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Sodium in PDB 4bz1: Structure of Dengue Virus Ediii in Complex with Fab 3E31

Protein crystallography data

The structure of Structure of Dengue Virus Ediii in Complex with Fab 3E31, PDB code: 4bz1 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) 53.504 / 2.15
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.802, 107.009, 134.896, 90.00, 90.00, 90.00
R / Rfree (%) 22.34 / 25.46

Other elements in 4bz1:

The structure of Structure of Dengue Virus Ediii in Complex with Fab 3E31 also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Dengue Virus Ediii in Complex with Fab 3E31 (pdb code 4bz1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Dengue Virus Ediii in Complex with Fab 3E31, PDB code: 4bz1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4bz1

Go back to Sodium Binding Sites List in 4bz1
Sodium binding site 1 out of 4 in the Structure of Dengue Virus Ediii in Complex with Fab 3E31


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 3E31 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na218

b:23.8
occ:1.00
HD22 H:ASN200 2.3 35.9 1.0
HA H:ASN159 2.7 31.6 1.0
OG H:SER160 3.0 39.2 1.0
HB H:THR198 3.1 29.9 1.0
ND2 H:ASN200 3.2 29.9 1.0
HG H:SER160 3.2 47.0 1.0
H H:SER160 3.4 33.9 1.0
N H:SER160 3.5 28.2 1.0
CA H:ASN159 3.5 26.4 1.0
HG22 H:THR198 3.5 28.6 1.0
HD21 H:ASN200 3.6 35.9 1.0
C H:ASN159 3.6 28.4 1.0
HB2 H:SER160 3.9 45.4 1.0
CB H:SER160 3.9 37.9 1.0
HG23 H:THR198 3.9 28.6 1.0
CB H:THR198 3.9 24.9 1.0
CG2 H:THR198 4.0 23.9 1.0
CG H:ASN200 4.1 26.8 1.0
OD1 H:ASN200 4.2 28.4 1.0
H H:ASN159 4.2 31.5 1.0
HG1 H:THR198 4.2 29.8 1.0
CA H:SER160 4.3 32.2 1.0
O H:ASN159 4.3 33.3 1.0
N H:ASN159 4.3 26.3 1.0
OD1 H:ASN159 4.5 30.3 1.0
HA H:SER160 4.6 38.6 1.0
HB3 H:ASN159 4.6 34.6 1.0
OG1 H:THR198 4.6 24.9 1.0
CB H:ASN159 4.6 28.8 1.0
NA H:NA219 4.7 36.4 1.0
O H:THR198 4.7 22.8 1.0
HB3 H:ASP211 4.8 35.6 1.0
HB3 H:SER160 4.8 45.4 1.0
HG21 H:THR198 4.9 28.6 1.0
O H:HOH2039 5.0 45.2 1.0
CG H:ASN159 5.0 29.8 1.0

Sodium binding site 2 out of 4 in 4bz1

Go back to Sodium Binding Sites List in 4bz1
Sodium binding site 2 out of 4 in the Structure of Dengue Virus Ediii in Complex with Fab 3E31


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 3E31 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na219

b:36.4
occ:1.00
OG1 H:THR198 2.3 24.9 1.0
HG1 H:THR196 2.4 42.5 1.0
HG1 H:THR198 2.4 29.8 1.0
OD1 H:ASN159 2.5 30.3 1.0
HB H:THR198 2.8 29.9 1.0
CB H:THR198 3.1 24.9 1.0
OG1 H:THR196 3.1 35.4 1.0
H H:THR198 3.1 29.3 1.0
N H:THR198 3.1 24.4 1.0
HA H:ILE197 3.2 31.9 1.0
O H:THR196 3.4 28.1 1.0
C H:ILE197 3.4 26.4 1.0
HB H:THR196 3.4 39.5 1.0
C H:THR196 3.4 28.6 1.0
CG H:ASN159 3.5 29.8 1.0
N H:ILE197 3.5 26.6 1.0
CA H:ILE197 3.6 26.6 1.0
CA H:THR198 3.7 22.9 1.0
CB H:THR196 3.7 32.9 1.0
HD22 H:ASN159 3.8 33.9 1.0
HE2 H:LYS213 3.8 55.2 1.0
H H:ILE197 4.0 31.9 1.0
ND2 H:ASN159 4.0 28.2 1.0
HG3 H:LYS213 4.0 38.0 1.0
HA H:ASN159 4.1 31.6 1.0
O H:ILE197 4.1 25.5 1.0
O H:HOH2038 4.2 43.1 1.0
HA H:THR198 4.2 27.4 1.0
CA H:THR196 4.2 31.1 1.0
CG2 H:THR198 4.4 23.9 1.0
HG22 H:THR198 4.5 28.6 1.0
CB H:ASN159 4.6 28.8 1.0
O H:HOH2050 4.6 53.3 1.0
NA H:NA218 4.7 23.8 1.0
CE H:LYS213 4.7 46.0 1.0
HB3 H:ASN159 4.8 34.6 1.0
CA H:ASN159 4.8 26.4 1.0
HD21 H:ASN159 4.8 33.9 1.0
HA H:LYS213 4.8 34.2 1.0
HG21 H:THR198 4.8 28.6 1.0
C H:THR198 4.9 21.4 1.0
HB2 H:LYS213 4.9 38.2 1.0
HA H:THR196 4.9 37.3 1.0
H H:ASN159 4.9 31.5 1.0
CG H:LYS213 4.9 31.6 1.0
HE3 H:LYS213 5.0 55.2 1.0
O H:THR198 5.0 22.8 1.0

