Zinc in PDB 7l79: Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01

Protein crystallography data

The structure of Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01, PDB code: 7l79 was solved by T.Zhou, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.92 / 2.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.792, 135.95, 136.908, 90, 90, 90
R / Rfree (%) 22 / 28

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01 (pdb code 7l79). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01, PDB code: 7l79:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 7l79

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Zinc binding site 1 out of 9 in the Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01


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 Broadly Hiv-1-Neutralizing Antibody VRC40.01 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:54.3
occ:1.00
HE2 H:HIS178 1.2 72.0 1.0
HG1 H:THR197 1.7 81.1 1.0
NE2 H:HIS178 2.0 60.3 1.0
OD1 L:ASN138 2.0 68.0 1.0
OD1 L:ASN137 2.1 65.2 1.0
OG1 H:THR197 2.3 67.8 1.0
O L:HOH410 2.3 47.6 1.0
HD21 L:ASN137 2.4 48.8 1.0
CG L:ASN137 2.8 45.8 1.0
ND2 L:ASN137 2.9 40.9 1.0
CD2 H:HIS178 3.0 51.3 1.0
CE1 H:HIS178 3.0 51.9 1.0
HD2 H:HIS178 3.1 61.3 1.0
CG L:ASN138 3.2 49.1 1.0
HE1 H:HIS178 3.3 62.0 1.0
O H:GLY176 3.5 54.1 1.0
CB H:THR197 3.5 65.8 1.0
HG21 H:THR197 3.6 80.5 1.0
HA2 H:GLY176 3.7 70.3 1.0
HB H:THR197 3.7 78.7 1.0
HD21 L:ASN138 3.7 54.2 1.0
HD22 L:ASN137 3.7 48.8 1.0
ND2 L:ASN138 3.9 45.4 1.0
CG2 H:THR197 4.0 67.4 1.0
ND1 H:HIS178 4.1 50.1 1.0
CG H:HIS178 4.1 48.1 1.0
CB L:ASN137 4.2 37.7 1.0
HB2 L:ASN138 4.2 49.6 1.0
H H:THR197 4.2 73.1 1.0
C H:GLY176 4.3 55.4 1.0
HG23 H:THR197 4.3 80.5 1.0
CA H:GLY176 4.3 58.9 1.0
CB L:ASN138 4.4 41.6 1.0
HB2 L:ASN137 4.4 45.0 1.0
HG L:SER174 4.4 50.7 1.0
HA3 H:GLY176 4.5 70.3 1.0
HB3 L:ASN137 4.7 45.0 1.0
HD22 L:ASN138 4.7 54.2 1.0
CA H:THR197 4.7 62.6 1.0
N H:THR197 4.8 61.2 1.0
H L:ASN138 4.9 50.9 1.0
N L:ASN138 4.9 42.6 1.0
HG22 H:THR197 4.9 80.5 1.0
HD1 H:HIS178 4.9 59.9 1.0

Zinc binding site 2 out of 9 in 7l79

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Zinc binding site 2 out of 9 in the Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01


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 Broadly Hiv-1-Neutralizing Antibody VRC40.01 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn301

b:41.3
occ:1.00
OE1 L:GLU195 2.1 78.6 1.0
OE2 L:GLU195 2.1 80.3 1.0
O L:HOH406 2.3 40.4 1.0
CD L:GLU195 2.4 71.0 1.0
HZ1 L:LYS149 2.4 57.6 1.0
HZ2 L:LYS149 3.0 57.6 1.0
NZ L:LYS149 3.1 48.2 1.0
HZ3 L:LYS149 3.5 57.6 1.0
CG L:GLU195 3.9 55.9 1.0
HE3 L:LYS149 4.2 54.1 1.0
HG2 L:GLU195 4.2 66.8 1.0
CE L:LYS149 4.3 45.3 1.0
HG3 L:GLU195 4.3 66.8 1.0
HG2 L:PRO204 4.3 62.4 1.0
HB3 L:PRO204 4.4 58.7 1.0
HE2 L:LYS149 4.6 54.1 1.0
HB3 L:GLU195 4.6 57.9 1.0
O L:HOH424 4.7 40.4 1.0
CB L:GLU195 4.8 48.5 1.0
HG3 L:PRO204 4.8 62.4 1.0
HB2 L:GLU195 4.8 57.9 1.0
CG L:PRO204 4.9 52.2 1.0
HB2 L:PRO204 4.9 58.7 1.0
CB L:PRO204 4.9 49.1 1.0

