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Sodium in PDB 3fiu: Structure of Nmn Synthetase From Francisella Tularensis

Enzymatic activity of Structure of Nmn Synthetase From Francisella Tularensis

All present enzymatic activity of Structure of Nmn Synthetase From Francisella Tularensis:
6.3.1.5;

Protein crystallography data

The structure of Structure of Nmn Synthetase From Francisella Tularensis, PDB code: 3fiu was solved by L.Sorci, D.Martynowski, Y.Eyobo, A.L.Osterman, H.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.432, 126.438, 152.531, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.3

Other elements in 3fiu:

The structure of Structure of Nmn Synthetase From Francisella Tularensis also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Nmn Synthetase From Francisella Tularensis (pdb code 3fiu). 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 Nmn Synthetase From Francisella Tularensis, PDB code: 3fiu:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3fiu

Go back to Sodium Binding Sites List in 3fiu
Sodium binding site 1 out of 4 in the Structure of Nmn Synthetase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Nmn Synthetase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na250

b:19.4
occ:1.00
 OD2 A:ASP202 2.4 23.7 1.0
O4 A:POP4001 2.7 18.4 1.0
O A:HOH750 2.7 43.7 1.0
O6 A:POP4001 2.9 18.6 1.0
O3P A:AMP3001 2.9 22.3 1.0
OD1 A:ASP202 2.9 24.4 1.0
O1P A:AMP3001 3.0 21.6 1.0
CG A:ASP202 3.0 25.7 1.0
P A:AMP3001 3.2 26.7 1.0
P2 A:POP4001 3.3 19.4 1.0
O A:SER193 3.6 23.4 1.0
C A:SER193 3.6 23.3 1.0
MG A:MG5002 3.7 21.0 1.0
N A:SER193 3.7 22.6 1.0
MG A:MG5001 3.8 20.1 1.0
O2P A:AMP3001 3.9 24.3 1.0
OE1 A:GLU147 3.9 14.8 1.0
N A:ALA194 3.9 24.0 1.0
CA A:SER193 4.1 23.2 1.0
O5 A:POP4001 4.2 17.4 1.0
CA A:ALA194 4.3 25.3 1.0
OH A:TYR210 4.4 25.8 1.0
C A:PRO192 4.4 23.8 1.0
O A:HOH272 4.5 20.5 1.0
CB A:ASP202 4.5 22.6 1.0
O A:HOH259 4.6 22.8 1.0
O A:POP4001 4.7 17.8 1.0
CB A:ALA194 4.8 25.6 1.0
O2 A:POP4001 4.8 17.1 1.0
O5' A:AMP3001 4.8 23.5 1.0
O3 A:POP4001 4.8 19.9 1.0
CB A:PRO192 4.9 22.0 1.0
CA A:PRO192 5.0 22.8 1.0
O A:HOH276 5.0 23.4 1.0

Sodium binding site 2 out of 4 in 3fiu

Go back to Sodium Binding Sites List in 3fiu
Sodium binding site 2 out of 4 in the Structure of Nmn Synthetase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Nmn Synthetase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na250

b:18.5
occ:1.00
 OD2 B:ASP202 2.4 26.0 1.0
O4 B:POP4001 2.5 19.3 1.0
O B:HOH616 2.6 42.7 1.0
O3P B:AMP3001 2.8 21.8 1.0
OD1 B:ASP202 2.9 21.0 1.0
O6 B:POP4001 3.0 16.0 1.0
CG B:ASP202 3.0 26.4 1.0
O1P B:AMP3001 3.1 19.7 1.0
P B:AMP3001 3.2 22.4 1.0
P2 B:POP4001 3.4 17.9 1.0
O B:SER193 3.5 19.7 1.0
C B:SER193 3.6 19.5 1.0
MG B:MG5002 3.7 20.7 1.0
MG B:MG5001 3.7 19.3 1.0
O2P B:AMP3001 3.8 18.3 1.0
OE1 B:GLU147 3.8 19.0 1.0
N B:SER193 3.8 20.0 1.0
N B:ALA194 3.9 21.3 1.0
CA B:SER193 4.2 21.1 1.0
O5 B:POP4001 4.3 20.5 1.0
O B:HOH264 4.3 21.0 1.0
OH B:TYR210 4.4 22.7 1.0
CA B:ALA194 4.4 22.7 1.0
CB B:ASP202 4.5 21.6 1.0
C B:PRO192 4.5 21.4 1.0
O B:HOH279 4.6 23.3 1.0
O B:POP4001 4.7 15.9 1.0
O5' B:AMP3001 4.8 22.3 1.0
CB B:PRO192 4.8 21.5 1.0
O2 B:POP4001 4.9 18.1 1.0
O3 B:POP4001 4.9 16.3 1.0
CB B:ALA194 4.9 20.6 1.0
CD B:GLU147 4.9 21.1 1.0
O B:HOH375 5.0 46.0 1.0
CA B:PRO192 5.0 20.9 1.0