Sodium binding site 3 out of 4 in 4bz1

Go back to Sodium Binding Sites List in 4bz1
Sodium binding site 3 out of 4 in the Structure of Dengue Virus Ediii in Complex with Fab 3E31


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 3E31 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na220

b:37.8
occ:1.00
O H:HOH2055 2.5 27.0 1.0
OG H:SER182 2.5 33.8 1.0
O H:HOH2045 2.6 37.5 1.0
HG L:SER182 3.0 42.2 1.0
HB3 L:SER182 3.0 42.0 1.0
H H:SER182 3.1 36.0 1.0
HA H:LEU181 3.1 42.3 1.0
N H:SER182 3.3 30.0 1.0
HB2 H:PHE170 3.4 37.9 1.0
OG L:SER182 3.5 35.2 1.0
HB3 H:SER182 3.5 38.0 1.0
CB H:SER182 3.5 31.7 1.0
HB3 L:SER168 3.5 51.1 1.0
CB L:SER182 3.7 35.0 1.0
C H:LEU181 3.8 31.4 1.0
CA H:LEU181 3.9 35.2 1.0
HG1 L:THR184 4.0 42.0 1.0
CA H:SER182 4.0 29.4 1.0
HB2 L:SER182 4.1 42.0 1.0
HB3 H:PHE170 4.1 37.9 1.0
CB H:PHE170 4.2 31.6 1.0
HB2 L:SER168 4.2 51.1 1.0
CB L:SER168 4.3 42.6 1.0
HB2 H:SER182 4.3 38.0 1.0
HG23 H:THR180 4.4 40.9 1.0
OG1 L:THR184 4.5 35.0 1.0
O H:LEU181 4.5 28.7 1.0
O H:THR180 4.5 39.0 1.0
HG L:SER168 4.6 57.0 1.0
HB2 H:LEU181 4.6 39.7 1.0
O L:SER182 4.7 31.0 1.0
CG H:PHE170 4.8 33.4 1.0
HA H:SER182 4.8 35.3 1.0
N H:LEU181 4.8 35.1 1.0
O H:PRO171 4.8 38.7 1.0
HD1 H:PHE170 4.9 38.1 1.0
O H:SER182 4.9 29.3 1.0
CA L:SER182 4.9 32.2 1.0
CB H:LEU181 4.9 33.1 1.0
C H:SER182 4.9 28.5 1.0
C L:SER182 4.9 31.5 1.0
OG L:SER168 4.9 47.5 1.0
C H:THR180 5.0 35.3 1.0

Sodium binding site 4 out of 4 in 4bz1

Go back to Sodium Binding Sites List in 4bz1
Sodium binding site 4 out of 4 in the Structure of Dengue Virus Ediii in Complex with Fab 3E31


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 3E31 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na221

b:58.8
occ:1.00
H H:PHE29 2.3 88.1 1.0
HB2 H:PHE29 2.4 80.8 1.0
HG H:SER77 2.8 86.7 1.0
N H:PHE29 3.0 73.4 1.0
O H:TYR27 3.1 74.3 1.0
CB H:PHE29 3.1 67.3 1.0
HB3 H:PHE29 3.2 80.8 1.0
HA H:THR28 3.2 96.6 1.0
OG H:SER77 3.4 72.3 1.0
CA H:PHE29 3.7 70.3 1.0
C H:THR28 4.0 75.2 1.0
CA H:THR28 4.0 80.5 1.0
HA H:PHE29 4.1 84.4 1.0
HB3 H:SER77 4.1 80.7 1.0
C H:TYR27 4.2 76.9 1.0
CB H:SER77 4.3 67.2 1.0
CG H:PHE29 4.4 61.7 1.0
N H:THR28 4.6 79.5 1.0
HB2 H:SER77 4.8 80.7 1.0
H H:TYR27 4.8 95.0 1.0
HD1 H:PHE29 4.9 70.2 1.0
H H:THR30 4.9 88.1 1.0
HA H:SER25 5.0 85.6 1.0

Reference:

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. Structure of Dengue Virus Ediii in Complex with Fab 3E31 To Be Published.
Page generated: Tue Dec 15 06:34:59 2020

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