Zinc binding site 3 out of 9 in 7l79

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Zinc binding site 3 out of 9 in the Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01


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 Broadly Hiv-1-Neutralizing Antibody VRC40.01 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn302

b:61.8
occ:1.00
HE2 L:HIS189 1.3 55.5 1.0
OD2 L:ASP185 2.2 106.2 1.0
OD1 L:ASP185 2.2 112.2 1.0
NE2 L:HIS189 2.2 46.5 1.0
O L:HOH426 2.3 55.5 1.0
O L:HOH420 2.3 40.4 1.0
CG L:ASP185 2.5 96.8 1.0
CD2 L:HIS189 3.1 45.1 1.0
CE1 L:HIS189 3.2 45.6 1.0
HD2 L:HIS189 3.3 53.9 1.0
HD2 L:LYS188 3.3 108.5 1.0
HE1 L:HIS189 3.4 54.4 1.0
HZ3 L:LYS188 3.9 110.0 1.0
CB L:ASP185 4.0 80.0 1.0
HB2 L:LYS188 4.0 98.3 1.0
HZ2 L:LYS188 4.2 110.0 1.0
CD L:LYS188 4.2 90.7 1.0
HA L:ASP185 4.2 87.1 1.0
O L:ASP185 4.3 69.5 1.0
CG L:HIS189 4.3 46.3 1.0
HB3 L:LYS188 4.3 98.3 1.0
ND1 L:HIS189 4.3 46.6 1.0
HB3 L:ASP185 4.4 95.7 1.0
NZ L:LYS188 4.4 92.0 1.0
HB2 L:ASP185 4.5 95.7 1.0
HD3 L:LYS188 4.6 108.5 1.0
CB L:LYS188 4.6 82.2 1.0
CA L:ASP185 4.6 72.8 1.0
C L:ASP185 4.9 69.1 1.0
CE L:LYS188 5.0 93.2 1.0

Zinc binding site 4 out of 9 in 7l79

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Zinc binding site 4 out of 9 in the Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01


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 Broadly Hiv-1-Neutralizing Antibody VRC40.01 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn303

b:53.7
occ:1.00
O L:HOH425 2.2 40.7 1.0
O L:VAL58 3.8 31.5 1.0
O L:HOH434 3.8 40.4 1.0
OD2 L:ASP60 3.8 58.2 1.0
O L:HOH435 3.9 42.8 1.0
CG L:ASP60 4.7 57.4 1.0
C L:VAL58 4.8 31.0 1.0
OD1 L:ASP60 4.9 57.4 1.0
N L:GLY57 5.0 34.2 1.0

Zinc binding site 5 out of 9 in 7l79

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Zinc binding site 5 out of 9 in the Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01


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 Broadly Hiv-1-Neutralizing Antibody VRC40.01 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn304