Sodium binding site 3 out of 4 in 3fiu

Go back to Sodium Binding Sites List in 3fiu
Sodium binding site 3 out of 4 in the Structure of Nmn Synthetase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Nmn Synthetase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na250

b:18.5
occ:1.00
 O4 C:POP4001 2.5 18.4 1.0
OD2 C:ASP202 2.6 23.1 1.0
O3P C:AMP3001 2.8 19.4 1.0
O C:HOH550 2.9 37.3 1.0
OD1 C:ASP202 2.9 19.2 1.0
O6 C:POP4001 3.0 19.1 1.0
O1P C:AMP3001 3.0 20.9 1.0
CG C:ASP202 3.1 23.9 1.0
P C:AMP3001 3.2 23.4 1.0
P2 C:POP4001 3.3 18.1 1.0
O C:SER193 3.5 19.2 1.0
C C:SER193 3.6 21.6 1.0
MG C:MG5002 3.7 20.3 1.0
MG C:MG5001 3.7 18.7 1.0
N C:SER193 3.7 21.0 1.0
O2P C:AMP3001 3.8 18.5 1.0
OE1 C:GLU147 3.9 13.5 1.0
N C:ALA194 4.0 22.4 1.0
CA C:SER193 4.2 21.5 1.0
O5 C:POP4001 4.2 16.5 1.0
OH C:TYR210 4.3 23.5 1.0
CA C:ALA194 4.4 24.9 1.0
O C:HOH270 4.5 20.2 1.0
C C:PRO192 4.5 21.2 1.0
O C:HOH255 4.5 22.5 1.0
CB C:ASP202 4.6 23.4 1.0
O C:POP4001 4.7 18.1 1.0
O2 C:POP4001 4.7 17.1 1.0
O5' C:AMP3001 4.7 22.2 1.0
CB C:PRO192 4.8 18.8 1.0
O3 C:POP4001 4.9 19.0 1.0
CA C:PRO192 4.9 20.2 1.0
O C:HOH263 5.0 23.6 1.0

Sodium binding site 4 out of 4 in 3fiu

Go back to Sodium Binding Sites List in 3fiu
Sodium binding site 4 out of 4 in the Structure of Nmn Synthetase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Nmn Synthetase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na250

b:19.7
occ:1.00
 O4 D:POP4001 2.6 18.9 1.0
OD2 D:ASP202 2.6 20.9 1.0
O3P D:AMP3001 2.7 21.3 1.0
O D:HOH500 2.7 37.7 1.0
OD1 D:ASP202 2.9 20.9 1.0
O1P D:AMP3001 3.0 20.7 1.0
O6 D:POP4001 3.0 20.9 1.0
CG D:ASP202 3.1 22.8 1.0
P D:AMP3001 3.1 23.9 1.0
P2 D:POP4001 3.3 19.9 1.0
O D:SER193 3.5 22.2 1.0
C D:SER193 3.6 22.6 1.0
MG D:MG5001 3.7 16.7 1.0
MG D:MG5002 3.7 20.1 1.0
O2P D:AMP3001 3.7 22.6 1.0
OE1 D:GLU147 3.7 16.9 1.0
N D:SER193 3.8 20.0 1.0
N D:ALA194 4.0 23.9 1.0
CA D:SER193 4.2 21.9 1.0
O5 D:POP4001 4.3 17.9 1.0
CA D:ALA194 4.4 26.1 1.0
O D:HOH273 4.4 20.8 1.0
OH D:TYR210 4.5 23.6 1.0
C D:PRO192 4.5 21.9 1.0
CB D:ASP202 4.6 19.6 1.0
O D:POP4001 4.6 17.5 1.0
O D:HOH272 4.6 23.5 1.0
O5' D:AMP3001 4.7 22.8 1.0
O2 D:POP4001 4.7 18.4 1.0
O3 D:POP4001 4.8 15.0 1.0
CB D:PRO192 4.9 22.1 1.0
CD D:GLU147 4.9 20.1 1.0
CB D:ALA194 5.0 24.8 1.0

Reference:

L.Sorci, D.Martynowski, D.A.Rodionov, Y.Eyobo, X.Zogaj, K.E.Klose, E.V.Nikolaev, G.Magni, H.Zhang, A.L.Osterman. Nicotinamide Mononucleotide Synthetase Is the Key Enzyme For An Alternative Route of Nad Biosynthesis in Francisella Tularensis Proc.Natl.Acad.Sci.Usa V. 106 3083 2009.
ISSN: ISSN 0027-8424
PubMed: 19204287
DOI: 10.1073/PNAS.0811718106
Page generated: Mon Oct 7 09:47:24 2024

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