Zinc in PDB 5wnb: Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G

Protein crystallography data

The structure of Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G, PDB code: 5wnb was solved by S.O.Fedechkin, N.L.George, J.T.Wolff, L.M.Kauvar, R.M.Dubois, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.38 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.760, 105.430, 121.820, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.8

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G (pdb code 5wnb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G, PDB code: 5wnb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 5wnb

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Zinc binding site 1 out of 14 in the Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:46.2
occ:1.00
 OD2 H:ASP106 1.9 63.3 1.0
NE2 H:HIS108 2.2 50.5 1.0
CE1 H:HIS108 2.6 50.2 1.0
CG H:ASP106 2.8 55.6 1.0
OD1 H:ASP106 3.3 57.6 1.0
CD2 H:HIS108 3.5 47.3 1.0
ND1 H:HIS108 3.8 49.3 1.0
CB H:ASP106 4.0 50.5 1.0
OD1 L:ASN53 4.3 50.3 1.0
CG H:HIS108 4.3 46.3 1.0
CA H:ASP106 4.6 50.4 1.0
O H:ASP106 4.9 44.6 1.0

Zinc binding site 2 out of 14 in 5wnb

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Zinc binding site 2 out of 14 in the Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn302

b:0.3
occ:1.00
 OD1 H:ASP77 2.3 57.9 1.0
OE1 H:GLU30 2.4 70.9 1.0
OE1 H:GLU2 2.5 71.7 1.0
CD H:GLU30 2.8 69.9 1.0
CG H:ASP77 3.3 54.0 1.0
OE2 H:GLU30 3.4 68.5 1.0
CD H:GLU2 3.4 70.6 1.0
CG H:GLU30 3.4 64.6 1.0
OD2 H:ASP77 3.6 50.8 1.0
OE2 H:GLU2 3.7 73.2 1.0
CB H:GLU30 3.7 64.2 1.0
O H:SER25 4.1 90.9 1.0
CA H:GLY24 4.5 41.5 1.0
CB H:ASP77 4.7 51.9 1.0
CG H:GLU2 4.7 67.0 1.0
C H:GLY24 4.7 58.1 1.0
N H:SER25 4.8 72.5 1.0
CD1 H:ILE98 4.8 27.5 1.0

Zinc binding site 3 out of 14 in 5wnb

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Zinc binding site 3 out of 14 in the Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn303

b:0.6
occ:1.00
 OE2 H:GLU31 2.0 0.7 1.0
O B:PRO172 2.3 73.9 1.0
CD H:GLU31 3.0 84.4 1.0
C B:PRO172 3.3 68.9 1.0
OE1 H:GLU31 3.3 76.7 1.0
CA B:PRO172 3.7 64.6 1.0
CG H:GLU31 4.3 74.5 1.0
CB B:PRO172 4.5 58.0 1.0
O B:VAL171 4.7 64.9 1.0
N B:PRO172 4.9 58.3 1.0

Zinc binding site 4 out of 14 in 5wnb

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Zinc binding site 4 out of 14 in the Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn304

b:46.6
occ:1.00
 OD1 L:ASN136 2.0 43.0 1.0
NE2 H:HIS175 2.1 37.1 1.0
OD1 L:ASN137 2.3 57.3 1.0
O L:HOH423 2.9 34.4 1.0
CG L:ASN136 2.9 40.7 1.0
CE1 H:HIS175 3.0 39.4 1.0
CD2 H:HIS175 3.1 33.8 1.0
ND2 L:ASN136 3.2 48.8 1.0
CG L:ASN137 3.5 54.2 1.0
OG1 H:THR194 3.8 49.1 1.0
O H:GLY173 4.0 52.9 1.0
ND1 H:HIS175 4.1 42.6 1.0
ND2 L:ASN137 4.2 52.9 1.0
CG H:HIS175 4.2 36.0 1.0
OG L:SER173 4.3 32.8 1.0
CB L:ASN136 4.3 40.1 1.0
CA H:GLY173 4.4 56.0 1.0
CB H:THR194 4.5 50.9 1.0
C H:GLY173 4.5 55.0 1.0
CB L:ASN137 4.6 47.2 1.0
N L:ASN137 4.7 41.4 1.0
CA L:ASN136 5.0 37.3 1.0

Zinc binding site 5 out of 14 in 5wnb

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Zinc binding site 5 out of 14 in the Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn301

b:39.6
occ:1.00
 ND1 L:HIS188 2.1 31.9 1.0
OD1 L:ASP150 2.5 37.2 1.0
CE1 L:HIS188 3.0 33.4 1.0
CG L:HIS188 3.2 28.8 1.0
CG L:ASP150 3.3 33.6 1.0
CB L:HIS188 3.6 27.5 1.0
CB L:ASP150 3.7 33.9 1.0
CA L:HIS188 3.7 30.2 1.0
NE2 L:HIS188 4.1 32.0 1.0
OD2 L:ASP150 4.2 37.5 1.0
CD2 L:HIS188 4.3 26.7 1.0
N L:LYS189 4.5 28.9 1.0
O L:LYS187 4.5 39.5 1.0
N L:HIS188 4.6 37.1 1.0
C L:HIS188 4.7 28.8 1.0
C L:LYS187 4.9 33.1 1.0

