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Chlorine in PDB 6vmz: Crystal Structure of A H5N1 Influenza Virus Hemagglutinin with CBS1117

Protein crystallography data

The structure of Crystal Structure of A H5N1 Influenza Virus Hemagglutinin with CBS1117, PDB code: 6vmz was solved by A.Antanasijevic, M.A.Durst, A.Lavie, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.47 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.710, 126.083, 249.639, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of A H5N1 Influenza Virus Hemagglutinin with CBS1117 (pdb code 6vmz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of A H5N1 Influenza Virus Hemagglutinin with CBS1117, PDB code: 6vmz:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6vmz

Go back to Chlorine Binding Sites List in 6vmz
Chlorine binding site 1 out of 6 in the Crystal Structure of A H5N1 Influenza Virus Hemagglutinin with CBS1117


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 A H5N1 Influenza Virus Hemagglutinin with CBS1117 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:0.5
occ:1.00
 CL1 A:R3P404 0.0 0.5 1.0
C14 A:R3P404 1.8 91.0 1.0
C13 A:R3P404 2.7 82.1 1.0
C9 A:R3P404 2.8 87.1 1.0
C8 A:R3P404 3.1 82.2 1.0
OG1 B:THR49 3.3 56.3 1.0
N1 A:R3P404 3.4 85.7 1.0
O A:R3P404 3.8 67.8 1.0
CG2 B:ILE45 3.8 63.0 1.0
O B:ILE45 3.9 57.2 1.0
C4 A:R3P404 3.9 87.4 1.0
C12 A:R3P404 4.0 83.6 1.0
C10 A:R3P404 4.1 86.0 1.0
CA B:ILE45 4.1 62.3 1.0
CH2 B:TRP21 4.2 60.6 1.0
CB B:ILE45 4.3 65.3 1.0
CG1 B:VAL48 4.3 54.6 1.0
CG1 B:ILE45 4.3 63.2 1.0
C5 A:R3P404 4.3 88.5 1.0
CB B:VAL48 4.4 53.5 1.0
N B:THR49 4.4 52.5 1.0
C B:ILE45 4.5 54.9 1.0
C11 A:R3P404 4.6 83.5 1.0
CB B:THR49 4.6 57.6 1.0
CA B:THR49 4.8 57.3 1.0
CZ3 B:TRP21 4.9 60.8 1.0
CZ2 B:TRP21 4.9 59.0 1.0

Chlorine binding site 2 out of 6 in 6vmz

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Chlorine binding site 2 out of 6 in the Crystal Structure of A H5N1 Influenza Virus Hemagglutinin with CBS1117


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 A H5N1 Influenza Virus Hemagglutinin with CBS1117 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:94.3
occ:1.00
 CL A:R3P404 0.0 94.3 1.0
C10 A:R3P404 1.8 86.0 1.0
C9 A:R3P404 2.8 87.1 1.0
C11 A:R3P404 2.8 83.5 1.0
C8 A:R3P404 3.0 82.2 1.0
O A:R3P404 3.3 67.8 1.0
N1 A:R3P404 3.7 85.7 1.0
OG1 A:THR325 3.7 51.5 1.0
O A:ALA39 4.0 56.7 1.0
C14 A:R3P404 4.1 91.0 1.0
C12 A:R3P404 4.1 83.6 1.0
CG2 A:THR325 4.3 52.2 1.0
CB A:THR325 4.3 47.9 1.0
CB A:HIS38 4.6 68.4 1.0
C13 A:R3P404 4.6 82.1 1.0
C A:ALA39 4.6 56.2 1.0
OE1 A:GLN40 4.8 83.7 1.0
N A:ALA39 4.8 58.5 1.0
C5 A:R3P404 4.9 88.5 1.0
C6 A:R3P404 4.9 89.9 1.0

Chlorine binding site 3 out of 6 in 6vmz

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Chlorine binding site 3 out of 6 in the Crystal Structure of A H5N1 Influenza Virus Hemagglutinin with CBS1117


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 A H5N1 Influenza Virus Hemagglutinin with CBS1117 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:97.7
occ:1.00
 CL1 C:R3P404 0.0 97.7 1.0
C14 C:R3P404 1.8 87.3 1.0
C13 C:R3P404 2.8 91.0 1.0
C9 C:R3P404 2.8 91.2 1.0
O C:R3P404 2.9 81.0 1.0
C8 C:R3P404 3.1 88.2 1.0
O C:ALA39 3.7 54.3 1.0
OG1 C:THR325 3.8 49.3 1.0
O C:HOH592 3.9 44.3 1.0
C10 C:R3P404 4.0 86.5 1.0
C12 C:R3P404 4.1 82.8 1.0
N1 C:R3P404 4.1 93.8 1.0
CG2 C:THR325 4.4 54.2 1.0
CB C:THR325 4.4 48.3 1.0
C C:ALA39 4.4 60.0 1.0
CB C:HIS38 4.4 58.4 1.0
OE1 C:GLN40 4.6 81.5 1.0
C11 C:R3P404 4.6 82.1 1.0
N C:ALA39 4.6 61.7 1.0
C6 C:R3P404 4.7 91.8 1.0
C5 C:R3P404 4.7 93.3 1.0

Chlorine binding site 4 out of 6 in 6vmz

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Chlorine binding site 4 out of 6 in the Crystal Structure of A H5N1 Influenza Virus Hemagglutinin with CBS1117


