Atomistry » Sodium » PDB 4j0p-4jer » 4jan
Atomistry »
  Sodium »
    PDB 4j0p-4jer »
      4jan »

Sodium in PDB 4jan: Crystal Structure of Broadly Neutralizing Antibody CH103 in Complex with Hiv-1 GP120

Protein crystallography data

The structure of Crystal Structure of Broadly Neutralizing Antibody CH103 in Complex with Hiv-1 GP120, PDB code: 4jan was solved by T.Zhou, S.Moquin, A.Zheng, S.Srivatsan, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.75 / 3.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.943, 208.651, 69.422, 90.00, 107.21, 90.00
R / Rfree (%) 19.6 / 25.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Broadly Neutralizing Antibody CH103 in Complex with Hiv-1 GP120 (pdb code 4jan). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Broadly Neutralizing Antibody CH103 in Complex with Hiv-1 GP120, PDB code: 4jan:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4jan

Go back to Sodium Binding Sites List in 4jan
Sodium binding site 1 out of 2 in the Crystal Structure of Broadly Neutralizing Antibody CH103 in Complex with Hiv-1 GP120


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Broadly Neutralizing Antibody CH103 in Complex with Hiv-1 GP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na301

b:40.4
occ:1.00
O L:GLY41 2.9 79.7 1.0
O H:GLY106 3.1 69.0 1.0
HB2 B:ARG189 3.1 0.1 1.0
HA2 L:GLY41 3.2 92.8 1.0
HA3 H:GLY106 3.3 80.9 1.0
HG11 H:VAL89 3.4 71.0 1.0
C L:GLY41 3.7 80.8 1.0
HG13 H:VAL89 3.8 71.0 1.0
C H:GLY106 3.8 68.1 1.0
CA L:GLY41 3.9 77.4 1.0
CA H:GLY106 4.0 67.4 1.0
CB B:ARG189 4.0 0.9 1.0
CG1 H:VAL89 4.1 59.2 1.0
HD2 B:ARG189 4.1 0.4 1.0
HA B:ARG189 4.2 0.2 1.0
HG21 H:VAL89 4.3 73.2 1.0
HG3 B:ARG189 4.3 0.3 1.0
O L:HOH402 4.4 44.7 1.0
HA2 H:GLY106 4.5 80.9 1.0
HB2 H:LEU108 4.5 80.2 1.0
CA B:ARG189 4.5 0.8 1.0
HA3 L:GLY41 4.5 92.8 1.0
HG22 H:VAL89 4.6 73.2 1.0
CG B:ARG189 4.6 0.1 1.0
H L:GLY41 4.6 85.5 1.0
N B:ARG189 4.7 0.5 1.0
HB3 B:ARG189 4.7 0.1 1.0
H B:ARG189 4.7 0.9 1.0
HG12 H:VAL89 4.7 71.0 1.0
O H:ARG105 4.8 85.8 1.0
CG2 H:VAL89 4.8 61.0 1.0
N L:GLY41 4.8 71.3 1.0
CD B:ARG189 4.8 0.4 1.0
HZ H:PHE91 4.9 76.0 1.0

Sodium binding site 2 out of 2 in 4jan

Go back to Sodium Binding Sites List in 4jan
Sodium binding site 2 out of 2 in the Crystal Structure of Broadly Neutralizing Antibody CH103 in Complex with Hiv-1 GP120


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Broadly Neutralizing Antibody CH103 in Complex with Hiv-1 GP120 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na301

b:65.5
occ:1.00
OE2 L:GLU3 2.3 87.0 1.0
HA3 H:GLY44 3.0 66.8 1.0
O L:GLY99 3.0 49.9 1.0
O H:LEU45 3.2 56.4 1.0
O H:LYS43 3.2 64.3 1.0
CD L:GLU3 3.4 84.6 1.0
H H:LEU45 3.5 63.0 1.0
HB2 L:PHE98 3.5 58.3 1.0
HA L:SER100 3.6 64.5 1.0
N H:LEU45 3.7 52.5 1.0
CA H:GLY44 3.7 55.6 1.0
C H:GLY44 3.8 53.0 1.0
C H:LEU45 4.0 54.8 1.0
HE2 L:TYR87 4.0 73.0 1.0
OE1 L:GLU3 4.0 86.4 1.0
C L:GLY99 4.1 49.7 1.0
C H:LYS43 4.1 62.5 1.0
O L:PHE98 4.2 44.4 1.0
HD2 L:TYR87 4.3 72.5 1.0
HB3 H:GLU46 4.3 68.3 1.0
N H:GLY44 4.3 60.2 1.0
HG2 L:GLU3 4.3 96.6 1.0
HB3 L:PHE98 4.4 58.3 1.0
CB L:PHE98 4.4 48.5 1.0
CA H:LEU45 4.4 53.6 1.0
CA L:SER100 4.4 53.7 1.0
HA2 H:GLY44 4.5 66.8 1.0
CG L:GLU3 4.5 80.5 1.0
C L:PHE98 4.5 45.4 1.0
O H:GLY44 4.6 49.5 1.0
HB3 H:LEU45 4.6 64.4 1.0
HB3 L:GLU3 4.6 91.1 1.0
N L:SER100 4.7 51.4 1.0
CE2 L:TYR87 4.7 60.8 1.0
CD2 L:TYR87 4.9 60.4 1.0
HA H:GLU46 4.9 65.9 1.0
N L:GLY99 4.9 47.1 1.0
N H:GLU46 4.9 53.8 1.0
H L:PHE98 5.0 53.8 1.0

Reference:

H.X.Liao, R.Lynch, T.Zhou, F.Gao, S.M.Alam, S.D.Boyd, A.Z.Fire, K.M.Roskin, C.A.Schramm, Z.Zhang, J.Zhu, L.Shapiro, J.C.Mullikin, S.Gnanakaran, P.Hraber, K.Wiehe, G.Kelsoe, G.Yang, S.M.Xia, D.C.Montefiori, R.Parks, K.E.Lloyd, R.M.Scearce, K.A.Soderberg, M.Cohen, G.Kamanga, M.K.Louder, L.M.Tran, Y.Chen, F.Cai, S.Chen, S.Moquin, X.Du, M.G.Joyce, S.Srivatsan, B.Zhang, A.Zheng, G.M.Shaw, B.H.Hahn, T.B.Kepler, B.T.Korber, P.D.Kwong, J.R.Mascola, B.F.Haynes. Co-Evolution of A Broadly Neutralizing Hiv-1 Antibody and Founder Virus. Nature V. 496 469 2013.
ISSN: ISSN 0028-0836
PubMed: 23552890
DOI: 10.1038/NATURE12053
Page generated: Tue Dec 15 06:46:05 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy