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Magnesium 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:

Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Nmn Synthetase From Francisella Tularensis (pdb code 3fiu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Nmn Synthetase From Francisella Tularensis, PDB code: 3fiu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3fiu

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Magnesium binding site 1 out of 8 in the Structure of Nmn Synthetase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Nmn Synthetase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5001

b:20.1
occ:1.00
 O4 A:POP4001 2.0 18.4 1.0
O2 A:POP4001 2.1 17.1 1.0
OD2 A:ASP41 2.1 21.5 1.0
OE1 A:GLU147 2.2 14.8 1.0
O1P A:AMP3001 2.2 21.6 1.0
O A:HOH251 2.2 16.9 1.0
CD A:GLU147 3.1 18.6 1.0
P2 A:POP4001 3.2 19.4 1.0
CG A:ASP41 3.2 20.1 1.0
P1 A:POP4001 3.3 19.1 1.0
O A:POP4001 3.3 17.8 1.0
OE2 A:GLU147 3.4 19.6 1.0
P A:AMP3001 3.4 26.7 1.0
CB A:ASP41 3.6 16.1 1.0
NA A:NA250 3.8 19.4 1.0
O3P A:AMP3001 3.9 22.3 1.0
O5' A:AMP3001 3.9 23.5 1.0
O A:HOH272 3.9 20.5 1.0
O3 A:POP4001 4.0 19.9 1.0
C5' A:AMP3001 4.1 20.2 1.0
O6 A:POP4001 4.1 18.6 1.0
O3' A:AMP3001 4.2 17.9 1.0
O5 A:POP4001 4.3 17.4 1.0
O A:HOH750 4.3 43.7 1.0
OD1 A:ASP41 4.3 20.7 1.0
O A:HOH259 4.3 22.8 1.0
NZ A:LYS171 4.4 21.7 1.0
O1 A:POP4001 4.4 19.0 1.0
CG A:GLU147 4.5 20.4 1.0
OG1 A:THR142 4.5 18.4 1.0
MG A:MG5002 4.6 21.0 1.0
O2P A:AMP3001 4.7 24.3 1.0
O A:HOH255 4.8 28.7 1.0
ND2 A:ASN144 4.8 21.7 1.0
C3' A:AMP3001 4.9 20.6 1.0
O A:THR142 5.0 19.5 1.0
CA A:ASP41 5.0 15.3 1.0

Magnesium binding site 2 out of 8 in 3fiu

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Magnesium binding site 2 out of 8 in the Structure of Nmn Synthetase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Nmn Synthetase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5002

b:21.0
occ:1.00
 O3P A:AMP3001 2.0 22.3 1.0
O3 A:POP4001 2.0 19.9 1.0
O A:HOH253 2.0 21.0 1.0
O6 A:POP4001 2.1 18.6 1.0
O A:HOH254 2.1 20.3 1.0
O A:SER193 2.2 23.4 1.0
P2 A:POP4001 3.1 19.4 1.0
P1 A:POP4001 3.2 19.1 1.0
P A:AMP3001 3.4 26.7 1.0
C A:SER193 3.4 23.3 1.0
O A:POP4001 3.4 17.8 1.0
NA A:NA250 3.7 19.4 1.0
O4 A:POP4001 3.8 18.4 1.0
O2 A:POP4001 3.8 17.1 1.0
O5' A:AMP3001 3.9 23.5 1.0
OG A:SER37 3.9 16.9 1.0
N A:SER193 4.0 22.6 1.0
O A:HOH290 4.1 22.7 1.0
O1P A:AMP3001 4.1 21.6 1.0
O A:HOH813 4.2 51.6 1.0
N A:ALA194 4.2 24.0 1.0
CA A:ALA194 4.2 25.3 1.0
CA A:SER193 4.3 23.2 1.0
O1 A:POP4001 4.4 19.0 1.0
O5 A:POP4001 4.4 17.4 1.0
O A:HOH377 4.4 29.9 1.0
CB A:SER37 4.4 18.0 1.0
O2P A:AMP3001 4.5 24.3 1.0
CA A:GLY39 4.6 17.9 1.0
MG A:MG5001 4.6 20.1 1.0
C A:ALA194 4.7 27.5 1.0
CB A:SER193 5.0 24.0 1.0