b:111.0
occ:1.00
HG1 L:THR178 1.8 64.3 1.0
OG1 L:THR178 2.3 53.8 1.0
HB L:THR178 3.4 55.4 1.0
CB L:THR178 3.4 46.4 1.0
HG L:SER176 3.6 51.0 1.0
OG L:SER176 3.8 42.8 1.0
HG21 H:VAL183 3.8 46.6 1.0
HG22 H:VAL183 3.9 46.6 1.0
H L:THR178 3.9 46.8 1.0
HB2 H:SER193 3.9 54.7 1.0
N L:THR178 4.0 39.2 1.0
HA L:GLU161 4.1 71.7 1.0
HB3 L:SER176 4.2 48.3 1.0
O L:SER176 4.2 36.3 1.0
O L:GLN160 4.3 49.0 1.0
HB2 L:SER162 4.3 47.4 1.0
CG2 H:VAL183 4.3 39.1 1.0
CA L:THR178 4.3 41.2 1.0
HA L:SER177 4.3 34.7 1.0
HG21 L:THR178 4.4 51.2 1.0
HG11 H:VAL183 4.4 48.9 1.0
C L:SER177 4.5 30.7 1.0
C L:SER176 4.5 36.8 1.0
CG2 L:THR178 4.5 42.9 1.0
CB L:SER176 4.5 40.5 1.0
HG13 H:VAL183 4.7 48.9 1.0
CA L:SER177 4.7 29.1 1.0
HG13 L:VAL133 4.8 37.1 1.0
N L:SER177 4.8 27.4 1.0
CB H:SER193 4.8 45.8 1.0
HA L:THR178 4.8 49.1 1.0
HA H:LEU192 4.8 51.7 1.0
HB3 H:SER193 4.8 54.7 1.0
HB3 L:GLN160 4.9 53.7 1.0
HG23 L:THR178 4.9 51.2 1.0
C L:GLN160 4.9 45.5 1.0
CA L:GLU161 5.0 60.0 1.0
HG23 H:VAL183 5.0 46.6 1.0
CG1 H:VAL183 5.0 41.0 1.0
HB3 L:SER162 5.0 47.4 1.0
H L:SER162 5.0 47.1 1.0

Zinc binding site 6 out of 9 in 7l79

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Zinc binding site 6 out of 9 in the Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01


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 Broadly Hiv-1-Neutralizing Antibody VRC40.01 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn305

b:89.7
occ:1.00
OD2 L:ASP30 2.2 61.3 1.0
O L:HOH405 2.2 57.4 1.0
OD1 L:ASP30 2.2 61.4 1.0
CG L:ASP30 2.5 59.2 1.0
NH2 L:ARG31 4.1 58.3 1.0
CB L:ASP30 4.1 53.0 1.0
O L:HOH427 4.4 40.4 1.0
NE L:ARG31 4.7 56.4 1.0
OH L:TYR28 4.8 42.0 1.0
CZ L:ARG31 4.9 57.0 1.0
O L:HOH411 4.9 40.4 1.0

Zinc binding site 7 out of 9 in 7l79

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Zinc binding site 7 out of 9 in the Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01


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 Broadly Hiv-1-Neutralizing Antibody VRC40.01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:59.9
occ:1.00
HE2 B:HIS189 1.4 66.7 1.0
OD2 B:ASP185 2.1 89.0 1.0
HZ1 B:LYS188 2.1 79.8 1.0
OD1 B:ASP185 2.1 91.8 1.0
NE2 B:HIS189 2.2 55.8 1.0
O B:HOH407 2.3 40.4 1.0
CG B:ASP185 2.4 77.8 1.0
HZ3 B:LYS188 2.7 79.8 1.0
NZ B:LYS188 2.8 66.8 1.0
CD2 B:HIS189 3.0 48.2 1.0
HD2 B:HIS189 3.1 57.6 1.0
HD3 B:LYS188 3.2 91.7 1.0
CE1 B:HIS189 3.3 49.0 1.0
HZ2 B:LYS188 3.3 79.8 1.0
HE1 B:HIS189 3.5 58.5 1.0
CE B:LYS188 3.9 73.7 1.0
CD B:LYS188 3.9 76.6 1.0
CB B:ASP185 4.0 60.5 1.0
HG2 B:LYS188 4.2 91.5 1.0
CG B:HIS189 4.2 47.5 1.0
ND1 B:HIS189 4.3 49.2 1.0
O B:ASP185 4.3 48.5 1.0
HE2 B:LYS188 4.4 88.2 1.0
HA B:ASP185 4.4 64.6 1.0
HB3 B:ASP185 4.4 72.3 1.0
HB3 B:LYS188 4.4 87.8 1.0
HB2 B:ASP185 4.4 72.3 1.0
HE3 B:LYS188 4.5 88.2 1.0
CG B:LYS188 4.6 76.5 1.0
CA B:ASP185 4.7 54.0 1.0
HD2 B:LYS188 4.7 91.7 1.0
HE22 B:GLN155 4.9 59.4 1.0
C B:ASP185 4.9 49.9 1.0

