Sodium in PDB 4jzz: Crystal Structure of CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group

The structure of Crystal Structure of CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group, PDB code: 4jzz was solved by P.Acharya, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.26 / 1.49
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	65.087, 164.719, 78.031, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 18.9

The binding sites of Sodium atom in the Crystal Structure of CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group (pdb code 4jzz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group, PDB code: 4jzz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Crystal Structure of CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group


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 CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:28.9 occ:1.00 O A:VAL372 2.8 19.0 1.0 O A:HOH713 2.8 33.2 1.0 N A:SER387 3.0 19.8 1.0 CA A:ASN386 3.4 18.6 1.0 OD1 A:ASN386 3.5 25.8 1.0 OG A:SER387 3.6 21.3 1.0 CA A:THR373 3.6 17.6 1.0 C A:ASN386 3.6 21.0 1.0 C A:VAL372 3.6 19.6 1.0 CG A:ASN386 3.9 26.0 1.0 O A:HOH642 3.9 27.0 1.0 N A:THR373 4.0 19.0 1.0 CG2 A:THR373 4.0 21.6 1.0 CA A:SER387 4.0 20.0 1.0 O A:CYS385 4.1 19.3 1.0 N A:THR388 4.1 22.1 1.0 CB A:ASN386 4.2 21.3 1.0 CG1 A:VAL372 4.2 29.2 1.0 CB A:THR373 4.2 16.6 1.0 CB A:SER387 4.3 19.5 1.0 C A:SER387 4.4 20.7 1.0 N A:ASN386 4.5 19.7 1.0 N2 A:NAG507 4.5 41.2 0.5 OG1 A:THR388 4.5 31.4 1.0 NA A:NA515 4.6 43.7 1.0 O7 A:NAG507 4.7 51.4 0.5 C A:CYS385 4.7 19.7 1.0 C A:THR373 4.7 17.2 1.0 ND2 A:ASN386 4.7 31.4 1.0 O A:ASN386 4.8 22.0 1.0 CA A:VAL372 4.9 18.5 1.0 N A:HIS374 4.9 18.3 1.0 C7 A:NAG507 5.0 45.4 0.5

Sodium binding site 2 out of 6 in the Crystal Structure of CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group


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 CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Na514 b:24.6 occ:1.00 O A:HOH852 2.7 23.9 1.0 OG A:SER256 2.8 16.3 1.0 N A:LEU261 2.8 15.2 1.0 CG1 A:VAL254 3.4 18.7 1.0 CA A:LEU260 3.4 14.7 1.0 O A:HOH618 3.5 23.3 1.0 CB A:VAL254 3.6 15.1 1.0 C A:LEU260 3.6 15.7 1.0 O A:VAL254 3.7 16.1 1.0 O A:LEU261 3.7 16.3 1.0 CB A:SER256 3.7 16.7 1.0 CA A:LEU261 3.8 14.2 1.0 O A:LEU259 3.8 16.9 1.0 CB A:LEU261 3.9 16.3 1.0 ND2 A:ASN478 3.9 16.1 1.0 CD2 A:LEU260 4.1 17.6 1.0 C A:VAL254 4.2 15.5 1.0 CG A:LEU261 4.2 18.3 1.0 C A:LEU261 4.2 14.8 1.0 CB A:LEU260 4.2 15.6 1.0 CA A:VAL254 4.5 14.9 1.0 N A:LEU260 4.5 14.6 1.0 C A:LEU259 4.6 16.9 1.0 N A:SER256 4.6 14.1 1.0 CG2 A:VAL254 4.7 19.5 1.0 CA A:SER256 4.8 14.2 1.0 CG A:LEU260 4.8 16.5 1.0 O A:LEU260 4.8 16.1 1.0 CD1 A:LEU261 4.9 20.3 1.0 CG A:ASN478 5.0 16.1 1.0 N A:VAL255 5.0 14.4 1.0

Sodium binding site 3 out of 6 in the Crystal Structure of CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Na515 b:43.7 occ:1.00 O A:HOH713 2.6 33.2 1.0 O A:HOH784 2.8 42.3 1.0 O A:SER364 3.5 28.6 1.0 CB A:PRO363 3.8 28.9 1.0 CG1 A:VAL372 3.8 29.2 1.0 O A:HOH835 4.3 43.3 1.0 N A:SER364 4.3 25.1 1.0 C A:SER364 4.4 28.6 1.0 OG1 A:THR388 4.4 31.4 1.0 NA A:NA509 4.6 28.9 1.0 CB A:SER364 4.6 26.0 1.0 N2 A:NAG507 4.6 41.2 0.5 O A:HOH898 4.7 52.3 1.0 O A:HOH642 4.7 27.0 1.0 CA A:SER364 4.7 22.4 1.0 C A:PRO363 4.8 25.1 1.0 O A:VAL372 4.8 19.0 1.0 O7 A:NAG507 4.8 51.4 0.5 CG A:PRO363 4.8 29.1 1.0 CA A:PRO363 4.9 25.1 1.0