Magnesium binding site 3 out of 8 in 3fiu

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Magnesium binding site 3 out of 8 in the Structure of Nmn Synthetase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Nmn Synthetase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5001

b:19.3
occ:1.00
 O4 B:POP4001 2.0 19.3 1.0
O1P B:AMP3001 2.1 19.7 1.0
O2 B:POP4001 2.1 18.1 1.0
OE1 B:GLU147 2.1 19.0 1.0
OD2 B:ASP41 2.2 21.5 1.0
O B:HOH252 2.2 14.6 1.0
CD B:GLU147 3.1 21.1 1.0
P2 B:POP4001 3.2 17.9 1.0
CG B:ASP41 3.3 20.4 1.0
P1 B:POP4001 3.3 16.8 1.0
P B:AMP3001 3.3 22.4 1.0
O B:POP4001 3.3 15.9 1.0
OE2 B:GLU147 3.4 19.8 1.0
CB B:ASP41 3.7 15.9 1.0
NA B:NA250 3.7 18.5 1.0
O3P B:AMP3001 3.8 21.8 1.0
O B:HOH264 3.8 21.0 1.0
O5' B:AMP3001 3.9 22.3 1.0
O3 B:POP4001 4.0 16.3 1.0
O6 B:POP4001 4.1 16.0 1.0
C5' B:AMP3001 4.2 21.0 1.0
O B:HOH279 4.2 23.3 1.0
O B:HOH616 4.2 42.7 1.0
O3' B:AMP3001 4.3 17.7 1.0
O5 B:POP4001 4.3 20.5 1.0
OD1 B:ASP41 4.4 22.3 1.0
O1 B:POP4001 4.4 14.4 1.0
CG B:GLU147 4.5 20.2 1.0
NZ B:LYS171 4.5 16.9 1.0
OG1 B:THR142 4.5 17.9 1.0
MG B:MG5002 4.6 20.7 1.0
O2P B:AMP3001 4.6 18.3 1.0
O B:HOH318 4.8 24.7 1.0
ND2 B:ASN144 4.9 17.2 1.0
C3' B:AMP3001 4.9 16.9 1.0
O B:THR142 4.9 17.0 1.0

Magnesium binding site 4 out of 8 in 3fiu

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Magnesium binding site 4 out of 8 in the Structure of Nmn Synthetase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Nmn Synthetase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5002

b:20.7
occ:1.00
 O3P B:AMP3001 1.9 21.8 1.0
O3 B:POP4001 2.0 16.3 1.0
O6 B:POP4001 2.1 16.0 1.0
O B:SER193 2.1 19.7 1.0
O B:HOH255 2.2 19.6 1.0
O B:HOH253 2.2 19.1 1.0
P2 B:POP4001 3.2 17.9 1.0
P1 B:POP4001 3.2 16.8 1.0
P B:AMP3001 3.3 22.4 1.0
C B:SER193 3.3 19.5 1.0
O B:POP4001 3.4 15.9 1.0
O4 B:POP4001 3.7 19.3 1.0
NA B:NA250 3.7 18.5 1.0
O5' B:AMP3001 3.8 22.3 1.0
O2 B:POP4001 3.9 18.1 1.0
OG B:SER37 3.9 18.2 1.0
N B:SER193 4.0 20.0 1.0
O B:HOH581 4.1 39.7 1.0
O1P B:AMP3001 4.1 19.7 1.0
N B:ALA194 4.2 21.3 1.0
CA B:ALA194 4.2 22.7 1.0
O B:HOH260 4.2 19.6 1.0
CA B:SER193 4.3 21.1 1.0
O2P B:AMP3001 4.4 18.3 1.0
O1 B:POP4001 4.4 14.4 1.0
CB B:SER37 4.5 17.0 1.0
O5 B:POP4001 4.5 20.5 1.0
MG B:MG5001 4.6 19.3 1.0
O B:HOH287 4.6 27.9 1.0
CA B:GLY39 4.7 15.5 1.0
C B:ALA194 4.7 23.4 1.0
CB B:SER193 5.0 21.4 1.0

