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Magnesium in PDB 3e27: Nicotinic Acid Mononucleotide (Namn) Adenylyltransferase From Bacillus Anthracis: Product Complex

Enzymatic activity of Nicotinic Acid Mononucleotide (Namn) Adenylyltransferase From Bacillus Anthracis: Product Complex

All present enzymatic activity of Nicotinic Acid Mononucleotide (Namn) Adenylyltransferase From Bacillus Anthracis: Product Complex:
2.7.7.18;

Protein crystallography data

The structure of Nicotinic Acid Mononucleotide (Namn) Adenylyltransferase From Bacillus Anthracis: Product Complex, PDB code: 3e27 was solved by D.Martynowski, Y.Eyobo, H.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.856, 137.413, 143.972, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 27.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Nicotinic Acid Mononucleotide (Namn) Adenylyltransferase From Bacillus Anthracis: Product Complex (pdb code 3e27). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Nicotinic Acid Mononucleotide (Namn) Adenylyltransferase From Bacillus Anthracis: Product Complex, PDB code: 3e27:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3e27

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Magnesium binding site 1 out of 4 in the Nicotinic Acid Mononucleotide (Namn) Adenylyltransferase From Bacillus Anthracis: Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nicotinic Acid Mononucleotide (Namn) Adenylyltransferase From Bacillus Anthracis: Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg190

b:40.3
occ:1.00
 OD1 A:ASP108 2.6 23.1 1.0
O14 A:DND191 3.0 25.3 1.0
NH2 A:ARG133 3.1 32.2 1.0
O12 A:DND191 3.1 31.1 1.0
C2B A:DND191 3.3 24.0 1.0
CG A:ASP108 3.5 26.2 1.0
O2B A:DND191 3.6 23.5 1.0
OD2 A:ASP108 3.6 26.4 1.0
PA A:DND191 3.8 24.9 1.0
O5B A:DND191 3.9 25.2 1.0
C3B A:DND191 4.0 24.5 1.0
O A:HOH230 4.1 35.8 1.0
PN A:DND191 4.2 26.4 1.0
O3P A:DND191 4.2 26.7 1.0
O A:HOH227 4.4 33.0 1.0
CZ A:ARG133 4.4 33.6 1.0
C8A A:DND191 4.4 23.2 1.0
CG A:MET109 4.5 27.3 1.0
C1B A:DND191 4.6 23.2 1.0
N9A A:DND191 4.7 24.6 1.0
O A:HOH226 4.9 27.4 1.0
CB A:ASP108 4.9 26.0 1.0
C5B A:DND191 4.9 23.8 1.0
C4B A:DND191 5.0 24.0 1.0

Magnesium binding site 2 out of 4 in 3e27

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Magnesium binding site 2 out of 4 in the Nicotinic Acid Mononucleotide (Namn) Adenylyltransferase From Bacillus Anthracis: Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nicotinic Acid Mononucleotide (Namn) Adenylyltransferase From Bacillus Anthracis: Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg190

b:36.8
occ:1.00
 O12 B:DND191 2.6 30.2 1.0
OD1 B:ASP108 2.7 27.9 1.0
O B:HOH294 3.1 32.5 1.0
O14 B:DND191 3.3 29.4 1.0
NH2 B:ARG133 3.3 42.5 1.0
O B:HOH297 3.4 39.9 1.0
C2B B:DND191 3.4 25.2 1.0
CG B:ASP108 3.6 27.3 1.0
O2B B:DND191 3.6 26.7 1.0
O5B B:DND191 3.8 27.1 1.0
OD2 B:ASP108 3.8 26.9 1.0
PN B:DND191 3.8 28.3 1.0
PA B:DND191 3.9 27.6 1.0
C3B B:DND191 4.0 23.7 1.0
O3P B:DND191 4.0 28.9 1.0
O B:HOH295 4.1 28.2 1.0
CG B:MET109 4.2 24.1 1.0
CE B:MET109 4.4 18.4 1.0
CZ B:ARG133 4.6 39.6 1.0
C8A B:DND191 4.6 26.0 1.0
O11 B:DND191 4.7 29.3 1.0
C1B B:DND191 4.7 25.5 1.0
C5B B:DND191 4.8 23.9 1.0
O B:HOH270 4.9 29.5 1.0
N9A B:DND191 4.9 26.8 1.0
C4B B:DND191 4.9 25.0 1.0
O5D B:DND191 4.9 27.4 1.0
CB B:ASP108 5.0 25.8 1.0

