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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: Mon Oct 7 16:13:57 2024

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