Magnesium binding site 5 out of 8 in 3fiu

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Magnesium binding site 5 out of 8 in the Structure of Nmn Synthetase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Nmn Synthetase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg5001

b:18.7
occ:1.00
 O4 C:POP4001 2.1 18.4 1.0
O1P C:AMP3001 2.1 20.9 1.0
O2 C:POP4001 2.1 17.1 1.0
OD2 C:ASP41 2.1 22.0 1.0
O C:HOH251 2.2 15.9 1.0
OE1 C:GLU147 2.2 13.5 1.0
CD C:GLU147 3.2 17.9 1.0
CG C:ASP41 3.2 17.2 1.0
P2 C:POP4001 3.3 18.1 1.0
P1 C:POP4001 3.3 17.9 1.0
P C:AMP3001 3.4 23.4 1.0
O C:POP4001 3.4 18.1 1.0
OE2 C:GLU147 3.4 24.7 1.0
CB C:ASP41 3.7 17.1 1.0
NA C:NA250 3.7 18.5 1.0
O3P C:AMP3001 3.8 19.4 1.0
O5' C:AMP3001 3.9 22.2 1.0
O C:HOH270 3.9 20.2 1.0
O3 C:POP4001 4.1 19.0 1.0
C5' C:AMP3001 4.1 16.6 1.0
O3' C:AMP3001 4.2 16.7 1.0
O C:HOH255 4.2 22.5 1.0
O6 C:POP4001 4.2 19.1 1.0
OD1 C:ASP41 4.3 21.4 1.0
O5 C:POP4001 4.3 16.5 1.0
O C:HOH550 4.4 37.3 1.0
O1 C:POP4001 4.4 17.4 1.0
OG1 C:THR142 4.4 17.9 1.0
NZ C:LYS171 4.5 17.8 1.0
CG C:GLU147 4.5 19.0 1.0
O2P C:AMP3001 4.6 18.5 1.0
MG C:MG5002 4.6 20.3 1.0
O C:HOH333 4.8 24.4 1.0
C3' C:AMP3001 4.8 13.7 1.0
O C:THR142 4.9 16.4 1.0
ND2 C:ASN144 4.9 17.6 1.0
C4' C:AMP3001 5.0 17.0 1.0

Magnesium binding site 6 out of 8 in 3fiu

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Magnesium binding site 6 out of 8 in the Structure of Nmn Synthetase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Nmn Synthetase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg5002

b:20.3
occ:1.00
 O3P C:AMP3001 2.0 19.4 1.0
O3 C:POP4001 2.0 19.0 1.0
O C:SER193 2.1 19.2 1.0
O C:HOH254 2.1 20.1 1.0
O C:HOH252 2.2 19.8 1.0
O6 C:POP4001 2.2 19.1 1.0
P1 C:POP4001 3.2 17.9 1.0
P2 C:POP4001 3.2 18.1 1.0
C C:SER193 3.3 21.6 1.0
P C:AMP3001 3.4 23.4 1.0
O C:POP4001 3.5 18.1 1.0
NA C:NA250 3.7 18.5 1.0
O4 C:POP4001 3.7 18.4 1.0
O2 C:POP4001 3.8 17.1 1.0
O5' C:AMP3001 3.9 22.2 1.0
OG C:SER37 4.0 18.2 1.0
N C:SER193 4.0 21.0 1.0
O1P C:AMP3001 4.2 20.9 1.0
O C:HOH407 4.2 35.4 1.0
O C:HOH266 4.2 20.3 1.0
N C:ALA194 4.2 22.4 1.0
CA C:SER193 4.2 21.5 1.0
CA C:ALA194 4.3 24.9 1.0
CB C:SER37 4.4 16.3 1.0
O2P C:AMP3001 4.4 18.5 1.0
O1 C:POP4001 4.5 17.4 1.0
O5 C:POP4001 4.5 16.5 1.0
O C:HOH297 4.6 29.9 1.0
MG C:MG5001 4.6 18.7 1.0
C C:ALA194 4.7 26.5 1.0
CA C:GLY39 4.7 14.8 1.0
O C:HOH713 4.8 40.4 1.0
CB C:SER193 4.9 22.9 1.0
O C:ALA194 5.0 29.4 1.0

