Calcium in PDB 5kzp: Structure of the HCV1-C1 Antibody-Antigen Complex

Protein crystallography data

The structure of Structure of the HCV1-C1 Antibody-Antigen Complex, PDB code: 5kzp was solved by K.H.Piepenbrink, E.J.Sundberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.49 / 2.26
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 47.070, 94.538, 126.758, 91.84, 94.95, 97.91
R / Rfree (%) 21.8 / 26.1

Calcium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Structure of the HCV1-C1 Antibody-Antigen Complex (pdb code 5kzp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 21 binding sites of Calcium where determined in the Structure of the HCV1-C1 Antibody-Antigen Complex, PDB code: 5kzp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 21 in 5kzp

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Calcium binding site 1 out of 21 in the Structure of the HCV1-C1 Antibody-Antigen Complex


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A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the HCV1-C1 Antibody-Antigen Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca302

b:76.0
occ:1.00
 OD2 L:ASP50 2.6 38.5 1.0
O H:HOH440 2.7 63.2 1.0
O H:ASP105 2.8 49.1 1.0
O L:HOH455 3.5 44.9 1.0
CG L:ASP50 3.5 34.2 1.0
O H:HOH467 3.7 61.4 1.0
C H:ASP105 3.9 40.5 1.0
OD1 L:ASP50 4.1 31.5 1.0
O L:HOH423 4.3 45.1 1.0
CB L:ASP50 4.4 29.4 1.0
CA H:ASP105 4.5 43.0 1.0

Calcium binding site 2 out of 21 in 5kzp

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Calcium binding site 2 out of 21 in the Structure of the HCV1-C1 Antibody-Antigen Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the HCV1-C1 Antibody-Antigen Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca303

b:65.1
occ:1.00
 O H:HOH462 2.3 56.4 1.0
O L:HOH474 2.4 72.7 1.0
N H:ASP62 3.1 28.1 1.0
O L:HOH460 3.5 34.7 1.0
CG H:ASP62 3.7 37.0 1.0
CA H:ALA61 3.7 21.8 1.0
O H:HOH447 3.8 45.6 1.0
O L:HOH430 3.8 52.5 1.0
OD1 H:ASP62 3.9 39.2 1.0
C H:ALA61 3.9 27.0 1.0
CB H:ASP62 3.9 34.7 1.0
OD2 H:ASP62 4.0 42.1 1.0
CB H:ALA61 4.0 21.6 1.0
O L:HOH481 4.1 32.3 1.0
CA H:ASP62 4.1 36.2 1.0
NH2 H:ARG65 4.7 31.1 1.0
O H:HOH418 4.8 29.7 1.0
CD2 L:TRP94 4.8 31.1 1.0
O H:HOH414 4.8 32.1 1.0
O H:TYR60 4.8 31.8 1.0
CE3 L:TRP94 4.9 30.2 1.0
CG L:TRP94 5.0 33.2 1.0
N H:ALA61 5.0 24.8 1.0

Calcium binding site 3 out of 21 in 5kzp

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Calcium binding site 3 out of 21 in the Structure of the HCV1-C1 Antibody-Antigen Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the HCV1-C1 Antibody-Antigen Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca301

b:89.9
occ:1.00
 O L:HOH416 2.5 56.9 1.0
O H:HOH448 2.7 53.3 1.0
O L:GLU165 3.4 35.2 1.0
C L:GLU165 4.4 35.5 1.0
CA L:ASP167 4.4 48.5 1.0
CB L:THR164 4.4 39.0 1.0
OD1 L:ASP167 4.4 54.2 1.0
ND1 H:HIS174 4.7 47.0 1.0
N L:GLU165 4.7 40.1 1.0
N L:ASP167 4.7 46.6 1.0
O L:GLN166 4.7 43.7 1.0
CB L:GLU165 4.8 42.2 1.0
C L:GLN166 4.8 44.0 1.0
CA L:GLU165 4.9 37.6 1.0
CB L:ASP167 4.9 47.5 1.0
OG1 L:THR164 4.9 46.0 1.0

