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Sodium in PDB 6qq3: The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet

Enzymatic activity of The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet

All present enzymatic activity of The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet:
3.2.1.17;

Protein crystallography data

The structure of The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet, PDB code: 6qq3 was solved by D.N.Axford, P.Docker, E.Dye, R.Morris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.72 / 1.53
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.448, 79.448, 37.882, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.1

Other elements in 6qq3:

The structure of The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet (pdb code 6qq3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet, PDB code: 6qq3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6qq3

Go back to Sodium Binding Sites List in 6qq3
Sodium binding site 1 out of 5 in the The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:18.7
occ:1.00
 O B:SER60 2.3 19.4 1.0
O B:CYS64 2.3 15.7 1.0
O B:HOH360 2.5 25.0 1.0
O B:ARG73 2.5 25.6 1.0
O B:HOH331 2.6 19.5 1.0
OG B:SER72 2.6 22.4 1.0
CB B:SER72 3.3 18.6 1.0
C B:CYS64 3.4 13.1 1.0
C B:SER60 3.5 15.9 1.0
C B:ARG73 3.5 25.2 1.0
CA B:ASN65 3.9 16.5 1.0
N B:ARG73 4.0 21.7 1.0
N B:ASN65 4.1 15.6 1.0
C B:SER72 4.1 31.6 1.0
CA B:SER60 4.1 12.7 1.0
CA B:SER72 4.4 24.0 1.0
CB B:SER60 4.4 13.4 1.0
CA B:ARG73 4.4 19.5 1.0
N B:CYS64 4.4 12.9 1.0
N B:ASN74 4.4 19.4 1.0
C B:ARG61 4.5 20.6 0.4
O B:ARG61 4.5 20.3 0.4
C B:ARG61 4.5 20.5 0.6
N B:ARG61 4.5 14.4 0.4
CA B:CYS64 4.5 12.9 1.0
CA B:ASN74 4.6 17.6 1.0
N B:ARG61 4.6 14.3 0.6
O B:SER72 4.6 28.1 1.0
O B:ARG61 4.6 20.1 0.6
CA B:ARG61 4.7 19.4 0.4
CB B:ASN74 4.7 18.6 1.0
CB B:THR69 4.7 17.0 1.0
N B:ASP66 4.7 14.3 1.0
O B:HOH372 4.8 17.4 1.0
CB B:ASN65 4.8 15.3 1.0
CA B:ARG61 4.8 19.8 0.6
OD1 B:ASN65 4.8 28.4 1.0
N B:TRP62 4.8 16.1 1.0
C B:ASN65 4.9 14.0 1.0
O B:THR69 4.9 24.8 1.0
O B:HOH363 5.0 42.1 1.0

Sodium binding site 2 out of 5 in 6qq3

Go back to Sodium Binding Sites List in 6qq3
Sodium binding site 2 out of 5 in the The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:25.9
occ:1.00
 OG B:SER24 2.4 19.2 0.2
O B:HOH330 2.6 52.2 1.0
OG B:SER24 2.9 18.9 0.8
N B:GLY26 3.0 16.1 1.0
O B:HOH326 3.2 37.8 1.0
CB B:SER24 3.4 17.6 0.2
CA B:GLY26 3.5 14.0 1.0
CB B:SER24 3.5 17.6 0.8
CA B:GLN121 3.6 24.5 1.0
CB B:GLN121 3.7 34.4 1.0
CD1 B:ILE124 3.9 31.4 1.0
N B:LEU25 4.0 16.2 1.0
N B:GLN121 4.1 23.6 1.0
C B:SER24 4.1 16.6 0.8
C B:LEU25 4.2 15.7 1.0
C B:SER24 4.3 16.7 0.2
CG1 B:ILE124 4.3 25.1 1.0
O B:VAL120 4.3 20.8 1.0
C B:VAL120 4.4 22.3 1.0
CG2 B:VAL120 4.4 22.9 1.0
CA B:SER24 4.4 16.6 0.8
CA B:SER24 4.5 16.7 0.2
C B:GLY26 4.5 12.5 1.0
CA B:LEU25 4.6 15.9 1.0
O B:SER24 4.6 15.3 0.8
N B:ASN27 4.7 12.4 1.0
OE1 B:GLN121 4.7 99.8 1.0
CD B:GLN121 4.8 89.0 1.0
CG B:GLN121 4.8 65.7 1.0
C B:GLN121 4.9 21.0 1.0
CB B:LEU25 4.9 18.5 1.0
O B:SER24 4.9 16.0 0.2
O B:HOH324 5.0 22.7 0.5