Sodium binding site 4 out of 6 in the Crystal Structure of CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Na516 b:23.4 occ:1.00 O A:PRO253 2.7 16.8 1.0 O A:HOH604 2.9 17.1 1.0 NE2 A:HIS66 2.9 18.3 1.0 NE1 A:TRP112 3.0 16.7 1.0 CZ A:PHE210 3.6 17.4 1.0 CE1 A:HIS66 3.7 17.1 1.0 C A:PRO253 3.9 16.7 1.0 CE2 A:TRP112 3.9 16.2 1.0 CD2 A:HIS66 3.9 15.7 1.0 CD1 A:TRP112 4.0 15.7 1.0 CG2 A:VAL255 4.1 15.3 1.0 CZ2 A:TRP112 4.1 16.8 1.0 CG A:PRO253 4.2 15.7 1.0 CG A:PRO212 4.2 18.3 1.0 CE2 A:PHE210 4.3 20.2 1.0 CB A:PRO253 4.4 15.2 1.0 CE1 A:PHE210 4.4 17.8 1.0 CG2 A:ILE108 4.4 17.0 1.0 N A:VAL255 4.6 14.4 1.0 CB A:PRO212 4.7 18.8 1.0 CA A:VAL254 4.7 14.9 1.0 CA A:PRO253 4.7 15.6 1.0 N A:VAL254 4.7 15.7 1.0 ND1 A:HIS66 4.9 18.1 1.0 CB A:VAL255 4.9 14.2 1.0 CD2 A:LEU111 5.0 21.8 1.0

Sodium binding site 5 out of 6 in the Crystal Structure of CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Na517 b:26.6 occ:1.00 O A:HOH621 2.8 20.7 1.0 O A:HOH604 2.8 17.1 1.0 O7 A:NAG504 2.8 22.9 1.0 O A:ASN377 2.9 21.8 1.0 O A:HOH819 3.3 40.3 1.0 CG A:PRO212 3.5 18.3 1.0 C8 A:NAG504 3.5 21.2 1.0 C7 A:NAG504 3.5 21.3 1.0 CE1 A:PHE210 3.6 17.8 1.0 CD A:PRO212 3.8 18.3 1.0 CG1 A:VAL254 4.0 18.7 1.0 C A:ASN377 4.1 18.6 1.0 CZ A:PHE210 4.4 17.4 1.0 CD1 A:PHE210 4.5 20.9 1.0 CB A:ASN377 4.5 20.9 1.0 N A:ASN377 4.6 17.8 1.0 CA A:ASN377 4.6 16.8 1.0 CA A:VAL254 4.7 14.9 1.0 CB A:VAL254 4.7 15.1 1.0 CG2 A:VAL254 4.8 19.5 1.0 N2 A:NAG504 4.9 19.8 1.0 N A:VAL255 4.9 14.4 1.0 O A:HOH607 4.9 20.1 1.0 CB A:PRO212 4.9 18.8 1.0

Sodium binding site 6 out of 6 in the Crystal Structure of CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of CD4-Mimetic Miniprotein M48U1 in Complex with Hiv-1 YU2 GP120 in C2221 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Na518 b:52.5 occ:1.00 O A:HOH875 2.2 36.7 1.0 OD2 A:ASP113 3.2 37.4 1.0 OE2 A:GLU429 3.6 54.9 1.0 CG2 A:ILE109 3.7 18.0 1.0 CD A:GLU429 3.7 47.0 1.0 OE1 A:GLU429 4.0 43.7 1.0 CB A:GLN428 4.1 23.1 1.0 CG A:ASP113 4.2 36.0 1.0 CG A:GLU429 4.2 36.2 1.0 OD1 A:ASP113 4.4 40.0 1.0 O A:GLN428 4.4 25.3 1.0 CB A:GLU429 4.4 27.1 1.0 C A:GLN428 4.6 24.0 1.0 O A:HOH848 4.9 48.7 1.0

P.Acharya, T.S.Luongo, M.K.Louder, K.Mckee, Y.Yang, Y.Do Kwon, J.R.Mascola, P.Kessler, L.Martin, P.D.Kwong. Structural Basis For Highly Effective Hiv-1 Neutralization By CD4-Mimetic Miniproteins Revealed By 1.5 A Cocrystal Structure of GP120 and M48U1. Structure V. 21 1018 2013.
ISSN: ISSN 0969-2126
PubMed: 23707685
DOI: 10.1016/J.STR.2013.04.015