Magnesium binding site 7 out of 8 in 3fiu

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Magnesium binding site 7 out of 8 in the Structure of Nmn Synthetase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Nmn Synthetase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg5001

b:16.7
occ:1.00
 O4 D:POP4001 2.0 18.9 1.0
O2 D:POP4001 2.0 18.4 1.0
O1P D:AMP3001 2.1 20.7 1.0
OD2 D:ASP41 2.1 20.7 1.0
OE1 D:GLU147 2.1 16.9 1.0
O D:HOH251 2.2 15.7 1.0
CD D:GLU147 3.1 20.1 1.0
P1 D:POP4001 3.2 18.7 1.0
CG D:ASP41 3.2 18.9 1.0
P2 D:POP4001 3.2 19.9 1.0
P D:AMP3001 3.3 23.9 1.0
O D:POP4001 3.3 17.5 1.0
OE2 D:GLU147 3.4 19.2 1.0
CB D:ASP41 3.7 16.3 1.0
NA D:NA250 3.7 19.7 1.0
O3P D:AMP3001 3.8 21.3 1.0
O5' D:AMP3001 3.8 22.8 1.0
O D:HOH273 3.9 20.8 1.0
O3 D:POP4001 4.0 15.0 1.0
O6 D:POP4001 4.1 20.9 1.0
O D:HOH272 4.2 23.5 1.0
C5' D:AMP3001 4.2 21.6 1.0
O3' D:AMP3001 4.2 16.9 1.0
O D:HOH500 4.2 37.7 1.0
O5 D:POP4001 4.3 17.9 1.0
OD1 D:ASP41 4.3 21.3 1.0
O1 D:POP4001 4.4 16.9 1.0
NZ D:LYS171 4.4 17.9 1.0
CG D:GLU147 4.5 18.8 1.0
OG1 D:THR142 4.6 18.9 1.0
MG D:MG5002 4.6 20.1 1.0
O2P D:AMP3001 4.6 22.6 1.0
O D:HOH317 4.6 27.8 1.0
C3' D:AMP3001 4.8 16.0 1.0
ND2 D:ASN144 4.9 16.9 1.0
O D:THR142 4.9 19.0 1.0

Magnesium binding site 8 out of 8 in 3fiu

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Magnesium binding site 8 out of 8 in the Structure of Nmn Synthetase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Nmn Synthetase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg5002

b:20.1
occ:1.00
 O3P D:AMP3001 1.9 21.3 1.0
O3 D:POP4001 2.0 15.0 1.0
O D:HOH253 2.1 21.9 1.0
O D:HOH252 2.1 21.8 1.0
O6 D:POP4001 2.2 20.9 1.0
O D:SER193 2.2 22.2 1.0
P1 D:POP4001 3.1 18.7 1.0
P2 D:POP4001 3.2 19.9 1.0
P D:AMP3001 3.3 23.9 1.0
C D:SER193 3.4 22.6 1.0
O D:POP4001 3.4 17.5 1.0
NA D:NA250 3.7 19.7 1.0
O4 D:POP4001 3.7 18.9 1.0
O5' D:AMP3001 3.8 22.8 1.0
O2 D:POP4001 3.8 18.4 1.0
OG D:SER37 3.9 17.5 1.0
N D:SER193 4.1 20.0 1.0
O1P D:AMP3001 4.1 20.7 1.0
O D:HOH289 4.2 21.9 1.0
N D:ALA194 4.3 23.9 1.0
CA D:ALA194 4.3 26.1 1.0
CA D:SER193 4.3 21.9 1.0
CB D:SER37 4.3 16.8 1.0
O1 D:POP4001 4.4 16.9 1.0
O2P D:AMP3001 4.4 22.6 1.0
O D:HOH322 4.4 26.9 1.0
O5 D:POP4001 4.5 17.9 1.0
MG D:MG5001 4.6 16.7 1.0
CA D:GLY39 4.6 16.3 1.0
C D:ALA194 4.7 27.8 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 Dec 14 08:08:44 2020

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