Magnesium binding site 3 out of 4 in 3e27

Go back to Magnesium Binding Sites List in 3e27
Magnesium binding site 3 out of 4 in the Nicotinic Acid Mononucleotide (Namn) Adenylyltransferase From Bacillus Anthracis: Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Nicotinic Acid Mononucleotide (Namn) Adenylyltransferase From Bacillus Anthracis: Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg190

b:40.9
occ:1.00
 OD1 C:ASP108 2.6 20.4 1.0
O12 C:DND191 2.9 25.3 1.0
O C:HOH256 2.9 38.7 1.0
O14 C:DND191 3.2 21.7 1.0
C2B C:DND191 3.4 19.3 1.0
CG C:ASP108 3.4 22.1 1.0
NH2 C:ARG133 3.4 32.4 1.0
OD2 C:ASP108 3.5 22.7 1.0
O C:HOH287 3.6 34.6 1.0
O2B C:DND191 3.6 17.5 1.0
C3B C:DND191 3.9 18.6 1.0
O5B C:DND191 3.9 21.2 1.0
O C:HOH226 4.0 26.9 1.0
PA C:DND191 4.0 22.2 1.0
PN C:DND191 4.1 24.1 1.0
CE C:MET109 4.3 20.3 1.0
O3P C:DND191 4.3 22.6 1.0
C8A C:DND191 4.5 23.0 1.0
CG C:MET109 4.6 19.9 1.0
C1B C:DND191 4.6 20.9 1.0
CZ C:ARG133 4.7 31.7 1.0
CB C:ASP108 4.8 22.0 1.0
O C:HOH291 4.8 29.5 1.0
N9A C:DND191 4.8 22.2 1.0
C4B C:DND191 4.9 19.5 1.0
C5B C:DND191 4.9 20.1 1.0
O3B C:DND191 4.9 17.4 1.0
O11 C:DND191 4.9 25.3 1.0

Magnesium binding site 4 out of 4 in 3e27

Go back to Magnesium Binding Sites List in 3e27
Magnesium binding site 4 out of 4 in the Nicotinic Acid Mononucleotide (Namn) Adenylyltransferase From Bacillus Anthracis: Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Nicotinic Acid Mononucleotide (Namn) Adenylyltransferase From Bacillus Anthracis: Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg190

b:39.6
occ:1.00
 O D:HOH297 2.4 30.1 1.0
OD1 D:ASP108 2.5 25.5 1.0
O12 D:DND191 3.0 32.0 1.0
C2B D:DND191 3.3 20.6 1.0
CG D:ASP108 3.4 26.8 1.0
NH2 D:ARG133 3.5 37.2 1.0
O14 D:DND191 3.5 26.4 1.0
O2B D:DND191 3.5 22.2 1.0
OD2 D:ASP108 3.6 27.9 1.0
O5B D:DND191 3.8 22.1 1.0
C3B D:DND191 3.9 20.7 1.0
PA D:DND191 4.0 26.0 1.0
PN D:DND191 4.1 28.8 1.0
O3P D:DND191 4.1 29.1 1.0
O D:HOH295 4.3 32.1 1.0
CG D:MET109 4.4 24.4 1.0
C8A D:DND191 4.5 22.4 1.0
C1B D:DND191 4.6 21.3 1.0
CE D:MET109 4.6 22.4 1.0
N9A D:DND191 4.7 23.0 1.0
CZ D:ARG133 4.8 38.2 1.0
CB D:ASP108 4.9 26.1 1.0
O3B D:DND191 4.9 20.1 1.0
C5B D:DND191 4.9 20.2 1.0
C4B D:DND191 4.9 18.1 1.0

Reference:

L.Sorci, Y.Pan, Y.Eyobo, I.Rodionova, N.Huang, O.Kurnasov, S.Zhong, A.D.Mackerell, H.Zhang, A.L.Osterman. Targeting Nad Biosynthesis in Bacterial Pathogens: Structure-Based Development of Inhibitors of Nicotinate Mononucleotide Adenylyltransferase Nadd. Chem.Biol. V. 16 849 2009.
ISSN: ISSN 1074-5521
PubMed: 19716475
DOI: 10.1016/J.CHEMBIOL.2009.07.006
Page generated: Wed Aug 14 12:50:22 2024

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