Sodium binding site 3 out of 5 in 6qq3

Go back to Sodium Binding Sites List in 6qq3
Sodium binding site 3 out of 5 in the The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:42.0
occ:1.00
 N B:LYS1 2.8 18.4 1.0
CA B:LYS1 3.6 19.4 1.0
CB B:LYS1 3.9 19.1 1.0
NE2 B:GLN41 4.0 16.0 1.0
CB B:SER86 4.3 28.4 1.0
O B:HOH318 4.4 17.7 1.0
CD B:GLN41 4.5 20.1 1.0
O B:HOH359 4.6 37.8 1.0
OG1 B:THR40 4.6 16.1 1.0
CG B:GLN41 4.7 17.2 1.0
CA B:SER86 4.9 19.8 1.0
N B:SER86 4.9 22.1 1.0
OG B:SER86 5.0 47.5 1.0

Sodium binding site 4 out of 5 in 6qq3

Go back to Sodium Binding Sites List in 6qq3
Sodium binding site 4 out of 5 in the The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na206

b:35.1
occ:1.00
 OD1 B:ASN44 3.0 30.6 0.4
N B:ARG45 3.1 16.8 0.6
N B:ARG45 3.1 16.9 0.4
O B:HOH305 3.4 38.4 1.0
CB B:ARG45 3.8 21.4 0.4
CA B:ASN44 3.8 14.5 0.6
CB B:ARG45 3.8 21.4 0.6
CA B:ASN44 3.8 14.6 0.4
C B:ASN44 3.9 14.5 0.6
C B:ASN44 4.0 14.5 0.4
CA B:ARG45 4.0 15.7 0.4
CA B:ARG45 4.0 15.6 0.6
CG B:ASN44 4.0 21.1 0.4
OD1 B:ASN44 4.1 19.3 0.6
O B:ARG45 4.3 21.1 0.6
O B:ARG45 4.4 22.1 0.4
CB B:ASN44 4.5 18.3 0.6
CB B:ASN44 4.6 18.4 0.4
O B:HOH345 4.6 30.3 0.5
C B:ARG45 4.7 18.8 0.6
C B:ARG45 4.7 18.9 0.4
O B:THR43 4.7 18.4 1.0
CG B:ASN44 4.7 18.8 0.6
N B:ASN44 4.9 15.0 0.6
N B:ASN44 4.9 15.0 0.4

Sodium binding site 5 out of 5 in 6qq3

Go back to Sodium Binding Sites List in 6qq3
Sodium binding site 5 out of 5 in the The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na207

b:39.6
occ:1.00
 N B:ILE88 3.3 21.3 1.0
O B:HOH347 3.3 52.3 1.0
O B:HOH302 3.5 45.0 1.0
CG1 B:ILE88 3.6 21.0 1.0
CA B:ASP87 3.8 19.0 1.0
OD1 B:ASP87 3.8 29.4 1.0
O B:SER86 3.8 26.8 1.0
O B:HOH381 3.9 51.4 1.0
C B:ASP87 4.1 23.4 1.0
CE1 B:HIS15 4.3 30.0 1.0
CB B:ILE88 4.3 17.8 1.0
CG2 B:ILE88 4.3 22.7 1.0
CZ B:PHE3 4.3 27.3 1.0
CA B:ILE88 4.3 16.8 1.0
CB B:ALA11 4.5 20.9 1.0
CD1 B:ILE88 4.5 24.3 1.0
CG B:ASP87 4.6 29.9 1.0
CB B:ASP87 4.6 22.8 1.0
C B:SER86 4.7 20.6 1.0
N B:ASP87 4.7 19.8 1.0
CE2 B:PHE3 4.8 22.6 1.0
NH2 B:ARG14 4.9 34.5 0.5

Reference:

D.N.Axford, P.Docker, E.Dye, R.Morris. The Room Temperature Structure of Lysozyme Via the Acoustic Levitation of A Droplet To Be Published.
Page generated: Tue Oct 8 12:56:14 2024

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