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 A H5N1 Influenza Virus Hemagglutinin with CBS1117 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:0.4
occ:1.00
 CL C:R3P404 0.0 0.4 1.0
C10 C:R3P404 1.8 86.5 1.0
C11 C:R3P404 2.7 82.1 1.0
C9 C:R3P404 2.7 91.2 1.0
N1 C:R3P404 3.0 93.8 1.0
C8 C:R3P404 3.1 88.2 1.0
OG1 D:THR49 3.3 61.2 1.0
CG1 D:VAL48 3.8 60.7 1.0
O D:ILE45 3.9 64.3 1.0
C12 C:R3P404 4.0 82.8 1.0
C14 C:R3P404 4.0 87.3 1.0
CB D:VAL48 4.1 60.8 1.0
CH2 D:TRP21 4.1 46.9 1.0
O C:R3P404 4.1 81.0 1.0
N D:THR49 4.2 54.2 1.0
CG2 D:ILE45 4.3 65.7 1.0
C5 C:R3P404 4.3 93.3 1.0
CA D:ILE45 4.3 63.9 1.0
C13 C:R3P404 4.5 91.0 1.0
CB D:THR49 4.6 58.1 1.0
C4 C:R3P404 4.6 93.1 1.0
C D:ILE45 4.6 61.4 1.0
CA D:THR49 4.6 57.2 1.0
CB D:ILE45 4.7 64.7 1.0
CB C:THR325 4.7 48.3 1.0
C D:VAL48 4.7 56.4 1.0
CG1 D:ILE45 4.7 69.0 1.0
CZ2 D:TRP21 4.8 51.9 1.0
CG2 C:THR325 4.9 54.2 1.0
CZ3 D:TRP21 4.9 49.4 1.0
CA D:VAL48 4.9 60.7 1.0

Chlorine binding site 5 out of 6 in 6vmz

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Chlorine binding site 5 out of 6 in the Crystal Structure of A H5N1 Influenza Virus Hemagglutinin with CBS1117


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 A H5N1 Influenza Virus Hemagglutinin with CBS1117 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl403

b:0.4
occ:1.00
 CL1 E:R3P403 0.0 0.4 1.0
C14 E:R3P403 1.8 0.1 1.0
C9 E:R3P403 2.8 0.0 1.0
C13 E:R3P403 2.8 99.8 1.0
OG1 F:THR49 2.9 72.0 1.0
C8 E:R3P403 3.1 99.2 1.0
N1 E:R3P403 3.2 0.5 1.0
O F:ILE45 3.6 75.7 1.0
CG1 F:VAL48 3.9 61.7 1.0
N F:THR49 3.9 65.8 1.0
CG2 F:ILE45 3.9 81.3 1.0
O E:R3P403 4.0 86.7 1.0
CB F:VAL48 4.0 61.0 1.0
C10 E:R3P403 4.0 97.6 1.0
C12 E:R3P403 4.1 0.9 1.0
CA F:ILE45 4.1 77.3 1.0
CB F:THR49 4.2 71.2 1.0
C F:ILE45 4.3 77.3 1.0
CA F:THR49 4.3 66.6 1.0
CB F:ILE45 4.4 79.6 1.0
C5 E:R3P403 4.4 0.1 1.0
C F:VAL48 4.5 63.1 1.0
CH2 F:TRP21 4.5 66.1 1.0
C11 E:R3P403 4.5 0.9 1.0
C4 E:R3P403 4.6 0.2 1.0
CG1 F:ILE45 4.6 81.5 1.0
CA F:VAL48 4.8 63.0 1.0

Chlorine binding site 6 out of 6 in 6vmz

Go back to Chlorine Binding Sites List in 6vmz
Chlorine binding site 6 out of 6 in the Crystal Structure of A H5N1 Influenza Virus Hemagglutinin with CBS1117


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 A H5N1 Influenza Virus Hemagglutinin with CBS1117 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl403

b:0.5
occ:1.00
 CL E:R3P403 0.0 0.5 1.0
C10 E:R3P403 1.8 97.6 1.0
C9 E:R3P403 2.7 0.0 1.0
C11 E:R3P403 2.8 0.9 1.0
O E:R3P403 2.9 86.7 1.0
C8 E:R3P403 3.0 99.2 1.0
O E:HOH526 3.8 55.9 1.0
N1 E:R3P403 3.8 0.5 1.0
OG1 E:THR325 3.9 57.2 1.0
C14 E:R3P403 4.0 0.1 1.0
C12 E:R3P403 4.1 0.9 1.0
CG2 E:THR325 4.4 59.9 1.0
CB E:THR325 4.4 55.8 1.0
C6 E:R3P403 4.4 0.9 1.0
O E:ALA39 4.4 53.2 1.0
C13 E:R3P403 4.6 99.8 1.0
OE1 E:GLN40 4.6 90.9 1.0
CB E:HIS38 4.6 73.2 1.0
C5 E:R3P403 4.7 0.1 1.0
C E:ALA39 4.9 56.5 1.0

Reference:

A.Antanasijevic, M.A.Durst, H.Cheng, I.N.Gaisina, J.T.Perez, B.Manicassamy, L.Rong, A.Lavie, M.Caffrey. Structure of Avian Influenza Hemagglutinin in Complex with A Small Molecule Entry Inhibitor. Life Sci Alliance V. 3 2020.
ISSN: ESSN 2575-1077
PubMed: 32611549
DOI: 10.26508/LSA.202000724
Page generated: Mon Jul 29 16:24:22 2024

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