Calcium in PDB 4jo1: Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Jr-Fl GP120

The structure of Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Jr-Fl GP120, PDB code: 4jo1 was solved by R.M.Pan, X.P.Kong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.23 / 2.03
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.514, 74.347, 84.438, 90.00, 90.01, 90.00
R / Rfree (%)	18.1 / 22.3

The binding sites of Calcium atom in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Jr-Fl GP120 (pdb code 4jo1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Jr-Fl GP120, PDB code: 4jo1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Jr-Fl 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 Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Jr-Fl GP120 within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca301 b:21.9 occ:1.00 O L:HOH426 3.2 24.1 1.0 O H:HOH408 3.3 21.9 1.0 N H:TRP47 3.3 16.1 1.0 O H:HOH550 3.3 37.3 1.0 N L:PHE98 3.3 17.4 1.0 CA H:GLU46 3.8 17.8 1.0 CA L:ALA97 3.9 14.8 1.0 CD2 L:PHE98 4.0 16.2 1.0 C H:GLU46 4.0 18.5 1.0 CB H:TRP47 4.0 15.0 1.0 CB L:PHE98 4.0 15.6 1.0 C L:ALA97 4.1 19.1 1.0 CG H:GLU46 4.2 16.9 1.0 CA H:TRP47 4.2 15.3 1.0 CA L:PHE98 4.3 17.9 1.0 O H:LEU45 4.4 17.8 1.0 CB H:GLU46 4.5 14.3 1.0 CG L:PHE98 4.5 14.3 1.0 O H:HOH440 4.5 29.1 1.0 O L:PHE98 4.6 15.3 1.0 O H:TRP47 4.6 14.8 1.0 CB L:ALA97 4.7 14.6 1.0 O L:HOH405 4.7 21.0 1.0 O L:ALA96 4.8 16.8 1.0 N H:GLU46 4.9 15.2 1.0 N L:ALA97 4.9 14.7 1.0 O H:HOH467 5.0 35.7 1.0 C L:PHE98 5.0 15.6 1.0 C H:TRP47 5.0 18.2 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Jr-Fl 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 Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Jr-Fl GP120 within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca302 b:39.3 occ:1.00 N L:SER9 3.2 17.1 1.0 O L:HOH550 3.5 31.5 1.0 CA L:PRO8 3.6 19.0 1.0 C L:PRO8 3.8 21.0 1.0 CB L:PRO8 4.0 20.2 1.0 OG L:SER9 4.1 34.9 1.0 CB L:SER9 4.1 22.2 1.0 CA L:SER9 4.3 19.7 1.0 CB L:THR7 4.7 22.4 1.0 CG2 L:THR7 4.7 23.6 1.0 CA L:THR7 4.8 19.7 1.0 N L:PRO8 4.9 21.1 1.0 O L:HOH487 4.9 41.0 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Jr-Fl GP120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Jr-Fl GP120 within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca301 b:28.3 occ:1.00 O H:HOH562 3.1 31.6 1.0 O H:HOH429 3.2 29.2 1.0 N H:TYR59 3.3 21.5 1.0 O L:HOH562 3.6 38.6 1.0 CA H:ALA58 3.8 15.4 1.0 CD1 H:TYR59 3.9 15.4 1.0 C H:ALA58 4.0 18.7 1.0 O H:TYR59 4.1 15.6 1.0 CA H:TYR59 4.2 17.0 1.0 CD H:LYS64 4.2 20.5 1.0 CB H:TYR59 4.2 15.4 1.0 CB H:ALA58 4.4 17.0 1.0 CG H:LYS64 4.5 19.8 1.0 CE H:LYS64 4.6 27.5 1.0 CG H:TYR59 4.6 19.2 1.0 C H:TYR59 4.6 22.7 1.0 O H:ALA57 4.7 18.5 1.0 O H:HOH409 4.7 19.8 1.0 O L:HOH462 4.9 36.4 1.0 CE1 H:TYR59 5.0 17.0 1.0 N H:ALA58 5.0 16.0 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Jr-Fl GP120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Jr-Fl GP120 within 5.0Å range: probe atom residue distance (Å) B Occ M:Ca301 b:19.3 occ:1.00 O I:HOH408 3.2 18.9 1.0 O M:HOH445 3.3 29.9 1.0 N I:TRP47 3.3 14.1 1.0 N M:PHE98 3.4 20.6 1.0 O I:HOH512 3.5 37.1 1.0 CA I:GLU46 3.8 15.0 1.0 CA M:ALA97 3.9 15.7 1.0 CD2 M:PHE98 4.0 13.1 1.0 CB I:TRP47 4.0 14.0 1.0 C I:GLU46 4.0 20.2 1.0 CB M:PHE98 4.0 13.9 1.0 C M:ALA97 4.1 20.5 1.0 CG I:GLU46 4.2 16.2 1.0 CA I:TRP47 4.2 16.0 1.0 CA M:PHE98 4.3 19.9 1.0 O I:LEU45 4.3 19.1 1.0 CB I:GLU46 4.5 14.2 1.0 CG M:PHE98 4.5 14.1 1.0 O M:PHE98 4.6 13.1 1.0 O I:TRP47 4.6 14.4 1.0 O I:HOH424 4.7 26.4 1.0 CB M:ALA97 4.7 13.8 1.0 O M:HOH559 4.8 21.4 1.0 N I:GLU46 4.8 14.6 1.0 O M:ALA96 4.9 18.6 1.0 N M:ALA97 4.9 15.3 1.0 C M:PHE98 5.0 14.9 1.0 C I:TRP47 5.0 16.8 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Jr-Fl GP120


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Rabbit Mab R56 Fab in Complex with V3 Crown of Hiv-1 Jr-Fl GP120 within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca301 b:27.6 occ:1.00 O I:HOH436 3.1 31.2 1.0 O I:HOH434 3.2 27.1 1.0 N I:TYR59 3.3 17.4 1.0 CA I:ALA58 3.8 14.8 1.0 CD1 I:TYR59 4.0 14.5 1.0 C I:ALA58 4.0 18.2 1.0 O I:TYR59 4.1 15.9 1.0 CA I:TYR59 4.3 18.1 1.0 CD I:LYS64 4.3 23.4 1.0 CB I:TYR59 4.3 14.1 1.0 CB I:ALA58 4.4 18.9 1.0 CG I:LYS64 4.5 20.0 1.0 CE I:LYS64 4.6 31.5 1.0 C I:TYR59 4.6 19.9 1.0 O I:ALA57 4.7 17.9 1.0 CG I:TYR59 4.7 16.8 1.0 O M:HOH412 4.8 21.0 1.0 O M:HOH534 4.8 31.6 1.0 N I:ALA58 4.9 14.8 1.0

R.Pan, J.M.Sampson, Y.Chen, M.Vaine, S.Wang, S.Lu, X.P.Kong. Rabbit Anti-Hiv-1 Monoclonal Antibodies Raised By Immunization Can Mimic the Antigen-Binding Modes of Antibodies Derived From Hiv-1-Infected Humans. J.Virol. V. 87 10221 2013.
ISSN: ISSN 0022-538X
PubMed: 23864637
DOI: 10.1128/JVI.00843-13