Sodium in PDB 3ma9: Crystal Structure of GP41 Derived Protein Complexed with Fab 8066

The structure of Crystal Structure of GP41 Derived Protein Complexed with Fab 8066, PDB code: 3ma9 was solved by M.Li, E.Gustchina, J.Louis, A.Gustchina, A.Wlodawer, M.Clore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.45 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.527, 124.698, 133.657, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.5

The binding sites of Sodium atom in the Crystal Structure of GP41 Derived Protein Complexed with Fab 8066 (pdb code 3ma9). 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 GP41 Derived Protein Complexed with Fab 8066, PDB code: 3ma9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of GP41 Derived Protein Complexed with Fab 8066


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 GP41 Derived Protein Complexed with Fab 8066 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na245 b:35.4 occ:1.00 OD1 H:ASN58 2.7 24.6 1.0 O L:VAL95 2.7 30.8 1.0 OG H:SER50 2.9 25.2 1.0 NE1 A:TRP30 3.0 34.8 1.0 CB H:SER50 3.1 20.7 1.0 CZ3 L:TRP90 3.5 27.2 1.0 CG H:ASN58 3.5 32.6 1.0 ND2 H:ASN58 3.5 32.0 1.0 OH H:TYR98 3.7 26.0 1.0 CE2 A:TRP30 3.8 35.2 1.0 C L:VAL95 3.8 35.0 1.0 CB L:VAL95 3.8 38.7 1.0 CG2 L:VAL95 3.9 27.8 1.0 CZ2 A:TRP30 3.9 29.0 1.0 CZ2 H:TRP47 3.9 24.9 1.0 CD1 A:TRP30 4.1 32.7 1.0 CE3 L:TRP90 4.1 32.7 1.0 CH2 L:TRP90 4.2 30.1 1.0 NE2 A:GLN34 4.3 28.3 1.0 CA L:VAL95 4.4 28.7 1.0 CA H:SER50 4.5 22.0 1.0 N H:SER50 4.7 24.7 1.0 CH2 H:TRP47 4.7 30.1 1.0 CZ H:TYR98 4.8 28.0 1.0 CE2 H:TRP47 4.8 28.0 1.0 NE1 H:TRP47 4.9 30.3 1.0 N L:ASP96 4.9 31.7 1.0 CB H:ASN58 5.0 26.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of GP41 Derived Protein Complexed with Fab 8066


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 GP41 Derived Protein Complexed with Fab 8066 within 5.0Å range: probe atom residue distance (Å) B Occ L:Na214 b:59.4 occ:1.00 O L:GLY24 3.0 39.7 1.0 OD1 L:ASN26 3.1 59.1 1.0 ND2 L:ASN68 3.2 44.6 1.0 C L:GLY24 3.5 42.0 1.0 O L:HOH233 3.7 22.0 1.0 CA L:GLY24 3.7 40.2 1.0 O L:ASP25 3.8 40.3 1.0 CB L:ASN68 3.8 44.1 1.0 O L:HOH375 4.0 34.5 1.0 CG L:ASN68 4.0 42.5 1.0 CG L:ASN26 4.2 51.6 1.0 C L:ASP25 4.4 41.3 1.0 N L:ASP25 4.5 35.9 1.0 N L:GLY24 4.6 40.6 1.0 ND2 L:ASN26 4.7 43.0 1.0

E.Gustchina, M.Li, J.M.Louis, D.E.Anderson, J.Lloyd, C.Frisch, C.A.Bewley, A.Gustchina, A.Wlodawer, G.M.Clore. Structural Basis of Hiv-1 Neutralization By Affinity Matured Fabs Directed Against the Internal Trimeric Coiled-Coil of GP41. Plos Pathog. V. 6 01182 2010.
ISSN: ISSN 1553-7366
PubMed: 21085615
DOI: 10.1371/JOURNAL.PPAT.1001182