Zinc binding site 8 out of 9 in 7l79

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Zinc binding site 8 out of 9 in the Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:40.4
occ:1.00
OE1 B:GLU195 2.0 65.8 1.0
OE2 B:GLU195 2.1 66.8 1.0
O B:HOH408 2.2 40.4 1.0
CD B:GLU195 2.3 58.1 1.0
HZ1 B:LYS149 2.4 42.7 1.0
HZ2 B:LYS149 3.0 42.7 1.0
NZ B:LYS149 3.1 35.8 1.0
HZ3 B:LYS149 3.5 42.7 1.0
CG B:GLU195 3.9 45.6 1.0
HG2 B:GLU195 4.2 54.4 1.0
HE3 B:LYS149 4.2 41.7 1.0
CE B:LYS149 4.3 35.0 1.0
HG3 B:GLU195 4.3 54.4 1.0
HG2 B:PRO204 4.5 41.1 1.0
HB3 B:GLU195 4.6 45.1 1.0
HE2 B:LYS149 4.6 41.7 1.0
O B:HOH417 4.7 40.4 1.0
CB B:GLU195 4.7 37.8 1.0
HB3 B:PRO204 4.8 41.6 1.0
HB2 B:GLU195 4.8 45.1 1.0

Zinc binding site 9 out of 9 in 7l79

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Zinc binding site 9 out of 9 in the Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Broadly Hiv-1-Neutralizing Antibody VRC40.01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:47.7
occ:1.00
HE2 A:HIS179 1.4 76.5 1.0
HD21 B:ASN137 1.9 55.6 1.0
OD1 B:ASN138 2.1 64.3 1.0
NE2 A:HIS179 2.1 64.0 1.0
OD1 B:ASN137 2.2 66.9 1.0
O B:HOH413 2.2 47.0 1.0
ND2 B:ASN137 2.5 46.6 1.0
HD21 B:ASN138 2.6 46.0 1.0
CG B:ASN137 2.6 49.1 1.0
CD2 A:HIS179 2.8 56.5 1.0
HD2 A:HIS179 2.8 67.5 1.0
CG B:ASN138 2.9 42.3 1.0
ND2 B:ASN138 3.0 38.6 1.0
CE1 A:HIS179 3.3 57.6 1.0
HD22 B:ASN137 3.3 55.6 1.0
HG1 A:THR198 3.5 54.1 1.0
HE1 A:HIS179 3.6 68.8 1.0
HG B:SER174 3.7 40.4 1.0
H B:ASN138 3.8 44.2 1.0
HD22 B:ASN138 3.9 46.0 1.0
HA2 A:GLY177 3.9 67.0 1.0
OG1 A:THR198 3.9 45.3 1.0
CG A:HIS179 4.0 52.9 1.0
O A:GLY177 4.1 57.6 1.0
CB B:ASN137 4.1 39.8 1.0
ND1 A:HIS179 4.2 56.2 1.0
N B:ASN138 4.3 37.1 1.0
CB B:ASN138 4.3 37.4 1.0
OG B:SER174 4.3 33.9 1.0
HG23 A:THR198 4.4 56.8 1.0
HG21 A:THR198 4.4 56.8 1.0
HA B:ASN137 4.5 44.3 1.0
HB3 B:ASN137 4.5 47.5 1.0
HB2 B:ASN138 4.6 44.6 1.0
HB2 B:ASN137 4.6 47.5 1.0
C A:GLY177 4.6 57.1 1.0
CA A:GLY177 4.7 56.1 1.0
CA B:ASN137 4.7 37.2 1.0
CG2 A:THR198 4.8 47.5 1.0
C B:ASN137 4.8 37.2 1.0
CA B:ASN138 4.8 37.4 1.0
HB3 B:ASN138 4.9 44.6 1.0
HA3 A:GLY177 4.9 67.0 1.0
CB A:THR198 5.0 45.7 1.0

Reference:

T.Zhou, T.Zhou, P.D.Kwong. N/A N/A.
ISSN: ESSN 2211-1247
Page generated: Fri Nov 5 16:53:48 2021

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