Calcium binding site 4 out of 21 in 5kzp

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Calcium binding site 4 out of 21 in the Structure of the HCV1-C1 Antibody-Antigen Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the HCV1-C1 Antibody-Antigen Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca302

b:60.0
occ:1.00
 O L:HOH469 2.3 54.3 1.0
O L:ARG54 2.4 31.1 1.0
O L:HOH447 2.5 47.3 1.0
O L:HOH471 2.6 57.2 1.0
OD1 L:ASN53 2.6 56.3 1.0
C L:ARG54 3.5 37.5 1.0
N L:ARG54 3.7 29.5 1.0
CG L:ASN53 3.8 50.2 1.0
O L:HOH448 4.0 60.2 1.0
CA L:ARG54 4.0 41.2 1.0
CB L:ARG54 4.3 40.3 1.0
C L:ASN53 4.4 31.3 1.0
ND2 L:ASN53 4.5 51.7 1.0
N L:ALA55 4.7 31.8 1.0
CA L:ASN53 4.8 35.1 1.0
OH L:TYR49 4.9 34.5 1.0
CB L:ASN53 4.9 39.0 1.0
CA L:ALA55 5.0 36.6 1.0

Calcium binding site 5 out of 21 in 5kzp

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Calcium binding site 5 out of 21 in the Structure of the HCV1-C1 Antibody-Antigen Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the HCV1-C1 Antibody-Antigen Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:0.4
occ:1.00
 O A:HOH604 2.6 33.2 1.0
O L:HOH404 3.6 46.9 1.0
O A:TRP420 3.7 40.3 1.0
CE2 L:TYR32 3.8 27.9 1.0
OH L:TYR32 3.9 39.5 1.0
NH1 L:ARG91 4.0 44.4 1.0
CZ L:TYR32 4.1 34.2 1.0
N A:TRP420 4.1 31.1 1.0
OG A:SER419 4.1 52.4 1.0
CB A:SER419 4.3 45.1 1.0
O L:SER92 4.5 27.1 1.0
CB B:LYS425 4.5 50.6 1.0
CA A:SER419 4.6 38.9 1.0
C A:TRP420 4.6 35.3 1.0
CD2 L:TYR32 4.7 29.4 1.0
C A:SER419 4.7 32.1 1.0
CD B:LYS425 4.8 46.8 1.0
O A:HOH605 4.8 62.8 1.0
CA A:TRP420 4.9 36.0 1.0

Calcium binding site 6 out of 21 in 5kzp

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Calcium binding site 6 out of 21 in the Structure of the HCV1-C1 Antibody-Antigen Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the HCV1-C1 Antibody-Antigen Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:75.5
occ:1.00
 O E:HOH437 2.3 71.2 1.0
O E:HOH408 2.5 46.1 1.0
O E:ASP105 2.6 38.4 1.0
OD2 I:ASP50 2.6 33.6 1.0
O I:HOH449 2.9 69.3 1.0
OD1 E:ASP105 3.3 55.1 1.0
CG I:ASP50 3.5 33.7 1.0
C E:ASP105 3.7 33.9 1.0
OD1 I:ASP50 4.1 34.2 1.0
O A:HOH607 4.2 79.2 1.0
CA E:ASP105 4.3 38.1 1.0
CB I:ASP50 4.4 30.3 1.0
CG E:ASP105 4.4 56.7 1.0
N E:ALA106 4.8 34.1 1.0
O A:HOH603 4.9 81.5 1.0
CB E:ALA106 4.9 27.3 1.0
CA E:ALA106 4.9 33.1 1.0

Calcium binding site 7 out of 21 in 5kzp

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Calcium binding site 7 out of 21 in the Structure of the HCV1-C1 Antibody-Antigen Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the HCV1-C1 Antibody-Antigen Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca301

b:64.7
occ:1.00
 O I:ARG54 2.3 33.8 1.0
OD1 I:ASN53 2.4 48.8 1.0
O I:HOH435 2.9 51.6 1.0
O I:HOH447 2.9 55.8 1.0
O I:HOH448 3.0 55.1 1.0
O I:HOH443 3.3 43.5 1.0
C I:ARG54 3.4 28.1 1.0
N I:ARG54 3.5 29.4 1.0
CG I:ASN53 3.6 42.0 1.0
CA I:ARG54 3.9 26.9 1.0
O I:HOH446 4.0 56.8 1.0
CB I:ARG54 4.2 28.5 1.0
C I:ASN53 4.2 32.8 1.0
ND2 I:ASN53 4.4 44.9 1.0
N I:ALA55 4.6 27.7 1.0
CA I:ASN53 4.6 32.7 1.0
CB I:ASN53 4.7 34.6 1.0
OH I:TYR49 4.7 35.2 1.0
CA I:ALA55 4.9 26.9 1.0
C I:ALA55 4.9 33.4 1.0
O I:ASN53 5.0 32.7 1.0

