Sodium in PDB 4bz2: Structure of Dengue Virus Ediii in Complex with Fab 2D73

The structure of Structure of Dengue Virus Ediii in Complex with Fab 2D73, PDB code: 4bz2 was solved by J.Li, D.Watterson, C.W.Chang, X.Q.Li, D.J.Ericsson, L.W.Qiu, J.P.Cai, J.Chen, S.R.Fry, M.A.Cooper, X.Y.Che, P.R.Young, B.Kobe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.592 / 2.03
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	108.655, 108.655, 108.564, 90.00, 90.00, 90.00
R / Rfree (%)	20.52 / 22.47

The structure of Structure of Dengue Virus Ediii in Complex with Fab 2D73 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Structure of Dengue Virus Ediii in Complex with Fab 2D73 (pdb code 4bz2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure of Dengue Virus Ediii in Complex with Fab 2D73, PDB code: 4bz2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Structure of Dengue Virus Ediii in Complex with Fab 2D73


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Dengue Virus Ediii in Complex with Fab 2D73 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1397 b:54.0 occ:1.00 O A:GLY381 2.7 44.0 1.0 O A:VAL379 2.8 35.4 1.0 HG13 A:VAL379 2.8 48.7 1.0 HA A:ILE337 2.9 53.2 1.0 HB2 A:PRO336 3.2 52.7 1.0 H A:GLY381 3.3 38.8 1.0 HA A:ILE380 3.3 50.9 1.0 O A:PRO336 3.3 38.6 1.0 C A:VAL379 3.4 37.4 1.0 HG2 A:GLU338 3.4 72.4 1.0 C A:PRO336 3.5 45.0 1.0 N A:GLY381 3.5 32.3 1.0 CA A:ILE337 3.6 44.4 1.0 H A:GLU338 3.6 51.1 1.0 N A:ILE337 3.6 44.7 1.0 HB A:VAL379 3.6 42.6 1.0 CG1 A:VAL379 3.6 40.6 1.0 C A:GLY381 3.8 37.7 1.0 O A:HOH2022 3.8 47.9 1.0 CA A:ILE380 3.8 42.4 1.0 C A:ILE380 3.8 37.2 1.0 N A:ILE380 3.8 43.5 1.0 HG12 A:VAL379 3.9 48.7 1.0 CB A:PRO336 4.0 43.9 1.0 N A:GLU338 4.1 42.6 1.0 CB A:VAL379 4.1 35.5 1.0 H A:ILE337 4.1 53.6 1.0 C A:ILE337 4.2 46.2 1.0 HB3 A:PRO336 4.2 52.7 1.0 CA A:GLY381 4.2 34.6 1.0 CA A:PRO336 4.3 40.2 1.0 CG A:GLU338 4.4 60.3 1.0 HG11 A:VAL379 4.4 48.7 1.0 CA A:VAL379 4.4 34.2 1.0 HG13 A:VAL382 4.4 71.0 1.0 H A:ILE380 4.5 52.2 1.0 HA2 A:GLY381 4.6 41.5 1.0 O A:ILE380 4.7 37.3 1.0 HA A:VAL382 4.7 61.3 1.0 HG3 A:GLU338 4.7 72.4 1.0 HA A:PRO336 4.8 48.2 1.0 HG11 A:VAL382 4.8 71.0 1.0 HG13 A:ILE337 4.9 63.1 1.0 N A:VAL382 4.9 44.9 1.0 CB A:ILE337 4.9 50.7 1.0 HB2 A:ALA386 5.0 57.5 1.0 HA A:VAL379 5.0 41.0 1.0 HB A:ILE337 5.0 60.8 1.0 CD A:GLU338 5.0 73.2 1.0

Sodium binding site 2 out of 8 in the Structure of Dengue Virus Ediii in Complex with Fab 2D73


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Dengue Virus Ediii in Complex with Fab 2D73 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1398 b:68.1 occ:1.00 OE2 A:GLU338 2.4 76.2 1.0 HE A:ARG340 2.6 75.6 1.0 CD A:GLU338 3.2 73.2 1.0 OE1 A:GLU338 3.3 74.7 1.0 NE A:ARG340 3.4 63.0 1.0 HH21 A:ARG340 3.5 77.1 1.0 HG21 A:VAL347 3.6 55.5 1.0 HG23 A:VAL347 3.6 55.5 1.0 HG22 A:VAL347 3.9 55.5 1.0 HD3 A:ARG340 3.9 57.8 1.0 CG2 A:VAL347 3.9 46.2 1.0 NH2 A:ARG340 4.1 64.3 1.0 CD A:ARG340 4.2 48.2 1.0 CZ A:ARG340 4.2 63.1 1.0 HG2 A:ARG340 4.4 45.6 1.0 CG A:GLU338 4.6 60.3 1.0 HG3 A:GLU338 4.7 72.4 1.0 CG A:ARG340 4.9 38.0 1.0 HH22 A:ARG340 4.9 77.1 1.0 O A:GLU345 4.9 44.5 1.0 HD2 A:ARG340 5.0 57.8 1.0

