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Zinc in PDB 4nrz: Crystal Structure of Hiv-1 Neutralizing Antibody M66.6

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Neutralizing Antibody M66.6, PDB code: 4nrz was solved by G.Ofek, Y.Yang, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.19 / 2.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.160, 118.873, 80.033, 90.00, 96.80, 90.00
R / Rfree (%) 17.7 / 21.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Hiv-1 Neutralizing Antibody M66.6 (pdb code 4nrz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Hiv-1 Neutralizing Antibody M66.6, PDB code: 4nrz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 4nrz

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Zinc binding site 1 out of 7 in the Crystal Structure of Hiv-1 Neutralizing Antibody M66.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Hiv-1 Neutralizing Antibody M66.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:47.9
occ:1.00
OE1 H:GLU32 2.5 54.3 1.0
NE2 H:HIS97 2.5 17.9 1.0
OE2 H:GLU32 2.8 57.7 1.0
CD H:GLU32 2.8 55.3 1.0
CD2 H:HIS97 3.1 12.4 1.0
CE1 H:HIS97 3.7 22.0 1.0
O H:SER31 3.9 33.8 1.0
CG H:GLU32 4.1 49.9 1.0
CG H:HIS97 4.4 16.4 1.0
OD1 H:ASN96 4.5 39.1 1.0
ND1 H:HIS97 4.6 22.5 1.0
OG H:SER31 4.8 66.1 1.0
C H:SER31 4.9 40.1 1.0

Zinc binding site 2 out of 7 in 4nrz

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Zinc binding site 2 out of 7 in the Crystal Structure of Hiv-1 Neutralizing Antibody M66.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Hiv-1 Neutralizing Antibody M66.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:44.9
occ:1.00
NE2 A:HIS97 2.0 24.2 1.0
OE2 A:GLU32 2.1 45.8 1.0
O A:HOH403 2.5 26.2 1.0
O A:HOH405 2.6 24.4 1.0
CD A:GLU32 2.8 40.7 1.0
CE1 A:HIS97 3.0 17.2 1.0
CD2 A:HIS97 3.0 22.7 1.0
OE1 A:GLU32 3.0 35.1 1.0
ND1 A:HIS97 4.1 15.6 1.0
CG A:HIS97 4.1 23.9 1.0
CG A:GLU32 4.2 40.1 1.0
O A:SER31 4.5 41.8 1.0
OD1 A:ASN96 4.6 40.9 1.0

Zinc binding site 3 out of 7 in 4nrz

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Zinc binding site 3 out of 7 in the Crystal Structure of Hiv-1 Neutralizing Antibody M66.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Hiv-1 Neutralizing Antibody M66.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:57.6
occ:1.00
O A:HOH419 2.9 26.2 1.0
NZ A:LYS12 3.5 32.5 1.0
O A:VAL11 3.9 21.9 1.0
CE A:LYS12 3.9 38.0 1.0
O A:HOH421 4.3 22.1 1.0
OE2 A:GLU16 4.3 62.9 1.0
CD A:LYS12 4.4 36.3 1.0
OE1 A:GLU10 4.9 37.5 1.0

Zinc binding site 4 out of 7 in 4nrz

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Zinc binding site 4 out of 7 in the Crystal Structure of Hiv-1 Neutralizing Antibody M66.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Hiv-1 Neutralizing Antibody M66.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn301

b:62.0
occ:1.00
ND2 L:ASN137 2.0 46.9 1.0
NE2 H:HIS164 2.3 46.1 1.0
OD1 L:ASN138 2.3 37.9 1.0
O L:HOH430 2.6 28.4 1.0
CG L:ASN137 2.9 39.9 1.0
CD2 H:HIS164 3.0 42.6 1.0
OD1 L:ASN137 3.0 37.1 1.0
CE1 H:HIS164 3.4 44.4 1.0
CG L:ASN138 3.4 30.7 1.0
ND2 L:ASN138 4.0 32.5 1.0
O H:GLY162 4.1 43.4 1.0
OG1 H:THR183 4.2 45.9 1.0
CG H:HIS164 4.2 36.4 1.0
CB L:ASN137 4.3 30.6 1.0
ND1 H:HIS164 4.3 44.8 1.0
CB L:ASN138 4.5 26.2 1.0
CG2 H:THR183 4.5 38.2 1.0
OG L:SER174 4.6 20.9 1.0
CA H:GLY162 4.7 41.9 1.0
C H:GLY162 4.7 40.6 1.0
N L:ASN138 4.8 25.4 1.0
O L:HOH415 4.9 29.0 1.0

