Sodium in PDB 6p8m: Crystal Structure of Antibody P-P3B3 A60C Heavy Chain in Complex with 426C Hiv-1 GP120 Core G459C

The structure of Crystal Structure of Antibody P-P3B3 A60C Heavy Chain in Complex with 426C Hiv-1 GP120 Core G459C, PDB code: 6p8m was solved by C.Weidle, M.Pancera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.59
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	146.796, 176.755, 108.573, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 26.8

The structure of Crystal Structure of Antibody P-P3B3 A60C Heavy Chain in Complex with 426C Hiv-1 GP120 Core G459C also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Antibody P-P3B3 A60C Heavy Chain in Complex with 426C Hiv-1 GP120 Core G459C (pdb code 6p8m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Antibody P-P3B3 A60C Heavy Chain in Complex with 426C Hiv-1 GP120 Core G459C, PDB code: 6p8m:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Antibody P-P3B3 A60C Heavy Chain in Complex with 426C Hiv-1 GP120 Core G459C


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 Antibody P-P3B3 A60C Heavy Chain in Complex with 426C Hiv-1 GP120 Core G459C within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1408 b:13.9 occ:1.00 HD3 C:PRO437 3.2 93.3 1.0 HA C:ALA436 3.6 64.8 1.0 OE1 C:GLN422 3.9 71.6 1.0 CD C:PRO437 4.1 77.5 1.0 O C:TYR435 4.2 75.2 1.0 HG22 C:ILE434 4.2 77.2 1.0 HG3 C:PRO437 4.4 91.9 1.0 HD2 C:PRO437 4.6 93.3 1.0 CA C:ALA436 4.6 53.8 1.0 HG21 C:ILE434 4.6 77.2 1.0 CG C:PRO437 4.8 76.4 1.0 CG2 C:ILE434 4.8 64.2 1.0 HB2 C:CYS119 4.9 48.9 1.0 C C:TYR435 5.0 74.0 1.0 CD C:GLN422 5.0 89.4 1.0 N C:PRO437 5.0 58.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Antibody P-P3B3 A60C Heavy Chain in Complex with 426C Hiv-1 GP120 Core G459C


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 Antibody P-P3B3 A60C Heavy Chain in Complex with 426C Hiv-1 GP120 Core G459C within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1409 b:27.8 occ:0.50 HG2 C:LYS421 3.6 0.6 1.0 HE3 C:LYS421 3.7 85.5 1.0 HG3 C:GLN422 4.4 90.5 1.0 HD12 C:ILE423 4.4 97.7 1.0 HE21 C:GLN422 4.5 0.8 1.0 H C:GLN422 4.5 61.2 1.0 CG C:LYS421 4.6 85.3 1.0 CE C:LYS421 4.6 71.0 1.0 HA C:LYS421 4.6 64.0 1.0 HB3 C:LYS421 4.7 85.9 1.0 H C:ILE423 4.8 69.9 1.0 HB C:ILE423 4.8 85.7 1.0 HE2 C:LYS421 4.8 85.5 1.0 HG13 C:ILE423 4.9 91.5 1.0 HG2 C:GLN422 4.9 90.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Antibody P-P3B3 A60C Heavy Chain in Complex with 426C Hiv-1 GP120 Core G459C


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 Antibody P-P3B3 A60C Heavy Chain in Complex with 426C Hiv-1 GP120 Core G459C within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1410 b:38.6 occ:0.50 HD22 C:LEU201 3.6 83.0 1.0 HZ1 C:LYS121 3.8 80.1 1.0 HD21 C:LEU201 4.2 83.0 1.0 CD2 C:LEU201 4.3 69.0 1.0 HD13 C:LEU201 4.4 70.7 1.0 NZ C:LYS121 4.6 66.6 1.0 HE2 C:LYS121 4.8 0.6 1.0 HZ3 C:LYS121 4.8 80.1 1.0 HD23 C:LEU201 5.0 83.0 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Antibody P-P3B3 A60C Heavy Chain in Complex with 426C Hiv-1 GP120 Core G459C


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 Antibody P-P3B3 A60C Heavy Chain in Complex with 426C Hiv-1 GP120 Core G459C within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:45.4 occ:1.00 O H:VAL111 3.4 81.6 1.0 HG1 H:THR87 3.6 98.7 1.0 HB3 H:SER84 3.7 92.7 1.0 HB3 H:SER112 3.8 80.2 1.0 OG1 H:THR87 4.4 82.0 1.0 CB H:SER84 4.5 77.1 1.0 HG21 H:THR87 4.5 88.4 1.0 HG H:SER84 4.5 83.0 1.0 OG H:SER84 4.6 69.0 1.0 CB H:SER112 4.6 66.6 1.0 HA H:SER84 4.6 0.8 1.0 HB2 H:SER112 4.6 80.2 1.0 C H:VAL111 4.6 74.6 1.0 H H:VAL111 4.9 77.9 1.0 HA H:SER112 4.9 88.6 1.0

K.R.Parks, A.Maccamy, J.Trichka, M.Gray, C.Weidle, A.Borst, A.Khechaduri, B.Takushi, J.Guenaga, R.Wyatt, R.Coler, C.Labranche, D.Veesler, D.C.Montefiori, M.Pancera, A.Mcguire, L.Stamatatos. Overcoming Key Steric Restrictions in the Maturation of VRC01-Class Hiv-1 Neutralizing Antibodies During Immunization To Be Published.