Sodium binding site 3 out of 8 in the Structure of Dengue Virus Ediii in Complex with Fab 2D73


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Dengue Virus Ediii in Complex with Fab 2D73 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1399 b:72.9 occ:1.00 O A:HOH2016 2.3 50.7 1.0 O A:HOH2019 2.7 44.2 1.0 O A:HOH2015 2.8 54.6 1.0 HG2 A:GLU314 3.2 53.1 1.0 HD2 A:ARG393 3.2 42.6 1.0 HA A:THR319 3.3 35.6 1.0 OG1 A:THR320 3.4 36.1 1.0 HE1 A:TRP391 3.5 38.0 1.0 C A:THR319 3.5 29.0 1.0 HG3 A:GLU314 3.5 53.1 1.0 O A:THR319 3.5 32.6 1.0 HG3 A:ARG393 3.6 40.6 1.0 HD2 A:PRO371 3.6 44.5 1.0 HG1 A:THR320 3.7 43.3 1.0 C A:GLY318 3.7 40.1 1.0 O A:GLY318 3.7 39.2 1.0 N A:THR319 3.7 33.2 1.0 CA A:THR319 3.7 29.7 1.0 CG A:GLU314 3.8 44.3 1.0 CD A:ARG393 3.9 35.5 1.0 NE A:ARG393 3.9 39.5 1.0 HZ2 A:TRP391 3.9 52.0 1.0 HE A:ARG393 3.9 47.4 1.0 HA2 A:GLY318 4.0 51.3 1.0 N A:THR320 4.0 29.2 1.0 H A:THR319 4.1 39.8 1.0 NE1 A:TRP391 4.2 31.7 1.0 CG A:ARG393 4.2 33.8 1.0 HB2 A:ARG393 4.3 38.4 1.0 H A:THR320 4.4 35.0 1.0 OE2 A:GLU314 4.4 50.2 1.0 HG2 A:PRO371 4.4 48.3 1.0 CA A:GLY318 4.4 42.8 1.0 CD A:GLU314 4.4 43.8 1.0 CZ A:ARG393 4.5 38.5 1.0 CB A:THR320 4.5 34.0 1.0 CD A:PRO371 4.6 37.1 1.0 CZ2 A:TRP391 4.6 43.4 1.0 HA A:GLU314 4.6 46.0 1.0 HA A:THR320 4.6 34.0 1.0 CA A:THR320 4.7 28.3 1.0 CE2 A:TRP391 4.7 31.6 1.0 HD3 A:ARG393 4.8 42.6 1.0 HB A:THR320 4.8 40.8 1.0 CB A:ARG393 4.8 32.0 1.0 HH11 A:ARG393 4.9 43.4 1.0 NH1 A:ARG393 4.9 36.1 1.0 CG A:PRO371 5.0 40.3 1.0 HG2 A:ARG393 5.0 40.6 1.0 HD3 A:PRO371 5.0 44.5 1.0

Sodium binding site 4 out of 8 in the Structure of Dengue Virus Ediii in Complex with Fab 2D73


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Dengue Virus Ediii in Complex with Fab 2D73 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na222 b:55.2 occ:1.00 CL H:CL223 2.5 0.1 1.0 O H:LYS43 2.7 50.8 1.0 H H:GLY42 2.9 71.9 1.0 HA2 H:GLY42 3.0 78.4 1.0 H H:LYS43 3.1 69.3 1.0 HE21 H:GLN39 3.1 61.9 1.0 N H:LYS43 3.2 57.7 1.0 C H:GLY42 3.3 61.8 1.0 CA H:GLY42 3.4 65.3 1.0 N H:GLY42 3.4 59.9 1.0 NE2 H:GLN39 3.5 51.6 1.0 HH L:TYR87 3.6 40.2 1.0 C H:LYS43 3.6 58.8 1.0 HE22 H:GLN39 3.7 61.9 1.0 HG2 H:GLN39 3.9 58.1 1.0 CA H:LYS43 4.0 59.3 1.0 O H:GLY42 4.0 63.6 1.0 CD H:GLN39 4.1 49.9 1.0 HG3 H:GLN39 4.1 58.1 1.0 OH L:TYR87 4.2 33.5 1.0 O H:SER40 4.2 55.7 1.0 CG H:GLN39 4.2 48.4 1.0 HA3 H:GLY42 4.4 78.4 1.0 HA H:LYS43 4.5 71.1 1.0 O L:HOH2034 4.6 54.8 1.0 CL L:CL214 4.6 85.8 1.0 C H:HIS41 4.6 58.7 1.0 HA H:HIS41 4.7 69.6 1.0 N H:SER44 4.8 51.0 1.0 HA H:SER44 4.9 63.3 1.0 OE1 H:GLN39 4.9 44.7 1.0

Sodium binding site 5 out of 8 in the Structure of Dengue Virus Ediii in Complex with Fab 2D73


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Dengue Virus Ediii in Complex with Fab 2D73 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na224 b:72.5 occ:1.00 OE1 H:GLU46 2.4 51.1 1.0 HB2 H:GLU46 2.9 54.1 1.0 H H:SER40 3.2 58.0 1.0 HD3 H:LYS38 3.2 48.5 1.0 HG2 H:LYS38 3.3 49.8 1.0 HB3 H:GLU46 3.4 54.1 1.0 HE2 H:LYS38 3.4 49.6 1.0 CD H:GLU46 3.4 60.4 1.0 CB H:GLU46 3.5 45.1 1.0 OG H:SER40 3.6 61.3 1.0 HG H:SER40 3.6 73.5 1.0 CD H:LYS38 3.8 40.4 1.0 CG H:LYS38 3.9 41.5 1.0 HA H:GLN39 4.0 51.6 1.0 CE H:LYS38 4.0 41.3 1.0 N H:SER40 4.0 48.3 1.0 O H:LYS38 4.1 40.4 1.0 HB2 H:SER40 4.1 72.8 1.0 HB3 H:LYS38 4.1 44.0 1.0 CG H:GLU46 4.1 54.8 1.0 O H:SER44 4.2 45.8 1.0 HZ1 H:LYS38 4.2 54.6 1.0 CB H:SER40 4.3 60.7 1.0 OE2 H:GLU46 4.4 65.9 1.0 C H:LYS38 4.4 43.0 1.0 CB H:LYS38 4.5 36.7 1.0 HB3 H:LYS43 4.6 80.2 1.0 HB2 H:LYS43 4.6 80.2 1.0 NZ H:LYS38 4.6 45.5 1.0 HG3 H:GLU46 4.6 65.8 1.0 CA H:GLN39 4.7 43.0 1.0 N H:GLN39 4.7 43.6 1.0 HD2 H:LYS38 4.7 48.5 1.0 HG3 H:LYS38 4.8 49.8 1.0 HG2 H:GLU46 4.8 65.8 1.0 CA H:SER40 4.8 53.1 1.0 CA H:GLU46 4.8 38.2 1.0 HE3 H:LYS38 4.8 49.6 1.0 C H:GLN39 4.9 47.5 1.0 HZ1 H:LYS63 4.9 0.2 1.0 HZ H:PHE64 4.9 62.6 1.0 N H:GLU46 4.9 42.4 1.0 H H:GLU46 4.9 50.9 1.0

Sodium binding site 6 out of 8 in the Structure of Dengue Virus Ediii in Complex with Fab 2D73


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Dengue Virus Ediii in Complex with Fab 2D73 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na225 b:58.5 occ:1.00 O H:SER7 2.4 45.9 1.0 HA H:THR115 2.6 56.7 1.0 HA2 H:GLY8 2.7 70.6 1.0 O H:GLY114 2.9 45.2 1.0 O H:HOH2002 2.9 42.8 1.0 HE21 H:GLN113 3.2 59.6 1.0 HG21 H:THR115 3.3 64.7 1.0 C H:SER7 3.4 53.0 1.0 OG1 H:THR115 3.4 47.6 1.0 CA H:GLY8 3.4 58.9 1.0 HD3 H:PRO9 3.4 76.2 1.0 CA H:THR115 3.5 47.2 1.0 C H:GLY8 3.6 54.1 1.0 NE2 H:GLN113 3.7 49.7 1.0 CB H:THR115 3.8 47.9 1.0 N H:GLY8 3.8 52.2 1.0 C H:GLY114 3.9 44.7 1.0 HG1 H:THR115 3.9 57.2 1.0 N H:PRO9 3.9 57.8 1.0 HE22 H:GLN113 4.0 59.6 1.0 CG2 H:THR115 4.0 53.9 1.0 H H:THR116 4.0 52.6 1.0 HB2 H:GLN6 4.0 48.9 1.0 HG2 H:GLN113 4.1 56.4 1.0 CD H:PRO9 4.1 63.5 1.0 O H:GLY8 4.2 55.5 1.0 N H:THR115 4.2 46.4 1.0 HA3 H:GLY8 4.2 70.6 1.0 HG3 H:PRO9 4.3 83.3 1.0 O H:GLN6 4.4 48.9 1.0 CD H:GLN113 4.5 50.2 1.0 HA H:PRO9 4.5 71.7 1.0 HB3 H:GLN6 4.6 48.9 1.0 HG22 H:THR115 4.6 64.7 1.0 C H:GLN6 4.6 47.4 1.0 N H:THR116 4.6 43.8 1.0 C H:THR115 4.6 46.7 1.0 HG23 H:THR115 4.6 64.7 1.0 CG H:GLN113 4.7 47.0 1.0 CA H:SER7 4.7 56.0 1.0 HG3 H:GLN113 4.7 56.4 1.0 H H:GLY8 4.7 62.6 1.0 N H:SER7 4.7 49.0 1.0 CB H:GLN6 4.7 40.8 1.0 HB H:THR115 4.8 57.5 1.0 CG H:PRO9 4.8 69.4 1.0 CA H:PRO9 4.8 59.8 1.0 HD2 H:PRO9 4.9 76.2 1.0