Zinc binding site 6 out of 14 in 5wnb

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Zinc binding site 6 out of 14 in the Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn302

b:58.3
occ:1.00
 O L:ACY304 2.1 46.7 1.0
OXT L:ACY304 2.3 65.0 1.0
NE2 L:HIS32 2.3 51.8 1.0
C L:ACY304 2.5 57.0 1.0
CD2 L:HIS32 3.2 49.3 1.0
CE1 L:HIS32 3.2 47.3 1.0
OG L:SER30 3.9 50.0 1.0
CH3 L:ACY304 3.9 51.4 1.0
OD1 L:ASN92 4.0 49.3 1.0
ND1 L:HIS32 4.3 43.8 1.0
CG L:HIS32 4.4 49.0 1.0
CB L:SER30 4.4 50.1 1.0
OD1 L:ASN31 4.7 45.4 1.0
CD2 B:PHE165 4.8 40.3 1.0
CG B:PHE165 4.9 37.7 1.0
CB B:PHE165 5.0 40.1 1.0

Zinc binding site 7 out of 14 in 5wnb

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Zinc binding site 7 out of 14 in the Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn303

b:57.8
occ:1.00
 OE1 M:GLU79 1.8 56.6 1.0
OE1 L:GLU81 1.8 57.6 1.0
OE1 M:GLU81 1.9 47.3 1.0
OE2 L:GLU79 1.9 43.5 1.0
CD M:GLU81 2.3 42.2 1.0
CD L:GLU81 2.4 38.8 1.0
OE2 M:GLU81 2.6 39.0 1.0
OE2 L:GLU81 2.6 37.9 1.0
CD L:GLU79 2.9 44.2 1.0
CD M:GLU79 3.0 53.7 1.0
CG L:GLU79 3.5 44.1 1.0
CG M:GLU81 3.6 46.3 1.0
CG L:GLU81 3.7 44.0 1.0
CG M:GLU79 3.7 42.0 1.0
OE1 L:GLU79 3.8 51.2 1.0
CB L:GLU79 3.8 38.7 1.0
CB M:GLU79 3.9 36.7 1.0
OE2 M:GLU79 4.0 55.0 1.0
NH2 L:ARG61 4.6 29.1 1.0
CB L:GLU81 4.8 41.8 1.0
CB M:GLU81 4.8 46.4 1.0
CD M:PRO80 4.9 36.3 1.0

Zinc binding site 8 out of 14 in 5wnb

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Zinc binding site 8 out of 14 in the Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn301

b:68.1
occ:1.00
 O I:HOH416 2.2 62.9 1.0
OD2 I:ASP77 2.2 60.6 1.0
CG I:ASP77 3.0 59.2 1.0
OE1 I:GLU30 3.0 69.7 1.0
OD1 I:ASP77 3.2 65.3 1.0
CD I:GLU30 3.8 66.3 1.0
OE2 I:GLU30 3.8 71.5 1.0
O I:ASN74 3.9 46.6 1.0
O I:LEU27 4.4 87.6 1.0
CB I:ASP77 4.5 53.5 1.0
CB I:PHE29 4.6 49.2 1.0
N I:PHE29 4.6 39.0 1.0

Zinc binding site 9 out of 14 in 5wnb

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Zinc binding site 9 out of 14 in the Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn302

b:53.0
occ:1.00
 OD2 I:ASP106 2.1 87.9 1.0
NE2 I:HIS108 2.2 48.2 1.0
CE1 I:HIS108 3.1 45.7 1.0
CD2 I:HIS108 3.2 49.5 1.0
CG I:ASP106 3.3 87.5 1.0
OD1 I:ASP106 3.9 91.1 1.0
ND1 I:HIS108 4.3 40.2 1.0
CG I:HIS108 4.3 49.0 1.0
CA I:ASP106 4.3 68.9 1.0
CB I:ASP106 4.4 80.1 1.0
CB I:THR103 4.7 40.5 1.0
C I:ASP106 4.8 66.1 1.0
O I:ASP106 4.9 71.2 1.0
CG2 I:THR103 4.9 37.5 1.0

Zinc binding site 10 out of 14 in 5wnb

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Zinc binding site 10 out of 14 in the Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Antibody 3D3 Bound to the Linear Epitope of Rsv G within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn303

b:72.4
occ:1.00
 OD1 M:ASN136 1.9 65.8 1.0
NE2 I:HIS175 2.1 48.8 1.0
OD1 M:ASN137 2.6 49.4 1.0
O M:HOH416 2.8 47.3 1.0
CG M:ASN136 2.9 57.4 1.0
CE1 I:HIS175 2.9 48.7 1.0
CD2 I:HIS175 3.2 50.1 1.0
ND2 M:ASN136 3.3 57.6 1.0
CG2 I:THR194 3.3 73.9 1.0
CG M:ASN137 3.5 55.5 1.0
ND2 M:ASN137 4.0 53.8 1.0
O I:GLY173 4.0 75.2 1.0
ND1 I:HIS175 4.1 49.5 1.0
CB M:ASN136 4.3 55.5 1.0
CG I:HIS175 4.3 50.0 1.0
OG M:SER173 4.4 55.0 1.0
OG1 I:THR194 4.5 75.9 1.0
CA I:GLY173 4.5 69.9 1.0
CB I:THR194 4.5 74.2 1.0
C I:GLY173 4.6 71.6 1.0
CB M:ASN137 4.6 47.2 1.0
N M:ASN137 4.9 46.4 1.0

Reference:

S.O.Fedechkin, N.L.George, J.T.Wolff, L.M.Kauvar, R.M.Dubois. Structures of Respiratory Syncytial Virus G Antigen Bound to Broadly Neutralizing Antibodies. Sci Immunol V. 3 2018.
ISSN: ESSN 2470-9468
PubMed: 29523582
DOI: 10.1126/SCIIMMUNOL.AAR3534
Page generated: Wed Dec 16 11:17:10 2020

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