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Sodium in PDB 6jd0: Structure of Mutant Human Cathepsin L, Engineered For Gag Binding

Enzymatic activity of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding

All present enzymatic activity of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding:
3.4.22.15;

Protein crystallography data

The structure of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding, PDB code: 6jd0 was solved by D.Choudhury, S.Biswas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.41 / 1.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.835, 64.172, 92.857, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.5

Other elements in 6jd0:

The structure of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Mutant Human Cathepsin L, Engineered For Gag Binding (pdb code 6jd0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Mutant Human Cathepsin L, Engineered For Gag Binding, PDB code: 6jd0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6jd0

Go back to Sodium Binding Sites List in 6jd0
Sodium binding site 1 out of 5 in the Structure of Mutant Human Cathepsin L, Engineered For Gag Binding


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na418

b:28.9
occ:1.00
CL A:CL415 2.6 46.3 1.0
HE1 A:PHE135 2.7 28.7 1.0
O A:GLY107 2.8 22.5 1.0
HA3 A:GLY107 2.8 25.1 1.0
HB2 A:LEU141 2.9 31.1 1.0
HD22 A:LEU141 3.1 30.6 1.0
CE1 A:PHE135 3.1 23.9 1.0
HA2 A:GLY107 3.3 25.1 1.0
CA A:GLY107 3.4 20.9 1.0
C A:GLY107 3.5 19.5 1.0
HZ A:PHE135 3.5 23.2 1.0
CZ A:PHE135 3.5 19.3 1.0
HB3 A:LEU141 3.6 31.1 1.0
CB A:LEU141 3.7 25.9 1.0
CD2 A:LEU141 3.8 25.5 1.0
HD23 A:LEU141 3.8 30.6 1.0
CD1 A:PHE135 3.8 20.9 1.0
HO A:POL438 4.0 59.4 1.0
HD1 A:PHE135 4.0 25.1 1.0
CG A:LEU141 4.3 22.8 1.0
HD13 A:LEU141 4.4 27.8 1.0
H12 A:POL438 4.4 49.3 1.0
H A:LEU141 4.5 31.8 1.0
CE2 A:PHE135 4.6 21.2 1.0
O A:POL438 4.6 49.5 1.0
HD21 A:LEU141 4.6 30.6 1.0
N A:GLY107 4.7 21.1 1.0
CG A:PHE135 4.8 20.6 1.0
N A:TYR108 4.8 21.1 1.0
CA A:LEU141 4.9 24.4 1.0
N A:LEU141 4.9 26.5 1.0
CD1 A:LEU141 4.9 23.2 1.0
C1 A:POL438 4.9 41.1 1.0
O A:LYS106 5.0 22.0 1.0

Sodium binding site 2 out of 5 in 6jd0

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Sodium binding site 2 out of 5 in the Structure of Mutant Human Cathepsin L, Engineered For Gag Binding


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na419

b:35.3
occ:1.00
O A:POL435 2.6 46.9 1.0
O1 A:PO4428 2.6 33.3 1.0
HA2 A:GLY286 2.7 28.2 1.0
O A:VAL112 2.9 21.3 1.0
HO A:POL435 2.9 56.3 1.0
HA A:LYS113 2.9 24.9 1.0
HB2 A:ASN114 3.1 29.2 1.0
C A:LYS113 3.4 21.7 1.0
CA A:LYS113 3.5 20.8 1.0
H12 A:POL435 3.5 61.0 1.0
C1 A:POL435 3.6 50.9 1.0
H A:GLU287 3.6 25.5 1.0
C A:VAL112 3.6 26.3 1.0
O3 A:PO4428 3.6 33.6 1.0
HG12 A:VAL112 3.6 29.4 1.0
CA A:GLY286 3.6 23.5 1.0
P A:PO4428 3.7 49.5 1.0
N A:ASN114 3.7 21.7 1.0
H21 A:POL435 3.7 30.0 1.0
O A:LYS113 3.8 20.1 1.0
HA3 A:GLY286 3.8 28.2 1.0
N A:LYS113 3.8 21.9 1.0
O A:HOH511 3.9 31.2 1.0
CB A:ASN114 3.9 24.3 1.0
H A:ASN114 3.9 26.0 1.0
HG3 A:GLU287 4.0 38.4 1.0
HB3 A:ASN114 4.1 29.2 1.0
N A:GLU287 4.2 21.2 1.0
C2 A:POL435 4.2 25.0 1.0
H A:GLY286 4.3 25.8 1.0
H11 A:POL435 4.4 61.0 1.0
C A:GLY286 4.4 20.4 1.0
CA A:ASN114 4.4 19.1 1.0
N A:GLY286 4.5 21.5 1.0
CG1 A:VAL112 4.5 24.5 1.0
HD22 A:ASN114 4.6 26.9 1.0
H22 A:POL435 4.6 30.0 1.0
H A:LYS113 4.6 26.3 1.0
HB A:VAL112 4.6 27.3 1.0
O4 A:PO4428 4.7 65.1 1.0
O2 A:PO4428 4.7 30.2 1.0
HA A:ASN114 4.7 22.9 1.0
CA A:VAL112 4.8 22.9 1.0
CB A:LYS113 4.9 22.8 1.0
CB A:VAL112 4.9 22.7 1.0
CG A:GLU287 4.9 32.0 1.0
HG11 A:VAL112 5.0 29.4 1.0

