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Sodium in PDB 5o8n: Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.

Enzymatic activity of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.

All present enzymatic activity of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.:
3.4.24.27;

Protein crystallography data

The structure of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation., PDB code: 5o8n was solved by D.N.Axford, C.Burton, P.Docker, M.Prince, P.D.Topham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.00 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.552, 93.552, 129.753, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 25.9

Other elements in 5o8n:

The structure of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation. also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Calcium (Ca) 4 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation. (pdb code 5o8n). 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 Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation., PDB code: 5o8n:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5o8n

Go back to Sodium Binding Sites List in 5o8n
Sodium binding site 1 out of 5 in the Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:71.4
occ:1.00
 NE2 A:GLN246 3.4 63.2 1.0
O A:HOH503 3.9 57.5 1.0
OH A:TYR242 3.9 63.3 1.0
CD A:GLN246 4.5 56.7 1.0
CG A:GLN246 4.6 39.9 1.0
CB A:GLN246 4.9 56.1 1.0
CZ A:TYR242 4.9 50.0 1.0

Sodium binding site 2 out of 5 in 5o8n

Go back to Sodium Binding Sites List in 5o8n
Sodium binding site 2 out of 5 in the Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:57.1
occ:1.00
 ND2 A:ASN19 3.6 60.6 1.0
N A:ASN19 3.6 37.5 1.0
OH A:TYR75 3.9 52.5 1.0
CB A:ASN19 4.0 48.4 1.0
CG A:ASN19 4.1 47.0 1.0
CE1 A:TYR75 4.3 46.5 1.0
CA A:LYS18 4.4 47.1 1.0
CA A:ASN19 4.4 41.9 1.0
CB A:LYS18 4.5 47.1 1.0
C A:LYS18 4.5 40.4 1.0
CZ A:TYR75 4.5 49.2 1.0
O A:ASN19 4.6 46.2 1.0

Sodium binding site 3 out of 5 in 5o8n

Go back to Sodium Binding Sites List in 5o8n
Sodium binding site 3 out of 5 in the Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:60.7
occ:1.00
 O A:HOH586 3.0 58.2 1.0
NH2 A:ARG35 3.2 48.7 1.0
NH1 A:ARG35 3.7 43.7 1.0
OD1 A:ASN21 3.8 43.9 1.0
CZ A:ARG35 3.9 46.5 1.0
O A:HOH542 3.9 47.9 1.0
O A:HOH584 4.4 50.6 1.0
CG A:ASN21 4.8 39.3 1.0

Sodium binding site 4 out of 5 in 5o8n

Go back to Sodium Binding Sites List in 5o8n
Sodium binding site 4 out of 5 in the Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:53.0
occ:0.50
 N A:ASP226 4.1 49.0 1.0
CA A:GLN225 4.8 51.1 1.0
CA A:ASP226 4.8 54.1 1.0

Sodium binding site 5 out of 5 in 5o8n

Go back to Sodium Binding Sites List in 5o8n
Sodium binding site 5 out of 5 in the Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Thermolysin at Room Temperature Via A Method of Acoustically Induced Rotation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:85.2
occ:0.50
 O A:HOH605 1.9 69.5 1.0
O A:HOH557 2.3 56.1 1.0
CB A:SER298 3.2 68.0 1.0
OG A:SER298 4.0 66.5 1.0
CA A:SER298 4.4 55.1 1.0
N A:SER298 4.4 57.5 1.0
CG2 A:THR293 5.0 66.0 1.0

Reference:

C.G.Burton, D.Axford, A.M.J.Edwards, R.J.Gildea, R.H.Morris, M.I.Newton, A.M.Orville, M.Prince, P.D.Topham, P.T.Docker. An Acoustic on-Chip Goniometer For Room Temperature Macromolecular Crystallography. Lab Chip V. 17 4225 2017.
ISSN: ISSN 1473-0189
PubMed: 29124258
DOI: 10.1039/C7LC00812K
Page generated: Tue Dec 15 11:23:59 2020

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