Calcium in PDB 4j6r: Crystal Structure of Broadly and Potently Neutralizing Antibody VRC23 in Complex with Hiv-1 GP120

The structure of Crystal Structure of Broadly and Potently Neutralizing Antibody VRC23 in Complex with Hiv-1 GP120, PDB code: 4j6r was solved by T.Zhou, S.Moquin, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.17 / 1.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.044, 68.692, 214.534, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.8

The binding sites of Calcium atom in the Crystal Structure of Broadly and Potently Neutralizing Antibody VRC23 in Complex with Hiv-1 GP120 (pdb code 4j6r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Broadly and Potently Neutralizing Antibody VRC23 in Complex with Hiv-1 GP120, PDB code: 4j6r:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Broadly and Potently Neutralizing Antibody VRC23 in Complex with Hiv-1 GP120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Broadly and Potently Neutralizing Antibody VRC23 in Complex with Hiv-1 GP120 within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca510 b:39.2 occ:1.00 HZ3 G:LYS421 2.3 50.8 1.0 H G:GLN422 2.5 38.6 1.0 H G:ILE423 2.6 41.2 1.0 HA G:LYS421 3.0 42.0 1.0 HB3 G:LYS421 3.1 40.8 1.0 NZ G:LYS421 3.2 42.4 1.0 HG2 G:LYS421 3.2 39.9 1.0 N G:GLN422 3.2 32.2 1.0 HB G:ILE423 3.3 47.3 1.0 HZ2 G:LYS421 3.3 50.8 1.0 O G:HOH862 3.4 58.8 1.0 N G:ILE423 3.4 34.3 1.0 HZ1 G:LYS421 3.6 50.8 1.0 CB G:LYS421 3.6 34.0 1.0 HG13 G:ILE423 3.6 58.9 1.0 CA G:LYS421 3.6 35.0 1.0 HH11 G:ARG327 3.6 90.6 1.0 HD12 G:ILE423 3.7 62.8 1.0 OE1 G:GLN422 3.7 50.7 1.0 HB2 G:GLN422 3.8 55.8 1.0 CG G:LYS421 3.8 33.3 1.0 C G:LYS421 3.9 31.8 1.0 CB G:ILE423 4.0 39.5 1.0 CG1 G:ILE423 4.1 49.1 1.0 HE3 G:LYS421 4.2 41.4 1.0 NH1 G:ARG327 4.2 75.5 1.0 CA G:GLN422 4.2 38.5 1.0 CE G:LYS421 4.2 34.5 1.0 HH12 G:ARG327 4.2 90.6 1.0 CA G:ILE423 4.2 37.6 1.0 O G:ILE423 4.3 33.4 1.0 C G:GLN422 4.3 36.8 1.0 CD1 G:ILE423 4.3 52.4 1.0 CD G:GLN422 4.4 42.6 1.0 CB G:GLN422 4.4 46.5 1.0 HB2 G:LYS421 4.5 40.8 1.0 HD2 G:ARG327 4.5 69.0 1.0 HG3 G:LYS421 4.6 39.9 1.0 CD G:LYS421 4.6 29.7 1.0 C G:ILE423 4.8 36.9 1.0 HD11 G:ILE423 4.8 62.8 1.0 HD3 G:ARG327 4.9 69.0 1.0 O G:ILE420 4.9 39.7 1.0 N G:LYS421 5.0 28.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Broadly and Potently Neutralizing Antibody VRC23 in Complex with Hiv-1 GP120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Broadly and Potently Neutralizing Antibody VRC23 in Complex with Hiv-1 GP120 within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca301 b:61.3 occ:1.00 HH11 L:ARG15 2.1 34.6 1.0 O L:HOH743 2.3 55.5 1.0 O L:HOH540 2.7 38.2 1.0 HD2 L:ARG15 2.8 38.4 1.0 NH1 L:ARG15 2.9 28.8 1.0 HD3 L:ARG15 3.0 38.4 1.0 O L:HOH537 3.2 38.1 1.0 O L:HOH440 3.3 22.3 1.0 HH12 L:ARG15 3.3 34.6 1.0 CD L:ARG15 3.3 32.0 1.0 HG2 L:PRO80 3.5 30.2 1.0 HG3 L:PRO80 3.6 30.2 1.0 H13 L:BU3305 3.7 69.3 1.0 CZ L:ARG15 3.9 30.8 1.0 CG L:PRO80 4.0 25.1 1.0 NE L:ARG15 4.1 35.9 1.0 HB2 L:ARG15 4.1 33.1 1.0 HO6 L:BU3305 4.2 67.4 1.0 OG L:SER171 4.2 20.6 1.0 HG L:SER171 4.3 24.8 1.0 O L:LYS169 4.4 22.3 1.0 HD3 L:PRO80 4.5 28.0 1.0 CG L:ARG15 4.6 36.8 1.0 HG21 L:ILE106 4.6 34.4 1.0 C1 L:BU3305 4.6 57.8 1.0 HB3 L:ARG15 4.6 33.1 1.0 CB L:ARG15 4.7 27.6 1.0 CD L:PRO80 4.8 23.4 1.0 H12 L:BU3305 4.8 69.3 1.0 O6 L:BU3305 4.8 56.2 1.0 HE L:ARG15 4.9 43.1 1.0 H11 L:BU3305 5.0 69.3 1.0

I.S.Georgiev, N.A.Doria-Rose, T.Zhou, Y.D.Kwon, R.P.Staupe, S.Moquin, G.Y.Chuang, M.K.Louder, S.D.Schmidt, H.R.Altae-Tran, R.T.Bailer, K.Mckee, M.Nason, S.O'dell, G.Ofek, M.Pancera, S.Srivatsan, L.Shapiro, M.Connors, S.A.Migueles, L.Morris, Y.Nishimura, M.A.Martin, J.R.Mascola, P.D.Kwong. Delineating Antibody Recognition in Polyclonal Sera From Patterns of Hiv-1 Isolate Neutralization. Science V. 340 751 2013.
ISSN: ISSN 0036-8075
PubMed: 23661761
DOI: 10.1126/SCIENCE.1233989