Sodium binding site 7 out of 8 in the Structure of Dengue Virus Ediii in Complex with Fab 2D73


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Dengue Virus Ediii in Complex with Fab 2D73 within 5.0Å range: probe atom residue distance (Å) B Occ L:Na215 b:53.8 occ:1.00 OD2 L:ASP70 2.4 39.9 1.0 O L:HOH2031 2.7 37.5 1.0 HB2 L:ASP70 2.8 45.8 1.0 O L:HOH2032 2.9 39.3 1.0 O L:HOH2038 3.0 53.9 1.0 CG L:ASP70 3.3 39.7 1.0 CB L:ASP70 3.5 38.2 1.0 H L:ASP70 3.7 42.4 1.0 H L:GLN69 3.8 38.2 1.0 HB2 L:GLN69 3.9 42.3 1.0 N L:ASP70 4.1 35.4 1.0 HB3 L:ASP70 4.2 45.8 1.0 O L:SER67 4.3 35.2 1.0 CA L:ASP70 4.5 33.8 1.0 OD1 L:ASP70 4.5 42.6 1.0 N L:GLN69 4.6 31.9 1.0 CB L:GLN69 4.8 35.2 1.0 HZ3 L:LYS24 4.9 81.7 1.0 C L:GLN69 4.9 34.4 1.0 HA3 L:GLY68 5.0 47.0 1.0

Sodium binding site 8 out of 8 in the Structure of Dengue Virus Ediii in Complex with Fab 2D73


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Dengue Virus Ediii in Complex with Fab 2D73 within 5.0Å range: probe atom residue distance (Å) B Occ L:Na216 b:59.8 occ:1.00 O L:SER60 2.5 50.5 1.0 O L:HOH2028 2.8 40.9 1.0 HA L:ARG61 3.0 54.6 1.0 HB3 L:SER63 3.2 46.0 1.0 HB3 L:SER76 3.5 58.0 1.0 O L:ARG61 3.5 41.2 1.0 C L:ARG61 3.5 45.3 1.0 C L:SER60 3.6 49.3 1.0 CA L:ARG61 3.7 45.5 1.0 HG L:SER76 3.9 58.5 1.0 HG L:SER63 4.0 54.8 1.0 CB L:SER63 4.0 38.3 1.0 N L:ARG61 4.1 45.8 1.0 OG L:SER63 4.1 45.7 1.0 N L:PHE62 4.2 43.8 1.0 O L:PHE62 4.2 43.5 1.0 OG L:SER76 4.2 48.7 1.0 C L:PHE62 4.2 43.1 1.0 CB L:SER76 4.2 48.3 1.0 H L:SER76 4.3 51.4 1.0 N L:SER63 4.5 37.9 1.0 H L:PHE62 4.6 52.6 1.0 HB2 L:SER60 4.6 67.0 1.0 HB2 L:SER63 4.6 46.0 1.0 CA L:PHE62 4.7 42.1 1.0 H L:SER63 4.8 45.4 1.0 HB2 L:SER76 4.8 58.0 1.0 CA L:SER63 4.8 35.3 1.0 CA L:SER60 4.9 52.1 1.0 HA L:PHE62 4.9 50.5 1.0 HA L:SER60 5.0 62.5 1.0 H L:ARG61 5.0 55.0 1.0

J.Li, D.Watterson, C.W.Chang, X.Q.Li, D.J.Ericsson, L.W.Qiu, J.P.Cai, J.Chen, S.R.Fry, M.A.Cooper, X.Y.Che, P.R.Young, B.Kobe. Tba To Be Published.