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Sodium in PDB 3ffz: Domain Organization in Clostridium Butulinum Neurotoxin Type E Is Unique: Its Implication in Faster Translocation

Enzymatic activity of Domain Organization in Clostridium Butulinum Neurotoxin Type E Is Unique: Its Implication in Faster Translocation

All present enzymatic activity of Domain Organization in Clostridium Butulinum Neurotoxin Type E Is Unique: Its Implication in Faster Translocation:
3.4.24.69;

Protein crystallography data

The structure of Domain Organization in Clostridium Butulinum Neurotoxin Type E Is Unique: Its Implication in Faster Translocation, PDB code: 3ffz was solved by D.Kumaran, S.Eswaramoorthy, S.Swaminathan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.49 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.430, 172.570, 137.265, 90.00, 99.84, 90.00
R / Rfree (%) 25.3 / 30.9

Other elements in 3ffz:

The structure of Domain Organization in Clostridium Butulinum Neurotoxin Type E Is Unique: Its Implication in Faster Translocation also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Domain Organization in Clostridium Butulinum Neurotoxin Type E Is Unique: Its Implication in Faster Translocation (pdb code 3ffz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Domain Organization in Clostridium Butulinum Neurotoxin Type E Is Unique: Its Implication in Faster Translocation, PDB code: 3ffz:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3ffz

Go back to Sodium Binding Sites List in 3ffz
Sodium binding site 1 out of 3 in the Domain Organization in Clostridium Butulinum Neurotoxin Type E Is Unique: Its Implication in Faster Translocation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Domain Organization in Clostridium Butulinum Neurotoxin Type E Is Unique: Its Implication in Faster Translocation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1301

b:62.8
occ:1.00
 O A:HOH1317 1.3 51.9 1.0
O A:LYS550 1.6 48.0 1.0
O A:ALA544 2.6 39.1 1.0
O A:GLU547 2.6 50.0 1.0
C A:LYS550 2.7 47.8 1.0
O A:GLN548 3.0 53.2 1.0
O A:HOH1312 3.3 58.9 1.0
N A:LYS550 3.4 49.2 1.0
CA A:LYS550 3.5 48.8 1.0
C A:ALA544 3.5 42.5 1.0
C A:GLN548 3.6 54.1 1.0
O A:HOH1313 3.6 42.7 1.0
CA A:ALA544 3.7 44.0 1.0
C A:GLU547 3.7 51.4 1.0
N A:ILE551 3.8 45.0 1.0
CB A:LYS550 3.9 50.0 1.0
CA A:ILE551 4.0 43.4 1.0
CA A:GLN548 4.1 55.3 1.0
CG1 A:ILE551 4.1 42.3 1.0
CB A:ALA544 4.1 46.4 1.0
C A:PRO549 4.2 50.4 1.0
O A:ALA525 4.3 31.4 1.0
N A:GLN548 4.3 53.3 1.0
N A:PRO549 4.4 53.0 1.0
CB A:ILE551 4.7 42.9 1.0
N A:LEU545 4.7 41.2 1.0
CA A:PRO549 4.8 52.0 1.0
O A:THR543 4.9 46.8 1.0
O A:PRO549 4.9 48.5 1.0
CA A:GLU547 4.9 51.5 1.0

Sodium binding site 2 out of 3 in 3ffz

Go back to Sodium Binding Sites List in 3ffz
Sodium binding site 2 out of 3 in the Domain Organization in Clostridium Butulinum Neurotoxin Type E Is Unique: Its Implication in Faster Translocation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Domain Organization in Clostridium Butulinum Neurotoxin Type E Is Unique: Its Implication in Faster Translocation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1302

b:38.5
occ:1.00
 O A:VAL593 2.1 54.4 1.0
O A:ILE596 2.2 47.6 1.0
O A:HOH1314 2.3 39.0 1.0
O A:ILE599 2.4 33.7 1.0
C A:ILE599 3.2 34.3 1.0
C A:VAL593 3.3 53.3 1.0
O A:ALA597 3.3 46.9 1.0
C A:ILE596 3.4 47.4 1.0
C A:ALA597 3.8 45.5 1.0
N A:ILE599 3.8 36.0 1.0
N A:SER600 3.9 32.3 1.0
CA A:SER600 4.0 30.9 1.0
CA A:ASP594 4.0 54.5 1.0
N A:ASP594 4.1 53.0 1.0
CA A:ALA597 4.1 44.8 1.0
CA A:ILE599 4.2 34.3 1.0
N A:ALA597 4.2 45.7 1.0
CA A:VAL593 4.2 52.6 1.0
CB A:VAL593 4.3 51.0 1.0
N A:VAL593 4.4 52.4 1.0
CA A:ILE596 4.5 47.9 1.0
CG1 A:VAL593 4.6 50.3 1.0
N A:ASP598 4.7 43.2 1.0
C A:ASP594 4.7 54.0 1.0
CB A:ILE596 4.7 48.1 1.0
N A:ILE596 4.7 49.5 1.0
CB A:SER600 4.8 27.0 1.0
C A:ASP598 4.8 38.1 1.0
CB A:ILE599 4.9 31.9 1.0
O A:ASP594 4.9 52.9 1.0
C A:SER600 5.0 32.5 1.0

Sodium binding site 3 out of 3 in 3ffz

Go back to Sodium Binding Sites List in 3ffz
Sodium binding site 3 out of 3 in the Domain Organization in Clostridium Butulinum Neurotoxin Type E Is Unique: Its Implication in Faster Translocation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Domain Organization in Clostridium Butulinum Neurotoxin Type E Is Unique: Its Implication in Faster Translocation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1302

b:55.8
occ:1.00
 O B:ILE599 2.0 63.3 1.0
O B:HOH1283 2.2 53.7 1.0
O B:VAL593 2.3 69.8 1.0
O B:ILE596 2.5 61.5 1.0
C B:ILE599 3.0 63.5 1.0
C B:VAL593 3.4 69.9 1.0
CA B:SER600 3.5 64.8 1.0
C B:ILE596 3.6 60.9 1.0
N B:SER600 3.6 63.6 1.0
CB B:VAL593 3.7 70.5 1.0
N B:ILE599 4.0 62.6 1.0
CA B:ALA597 4.0 60.3 1.0
CA B:VAL593 4.0 70.1 1.0
CA B:ILE599 4.1 63.1 1.0
N B:VAL593 4.1 69.8 1.0
C B:ALA597 4.2 60.4 1.0
N B:ALA597 4.2 60.2 1.0
CB B:SER600 4.4 64.2 1.0
CG2 B:VAL593 4.5 67.5 1.0
C B:SER600 4.5 66.0 1.0
O B:ALA597 4.5 60.1 1.0
N B:ASP594 4.5 69.4 1.0
N B:ASP598 4.6 61.5 1.0
O B:SER600 4.6 67.3 1.0
CG1 B:VAL593 4.7 70.3 1.0
CA B:ILE596 4.7 60.5 1.0
CA B:ASP594 4.8 69.5 1.0
CB B:ILE599 4.8 62.4 1.0
N B:ILE596 4.9 62.4 1.0
C B:ASP598 4.9 62.3 1.0

Reference:

D.Kumaran, S.Eswaramoorthy, W.Furey, J.Navaza, M.Sax, S.Swaminathan. Domain Organization in Clostridium Botulinum Neurotoxin Type E Is Unique: Its Implication in Faster Translocation. J.Mol.Biol. V. 386 233 2009.
ISSN: ISSN 0022-2836
PubMed: 19118561
DOI: 10.1016/J.JMB.2008.12.027
Page generated: Mon Oct 7 09:45:28 2024

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