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Magnesium in PDB 2r5w: Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase From Francisella Tularensis

Enzymatic activity of Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase From Francisella Tularensis

All present enzymatic activity of Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase From Francisella Tularensis:
2.7.7.1;

Protein crystallography data

The structure of Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase From Francisella Tularensis, PDB code: 2r5w was solved by N.Huang, L.Sorci, X.Zhang, C.Brautigan, X.Li, N.Raffaelli, N.Grishin, A.Osterman, H.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.53 / 2.30
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 124.909, 163.152, 180.792, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 25.3

Other elements in 2r5w:

The structure of Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase From Francisella Tularensis also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase From Francisella Tularensis (pdb code 2r5w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase From Francisella Tularensis, PDB code: 2r5w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2r5w

Go back to Magnesium Binding Sites List in 2r5w
Magnesium binding site 1 out of 6 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase 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 Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg348

b:34.6
occ:1.00
O B:HOH357 2.1 32.2 1.0
O B:HOH358 2.1 35.8 1.0
OE1 B:GLU254 2.2 37.8 1.0
O B:GLY234 2.2 30.4 1.0
OD1 B:ASP308 2.3 50.5 1.0
MG B:MG350 2.5 39.2 1.0
CL B:CL351 2.6 37.5 1.0
CG B:ASP308 3.0 49.3 1.0
OD2 B:ASP308 3.0 47.8 1.0
CD B:GLU254 3.3 34.9 1.0
C B:GLY234 3.3 30.4 1.0
OE1 B:GLU250 3.6 29.6 1.0
CA B:GLY235 3.6 30.2 1.0
OE2 B:GLU254 3.7 31.1 1.0
N B:GLY235 3.9 30.1 1.0
O B:HOH461 4.0 48.1 1.0
O B:HOH386 4.4 38.1 1.0
O B:HOH472 4.5 48.2 1.0
CG B:GLU254 4.5 35.5 1.0
CB B:ASP308 4.5 47.4 1.0
CA B:GLY234 4.5 30.2 1.0
CD B:GLU250 4.5 32.4 1.0
N B:GLY234 4.5 30.5 1.0
O B:HOH353 4.6 50.5 1.0
MG B:MG349 4.7 39.4 1.0
O B:HOH360 4.7 36.8 1.0
NH1 B:ARG221 4.8 39.9 1.0

Magnesium binding site 2 out of 6 in 2r5w

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Magnesium binding site 2 out of 6 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase 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 Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg349

b:39.4
occ:1.00
O B:HOH356 2.1 28.8 1.0
O B:HOH355 2.2 31.9 1.0
OE2 B:GLU250 2.2 36.1 1.0
O B:HOH386 2.3 38.1 1.0
O B:HOH354 2.3 30.1 1.0
CL B:CL351 2.8 37.5 1.0
MG B:MG350 3.1 39.2 1.0
CD B:GLU250 3.1 32.4 1.0
OE1 B:GLU250 3.3 29.6 1.0
OE2 B:GLU253 4.0 44.2 1.0
O B:HOH353 4.1 50.5 1.0
N B:PHE236 4.2 32.0 1.0
NH2 B:ARG249 4.2 27.1 1.0
O B:HOH461 4.3 48.1 1.0
CG B:GLU250 4.5 32.3 1.0
O B:PHE236 4.5 35.8 1.0
CA B:GLY235 4.6 30.2 1.0
OE1 B:GLU238 4.7 48.4 1.0
MG B:MG348 4.7 34.6 1.0
O B:HOH539 4.7 54.7 1.0
C B:GLY235 4.8 30.5 1.0
OD2 B:ASP308 4.8 47.8 1.0
OD2 B:ASP307 4.9 44.3 1.0

Magnesium binding site 3 out of 6 in 2r5w

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Magnesium binding site 3 out of 6 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase 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 Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg350

b:39.2
occ:1.00
OE1 B:GLU250 2.1 29.6 1.0
OE1 B:GLU254 2.2 37.8 1.0
O B:HOH353 2.3 50.5 1.0
OD2 B:ASP308 2.4 47.8 1.0
MG B:MG348 2.5 34.6 1.0
CL B:CL351 2.6 37.5 1.0
MG B:MG349 3.1 39.4 1.0
CD B:GLU250 3.1 32.4 1.0
CD B:GLU254 3.3 34.9 1.0
CG B:ASP308 3.4 49.3 1.0
OE2 B:GLU250 3.4 36.1 1.0
OD1 B:ASP308 3.6 50.5 1.0
CG B:GLU254 3.8 35.5 1.0
O B:GLY234 3.9 30.4 1.0
OE2 B:GLU253 4.0 44.2 1.0
O B:HOH461 4.0 48.1 1.0
O B:HOH386 4.1 38.1 1.0
OD2 B:ASP307 4.2 44.3 1.0
O B:HOH356 4.2 28.8 1.0
O B:HOH358 4.2 35.8 1.0
OE2 B:GLU254 4.4 31.1 1.0
CA B:GLY235 4.5 30.2 1.0
CG B:GLU250 4.5 32.3 1.0
C B:GLY234 4.5 30.4 1.0
O B:HOH357 4.6 32.2 1.0
CB B:ASP308 4.8 47.4 1.0
N B:GLY235 4.8 30.1 1.0
O B:HOH355 4.8 31.9 1.0
CG B:ASP307 4.8 45.4 1.0
CB B:GLU250 4.9 30.3 1.0