Sodium binding site 3 out of 5 in 6jd0

Go back to Sodium Binding Sites List in 6jd0
Sodium binding site 3 out of 5 in the Structure of Mutant Human Cathepsin L, Engineered For Gag Binding


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na420

b:49.2
occ:1.00
O2 A:PO4424 3.0 63.8 1.0
OE2 A:GLU244 3.1 33.5 1.0
NA A:NA422 3.1 50.5 1.0
O2 A:PO4425 3.8 89.0 1.0
CD A:GLU244 4.1 40.9 1.0
P A:PO4424 4.2 91.7 1.0
O3 A:PO4424 4.2 87.2 1.0
OE1 A:GLU244 4.4 42.0 1.0
HE3 A:LYS243 4.8 67.6 1.0
O1 A:PO4424 5.0 61.9 1.0

Sodium binding site 4 out of 5 in 6jd0

Go back to Sodium Binding Sites List in 6jd0
Sodium binding site 4 out of 5 in the Structure of Mutant Human Cathepsin L, Engineered For Gag Binding


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na421

b:58.2
occ:1.00
O3 A:PO4423 2.2 63.1 1.0
HH22 A:ARG50 2.3 55.6 1.0
O A:GLU43 2.9 30.0 1.0
HB2 A:GLN47 2.9 54.0 1.0
HB3 A:GLU43 3.0 35.9 1.0
NH2 A:ARG50 3.1 46.3 1.0
HH21 A:ARG50 3.4 55.6 1.0
HA A:GLU43 3.6 36.2 1.0
C A:GLU43 3.6 28.7 1.0
H A:GLN47 3.7 43.3 1.0
P A:PO4423 3.7 82.7 1.0
CB A:GLU43 3.8 29.9 1.0
HH12 A:ARG50 3.8 53.5 1.0
CA A:GLU43 3.9 30.2 1.0
CB A:GLN47 3.9 45.0 1.0
HG2 A:GLU43 4.1 43.0 1.0
OE1 A:GLN47 4.1 60.9 1.0
N A:GLN47 4.2 36.1 1.0
CZ A:ARG50 4.2 51.0 1.0
HB3 A:GLN47 4.3 54.0 1.0
HB2 A:ASN46 4.3 39.4 1.0
NH1 A:ARG50 4.4 44.6 1.0
HA A:GLN47 4.4 46.0 1.0
O2 A:PO4423 4.4 61.6 1.0
O1 A:PO4423 4.4 48.6 1.0
CA A:GLN47 4.4 38.4 1.0
HB2 A:GLU43 4.5 35.9 1.0
CG A:GLU43 4.5 35.8 1.0
O4 A:PO4423 4.5 87.6 1.0
N A:LEU44 4.7 27.5 1.0
HA A:LEU44 4.7 36.1 1.0
HG3 A:GLN47 4.7 67.5 1.0
CG A:GLN47 4.8 56.2 1.0
CD A:GLN47 4.9 61.0 1.0

Sodium binding site 5 out of 5 in 6jd0

Go back to Sodium Binding Sites List in 6jd0
Sodium binding site 5 out of 5 in the Structure of Mutant Human Cathepsin L, Engineered For Gag Binding


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Mutant Human Cathepsin L, Engineered For Gag Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na422

b:50.5
occ:1.00
HG1 A:THR57 2.1 32.4 1.0
OE2 A:GLU244 2.2 33.5 1.0
HB2 A:GLU244 2.4 34.3 1.0
OG1 A:THR57 2.9 27.0 1.0
NA A:NA420 3.1 49.2 1.0
HG3 A:LYS243 3.3 27.9 1.0
CB A:GLU244 3.3 28.6 1.0
CD A:GLU244 3.3 40.9 1.0
HG21 A:THR57 3.4 32.6 1.0
HB3 A:GLU244 3.5 34.3 1.0
CG A:GLU244 3.8 32.8 1.0
HG2 A:LYS243 3.9 27.9 1.0
O2 A:PO4425 3.9 89.0 1.0
CB A:THR57 3.9 23.3 1.0
CG A:LYS243 4.0 23.2 1.0
CG2 A:THR57 4.0 27.1 1.0
HE3 A:LYS243 4.1 67.6 1.0
HB A:THR57 4.1 27.9 1.0
HG3 A:GLU244 4.1 39.4 1.0
HG23 A:THR57 4.1 32.6 1.0
H A:GLU244 4.3 27.7 1.0
OE1 A:GLU244 4.4 42.0 1.0
CA A:GLU244 4.4 21.3 1.0
N A:GLU244 4.5 23.1 1.0
HB3 A:LYS243 4.5 26.9 1.0
HG2 A:GLU244 4.7 39.4 1.0
O3 A:PO4425 4.8 60.1 1.0
CB A:LYS243 4.9 22.4 1.0
HG22 A:THR57 4.9 32.6 1.0
CE A:LYS243 4.9 56.3 1.0
H A:THR57 4.9 30.9 1.0
P A:PO4425 5.0 0.8 1.0
C A:GLU244 5.0 21.0 1.0

Reference:

D.Choudhury, S.Biswas. Structure of Mutant Human Cathepsin L, Engineered For Gag Binding To Be Published.
Page generated: Tue Dec 15 12:25:23 2020

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