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Copper in PDB 5jxa: Crystal Structure of Ligand-Free VRC03 Antigen-Binding Fragment.

Protein crystallography data

The structure of Crystal Structure of Ligand-Free VRC03 Antigen-Binding Fragment., PDB code: 5jxa was solved by T.Zhou, S.Moquin, M.G.Joyce, J.R.Mascola, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.95 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.185, 50.804, 71.757, 90.00, 108.15, 90.00
R / Rfree (%) 16 / 18

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Ligand-Free VRC03 Antigen-Binding Fragment. (pdb code 5jxa). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Crystal Structure of Ligand-Free VRC03 Antigen-Binding Fragment., PDB code: 5jxa:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 5jxa

Go back to Copper Binding Sites List in 5jxa
Copper binding site 1 out of 3 in the Crystal Structure of Ligand-Free VRC03 Antigen-Binding Fragment.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Ligand-Free VRC03 Antigen-Binding Fragment. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu304

b:74.3
occ:1.00
NE2 H:HIS164 2.1 30.2 1.0
O H:HOH426 2.1 31.9 1.0
HD21 L:ASN138 2.3 58.3 1.0
HD21 L:ASN137 2.4 38.6 1.0
OD1 L:ASN138 2.5 33.2 1.0
O L:HOH512 2.8 41.2 1.0
CD2 H:HIS164 2.8 26.4 1.0
HD2 H:HIS164 2.8 31.7 1.0
ND2 L:ASN138 2.8 48.6 1.0
OD1 L:ASN137 2.9 30.8 1.0
CG L:ASN138 2.9 35.4 1.0
ND2 L:ASN137 3.0 32.2 1.0
CE1 H:HIS164 3.3 29.6 1.0
CG L:ASN137 3.3 27.8 1.0
HD22 L:ASN138 3.6 58.3 1.0
HG L:SER174 3.6 22.3 1.0
HE1 H:HIS164 3.6 35.5 1.0
HA2 H:GLY162 3.7 35.2 1.0
HD22 L:ASN137 3.7 38.6 1.0
O L:HOH570 3.9 38.7 1.0
HG1 H:THR183 4.0 32.4 1.0
O H:GLY162 4.0 29.2 1.0
CG H:HIS164 4.0 24.5 1.0
ND1 H:HIS164 4.2 27.0 1.0
OG L:SER174 4.3 18.6 1.0
CB L:ASN138 4.3 23.4 1.0
O H:HOH559 4.3 44.6 1.0
H L:ASN138 4.5 21.6 1.0
CA H:GLY162 4.5 29.3 1.0
C H:GLY162 4.5 29.3 1.0
OG1 H:THR183 4.5 27.0 1.0
HB2 L:ASN138 4.5 28.1 1.0
N L:ASN138 4.7 18.0 1.0
CB L:ASN137 4.7 22.2 1.0
HG23 H:THR183 4.8 30.8 1.0
HA L:ASN138 4.9 23.6 1.0
HA3 H:GLY162 4.9 35.2 1.0
O L:HOH571 4.9 19.8 1.0
CA L:ASN138 4.9 19.7 1.0
HB3 L:ASN138 4.9 28.1 1.0
HA L:ASN137 4.9 20.8 1.0
HG21 H:THR183 5.0 30.8 1.0

Copper binding site 2 out of 3 in 5jxa

Go back to Copper Binding Sites List in 5jxa
Copper binding site 2 out of 3 in the Crystal Structure of Ligand-Free VRC03 Antigen-Binding Fragment.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Ligand-Free VRC03 Antigen-Binding Fragment. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cu301