Magnesium binding site 4 out of 6 in 2r5w

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Magnesium binding site 4 out of 6 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase 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 Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg348

b:31.1
occ:1.00
O A:HOH427 2.0 22.0 1.0
O A:HOH356 2.1 28.7 1.0
O A:GLY234 2.1 23.9 1.0
OE2 A:GLU254 2.2 27.7 1.0
OD1 A:ASP308 2.3 30.3 1.0
CL A:CL351 2.7 31.4 1.0
MG A:MG350 2.7 30.8 1.0
CG A:ASP308 3.1 33.6 1.0
O A:HOH355 3.1 42.9 1.0
C A:GLY234 3.2 23.9 1.0
CD A:GLU254 3.2 26.1 1.0
OD2 A:ASP308 3.3 29.0 1.0
CA A:GLY235 3.5 22.3 1.0
OE1 A:GLU254 3.7 26.9 1.0
N A:GLY235 3.8 21.4 1.0
OE1 A:GLU250 3.9 27.7 1.0
O A:HOH447 4.0 39.8 1.0
O A:HOH491 4.1 37.5 1.0
O A:HOH357 4.2 34.5 1.0
O A:HOH390 4.5 32.6 1.0
CA A:GLY234 4.5 24.2 1.0
CG A:GLU254 4.5 25.0 1.0
N A:GLY234 4.5 24.3 1.0
CB A:ASP308 4.5 31.7 1.0
NH1 A:ARG221 4.5 36.2 1.0
CD A:GLU250 4.7 23.2 1.0
O A:HOH388 4.8 27.2 1.0
C A:GLY235 5.0 24.6 1.0

Magnesium binding site 5 out of 6 in 2r5w

Go back to Magnesium Binding Sites List in 2r5w
Magnesium binding site 5 out of 6 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase 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 Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg349

b:30.1
occ:1.00
O A:HOH357 2.0 34.5 1.0
O A:HOH352 2.1 29.9 1.0
O A:HOH353 2.2 26.1 1.0
OE2 A:GLU250 2.2 27.8 1.0
O A:HOH354 2.3 28.4 1.0
CL A:CL351 3.1 31.4 1.0
CD A:GLU250 3.2 23.2 1.0
OE1 A:GLU250 3.5 27.7 1.0
MG A:MG350 3.6 30.8 1.0
NH2 A:ARG249 4.0 23.2 1.0
N A:PHE236 4.1 24.5 1.0
O A:HOH414 4.1 36.7 1.0
OE1 A:GLU253 4.2 26.7 1.0
O A:HOH388 4.2 27.2 1.0
O A:HOH485 4.2 42.2 1.0
O A:HOH447 4.2 39.8 1.0
O A:HOH480 4.2 56.7 1.0
O A:PHE236 4.3 23.3 1.0
CG A:GLU250 4.6 27.7 1.0
OE1 A:GLU238 4.6 46.1 1.0
CA A:GLY235 4.7 22.3 1.0
C A:GLY235 4.8 24.6 1.0
CB A:PHE236 4.8 25.2 1.0
CA A:PHE236 4.9 24.1 1.0
O A:HOH355 4.9 42.9 1.0
CZ A:ARG249 4.9 25.1 1.0
NH1 A:ARG249 4.9 21.6 1.0

Magnesium binding site 6 out of 6 in 2r5w

Go back to Magnesium Binding Sites List in 2r5w
Magnesium binding site 6 out of 6 in the Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase 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 Crystal Structure of A Bifunctional Nmn Adenylyltransferase/Adp Ribose Pyrophosphatase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg350

b:30.8
occ:1.00
OE2 A:GLU254 2.1 27.7 1.0
OE1 A:GLU250 2.2 27.7 1.0
O A:HOH357 2.2 34.5 1.0
O A:HOH388 2.2 27.2 1.0
OD2 A:ASP308 2.3 29.0 1.0
CL A:CL351 2.6 31.4 1.0
MG A:MG348 2.7 31.1 1.0
CD A:GLU254 3.1 26.1 1.0
CG A:ASP308 3.2 33.6 1.0
CD A:GLU250 3.2 23.2 1.0
OD1 A:ASP308 3.4 30.3 1.0
CG A:GLU254 3.5 25.0 1.0
OE2 A:GLU250 3.5 27.8 1.0
MG A:MG349 3.6 30.1 1.0
O A:GLY234 3.8 23.9 1.0
O A:HOH480 3.9 56.7 1.0
O A:HOH447 4.0 39.8 1.0
OE1 A:GLU253 4.2 26.7 1.0
O A:HOH427 4.2 22.0 1.0
OE1 A:GLU254 4.2 26.9 1.0
C A:GLY234 4.4 23.9 1.0
CA A:GLY235 4.5 22.3 1.0
CG A:GLU250 4.5 27.7 1.0
O A:HOH355 4.5 42.9 1.0
OD2 A:ASP307 4.6 40.4 1.0
O A:HOH352 4.6 29.9 1.0
CB A:ASP308 4.6 31.7 1.0
O A:HOH356 4.7 28.7 1.0
N A:GLY235 4.7 21.4 1.0
CB A:GLU250 4.8 21.5 1.0
CG A:ASP307 5.0 36.7 1.0

Reference:

N.Huang, L.Sorci, X.Zhang, C.A.Brautigam, X.Li, N.Raffaelli, G.Magni, N.V.Grishin, A.L.Osterman, H.Zhang. Bifunctional Nmn Adenylyltransferase/Adp-Ribose Pyrophosphatase: Structure and Function in Bacterial Nad Metabolism. Structure V. 16 196 2008.
ISSN: ISSN 0969-2126
PubMed: 18275811
DOI: 10.1016/J.STR.2007.11.017
Page generated: Mon Dec 14 07:37:55 2020

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