Calcium binding site 8 out of 21 in 5kzp

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Calcium binding site 8 out of 21 in the Structure of the HCV1-C1 Antibody-Antigen Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the HCV1-C1 Antibody-Antigen Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca302

b:81.9
occ:1.00
 OD2 J:ASP50 2.3 33.9 1.0
O F:ASP105 2.5 40.1 1.0
O F:HOH418 2.7 68.0 1.0
OD1 F:ASP105 2.8 74.4 1.0
O F:HOH427 3.1 39.2 1.0
CG J:ASP50 3.3 34.4 1.0
C F:ASP105 3.6 41.4 1.0
OD1 J:ASP50 4.0 35.8 1.0
CG F:ASP105 4.0 70.5 1.0
CA F:ASP105 4.2 43.9 1.0
CB J:ASP50 4.3 32.1 1.0
N F:ALA106 4.7 40.8 1.0
O J:HOH463 4.7 46.9 1.0
CB F:ASP105 4.7 54.4 1.0
CB F:ALA106 4.8 33.1 1.0
CA F:ALA106 4.9 37.9 1.0
O J:HOH452 5.0 50.4 1.0
OD2 F:ASP105 5.0 74.8 1.0

Calcium binding site 9 out of 21 in 5kzp

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Calcium binding site 9 out of 21 in the Structure of the HCV1-C1 Antibody-Antigen Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of the HCV1-C1 Antibody-Antigen Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca303

b:97.0
occ:1.00
 O F:HOH442 2.6 69.7 1.0
O F:HOH452 2.9 65.7 1.0
O F:PHE27 3.7 48.0 1.0
N F:GLY26 3.8 49.1 1.0
ND2 F:ASN77 3.8 71.9 1.0
O F:HOH411 4.3 61.2 1.0
N F:PHE27 4.4 40.3 1.0
CA F:SER25 4.5 50.4 1.0
CA F:GLY26 4.5 49.0 1.0
C F:SER25 4.6 49.9 1.0
C F:PHE27 4.6 44.3 1.0
C F:GLY26 4.8 49.9 1.0

Calcium binding site 10 out of 21 in 5kzp

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Calcium binding site 10 out of 21 in the Structure of the HCV1-C1 Antibody-Antigen Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of the HCV1-C1 Antibody-Antigen Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca304

b:74.7
occ:1.00
 O F:HOH449 2.3 51.5 1.0
N F:ASP62 3.1 27.9 1.0
O J:HOH458 3.4 39.7 1.0
O F:HOH435 3.5 32.4 1.0
CG F:ASP62 3.6 36.1 1.0
OD2 F:ASP62 3.7 50.6 1.0
CB F:ASP62 3.8 27.3 1.0
CA F:ALA61 3.8 29.4 1.0
OD1 F:ASP62 3.9 36.6 1.0
C F:ALA61 4.0 28.8 1.0
CA F:ASP62 4.1 27.2 1.0
CB F:ALA61 4.1 23.6 1.0
O F:HOH422 4.6 51.5 1.0
O F:HOH421 4.7 47.7 1.0
O F:HOH412 4.8 28.7 1.0

Reference:

B.G.Pierce, E.N.Boucher, K.H.Piepenbrink, M.Ejemel, C.A.Rapp, W.D.Thomas, E.J.Sundberg, Z.Weng, Y.Wang. Structure-Based Design of Hepatitis C Virus Vaccines That Elicit Neutralizing Antibody Responses to A Conserved Epitope. J. Virol. V. 91 2017.
ISSN: ESSN 1098-5514
PubMed: 28794021
DOI: 10.1128/JVI.01032-17
Page generated: Sat Dec 12 05:34:45 2020

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