b:20.6
occ:1.00
OD2 L:ASP151 2.0 20.5 1.0
ND1 L:HIS189 2.1 24.8 1.0
O L:HOH499 2.4 25.7 1.0
HB2 L:ASP151 2.7 19.3 1.0
CG L:ASP151 2.9 18.2 1.0
CE1 L:HIS189 3.0 27.4 1.0
CB L:ASP151 3.1 16.1 1.0
HB3 L:ASP151 3.1 19.3 1.0
HE1 L:HIS189 3.1 32.8 1.0
CG L:HIS189 3.1 21.4 1.0
HB3 L:HIS189 3.2 24.7 1.0
HA L:HIS189 3.2 26.8 1.0
CB L:HIS189 3.5 20.6 1.0
CA L:HIS189 3.9 22.3 1.0
O L:HOH407 4.0 18.6 1.0
O L:LYS188 4.1 26.1 1.0
OD1 L:ASP151 4.1 17.9 1.0
NE2 L:HIS189 4.1 28.4 1.0
H L:LYS190 4.2 25.3 1.0
CD2 L:HIS189 4.2 25.6 1.0
HB2 L:HIS189 4.5 24.7 1.0
CA L:ASP151 4.6 15.8 1.0
HG12 L:VAL150 4.7 21.1 1.0
N L:HIS189 4.8 22.5 1.0
C L:LYS188 4.8 26.9 1.0
N L:LYS190 4.8 21.1 1.0
HE2 L:HIS189 4.9 34.1 1.0
C L:HIS189 4.9 22.8 1.0

Copper binding site 3 out of 3 in 5jxa

Go back to Copper Binding Sites List in 5jxa
Copper binding site 3 out of 3 in the Crystal Structure of Ligand-Free VRC03 Antigen-Binding Fragment.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Ligand-Free VRC03 Antigen-Binding Fragment. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cu302

b:0.0
occ:1.00
HH21 L:ARG39 1.9 72.4 1.0
HE22 L:GLN37 2.3 22.3 1.0
NH2 L:ARG39 2.6 60.3 1.0
OD1 L:ASP82 2.8 23.4 1.0
HH12 L:ARG45 2.8 35.7 1.0
HH22 L:ARG39 2.8 72.4 1.0
HZ L:PHE62 3.1 24.5 1.0
NE2 L:GLN37 3.1 18.6 1.0
HH21 L:ARG61 3.2 31.9 1.0
HA L:ASP82 3.4 24.0 1.0
NH1 L:ARG45 3.4 29.7 1.0
HH11 L:ARG45 3.4 35.7 1.0
HE2 L:PHE62 3.6 24.2 1.0
HE L:ARG39 3.7 56.8 1.0
HE21 L:GLN37 3.7 22.3 1.0
HB3 L:GLU81 3.7 43.8 1.0
O L:GLU81 3.7 25.6 1.0
CZ L:ARG39 3.7 54.6 1.0
HB2 L:GLU81 3.8 43.8 1.0
HH22 L:ARG61 3.8 31.9 1.0
NH2 L:ARG61 3.8 26.6 1.0
CZ L:PHE62 3.8 20.4 1.0
OE1 L:GLN37 3.9 19.9 1.0
CD L:GLN37 3.9 18.7 1.0
CG L:ASP82 4.0 22.6 1.0
C L:GLU81 4.0 25.3 1.0
NE L:ARG39 4.1 47.3 1.0
CE2 L:PHE62 4.1 20.2 1.0
CB L:GLU81 4.2 36.5 1.0
CA L:ASP82 4.2 20.0 1.0
N L:ASP82 4.3 22.0 1.0
CB L:ASP82 4.6 19.0 1.0
CZ L:ARG45 4.7 31.1 1.0
HH22 L:ARG45 4.7 37.2 1.0
CA L:GLU81 4.8 28.4 1.0
OE1 L:GLU81 4.8 69.8 1.0
H L:ASP82 4.8 26.4 1.0
NH1 L:ARG39 4.9 54.2 1.0
HB3 L:ASP82 4.9 22.8 1.0
OD2 L:ASP82 4.9 25.5 1.0
CZ L:ARG61 4.9 29.3 1.0
CE1 L:PHE62 5.0 21.1 1.0
HE L:ARG61 5.0 34.1 1.0

Reference:

T.M.Davenport, J.Gorman, M.G.Joyce, T.Zhou, C.Soto, M.Guttman, S.Moquin, Y.Yang, B.Zhang, N.A.Doria-Rose, S.L.Hu, J.R.Mascola, P.D.Kwong, K.K.Lee. Somatic Hypermutation-Induced Changes in the Structure and Dynamics of Hiv-1 Broadly Neutralizing Antibodies. Structure V. 24 1346 2016.
ISSN: ISSN 1878-4186
PubMed: 27477385
DOI: 10.1016/J.STR.2016.06.012
Page generated: Sun Dec 13 11:18:07 2020

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