Zinc binding site 5 out of 7 in 4nrz

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Zinc binding site 5 out of 7 in the Crystal Structure of Hiv-1 Neutralizing Antibody M66.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Hiv-1 Neutralizing Antibody M66.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn302

b:41.8
occ:1.00
NE2 L:HIS28 2.0 26.3 1.0
O L:HOH427 2.5 13.1 1.0
CD2 L:HIS28 2.8 24.9 1.0
CE1 L:HIS28 3.1 32.7 1.0
CG L:HIS28 4.0 29.3 1.0
ND1 L:HIS28 4.1 36.0 1.0
CG2 L:THR69 4.5 32.2 1.0
OG1 L:THR69 4.6 37.2 1.0

Zinc binding site 6 out of 7 in 4nrz

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Zinc binding site 6 out of 7 in the Crystal Structure of Hiv-1 Neutralizing Antibody M66.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Hiv-1 Neutralizing Antibody M66.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn303

b:94.9
occ:1.00
O L:HOH426 2.5 16.3 1.0
OD2 L:ASP185 2.5 61.5 1.0
O L:HOH431 2.7 45.3 1.0
NE2 L:HIS189 2.7 70.4 1.0
CG L:ASP185 3.4 68.2 1.0
OD1 L:ASP185 3.6 77.6 1.0
CD2 L:HIS189 3.6 67.7 1.0
CE1 L:HIS189 3.7 72.2 1.0
NZ L:LYS188 3.9 0.9 1.0
CD L:LYS188 4.0 93.6 1.0
CE L:LYS188 4.5 0.4 1.0
O L:HOH449 4.6 55.1 1.0
CB L:ASP185 4.8 62.4 1.0
CG L:HIS189 4.8 65.6 1.0
ND1 L:HIS189 4.8 70.3 1.0

Zinc binding site 7 out of 7 in 4nrz

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Zinc binding site 7 out of 7 in the Crystal Structure of Hiv-1 Neutralizing Antibody M66.6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Hiv-1 Neutralizing Antibody M66.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:63.5
occ:1.00
OD1 B:ASN138 1.7 53.3 1.0
NE2 A:HIS164 2.1 40.6 1.0
ND2 B:ASN137 2.3 28.7 1.0
O B:HOH423 2.5 49.7 1.0
CG B:ASN138 2.8 41.5 1.0
O B:HOH412 3.0 31.2 1.0
CD2 A:HIS164 3.1 30.1 1.0
CE1 A:HIS164 3.1 39.2 1.0
CG B:ASN137 3.2 37.0 1.0
OD1 B:ASN137 3.2 43.2 1.0
ND2 B:ASN138 3.4 28.7 1.0
O A:GLY162 4.1 49.6 1.0
CB B:ASN138 4.1 38.8 1.0
ND1 A:HIS164 4.2 39.4 1.0
CG A:HIS164 4.2 29.6 1.0
OG1 A:THR183 4.3 46.3 1.0
OG B:SER174 4.5 23.8 1.0
CB B:ASN137 4.6 30.7 1.0
CA A:GLY162 4.6 36.9 1.0
N B:ASN138 4.6 27.9 1.0
C A:GLY162 4.6 42.6 1.0
CG2 A:THR183 4.8 34.5 1.0
O B:HOH404 4.9 22.4 1.0
CA B:ASN138 4.9 35.0 1.0

Reference:

G.Ofek, B.Zirkle, Y.Yang, Z.Zhu, K.Mckee, B.Zhang, G.Y.Chuang, I.S.Georgiev, S.O'dell, N.Doria-Rose, J.R.Mascola, D.S.Dimitrov, P.D.Kwong. Structural Basis For Hiv-1 Neutralization By 2F5-Like Antibodies M66 and M66.6. J.Virol. V. 88 2426 2014.
ISSN: ISSN 0022-538X
PubMed: 24335316
DOI: 10.1128/JVI.02837-13
Page generated: Wed Dec 16 05:37:33 2020

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