4.9 47.2 1.0

Reference:

A.I.Flyak, S.Ruiz, M.D.Colbert, T.Luong, J.E.Crowe Jr., J.R.Bailey, P.J.Bjorkman. Hcv Broadly Neutralizing Antibodies Use A CDRH3 Disulfide Motif to Recognize An E2 Glycoprotein Site That Can Be Targeted For Vaccine Design. Cell Host Microbe V. 24 703 2018.
ISSN: ESSN 1934-6069
PubMed: 30439340
DOI: 10.1016/J.CHOM.2018.10.009
Page generated: Thu Jul 11 02:17:49 2024

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