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Magnesium in PDB 2buf: Arginine Feed-Back Inhibitable Acetylglutamate Kinase

Enzymatic activity of Arginine Feed-Back Inhibitable Acetylglutamate Kinase

All present enzymatic activity of Arginine Feed-Back Inhibitable Acetylglutamate Kinase:
2.7.2.8;

Protein crystallography data

The structure of Arginine Feed-Back Inhibitable Acetylglutamate Kinase, PDB code: 2buf was solved by S.Ramon-Maiques, M.L.Fernandez-Murga, A.Vagin, I.Fita, V.Rubio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.00 / 2.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.860, 98.780, 162.900, 91.49, 92.03, 107.56
R / Rfree (%) 24.9 / 26.7

Other elements in 2buf:

The structure of Arginine Feed-Back Inhibitable Acetylglutamate Kinase also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Arginine Feed-Back Inhibitable Acetylglutamate Kinase (pdb code 2buf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Arginine Feed-Back Inhibitable Acetylglutamate Kinase, PDB code: 2buf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2buf

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Magnesium binding site 1 out of 8 in the Arginine Feed-Back Inhibitable Acetylglutamate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Arginine Feed-Back Inhibitable Acetylglutamate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1301

b:50.6
occ:1.00
 O2A B:ADP1300 2.4 63.9 1.0
O1B B:ADP1300 2.5 70.9 1.0
PB B:ADP1300 3.5 69.2 1.0
PA B:ADP1300 3.6 64.5 1.0
O3A B:ADP1300 3.6 68.0 1.0
ND2 B:ASN197 3.7 56.4 1.0
O3B B:ADP1300 3.7 66.6 1.0
OD1 B:ASP199 3.8 58.3 1.0
OD1 B:ASN197 3.8 59.3 1.0
CG B:ASN197 4.2 56.4 1.0
O B:GLY251 4.2 62.0 1.0
CA B:GLY251 4.4 59.9 1.0
OE1 B:NLG1302 4.5 57.1 1.0
O5' B:ADP1300 4.6 64.6 1.0
CG B:ASP199 4.6 55.8 1.0
O1A B:ADP1300 4.6 62.2 1.0
NZ B:LYS255 4.7 71.3 1.0
C B:GLY251 4.7 59.8 1.0
NZ B:LYS33 4.8 54.8 1.0
OE2 B:NLG1302 4.8 57.6 1.0
CE B:LYS255 4.8 70.0 1.0
O2B B:ADP1300 4.9 68.0 1.0
OD2 B:ASP199 5.0 56.7 1.0
CD B:NLG1302 5.0 57.9 1.0

Magnesium binding site 2 out of 8 in 2buf

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Magnesium binding site 2 out of 8 in the Arginine Feed-Back Inhibitable Acetylglutamate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Arginine Feed-Back Inhibitable Acetylglutamate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1301

b:0.7
occ:1.00
 O2A C:ADP1300 2.4 0.7 1.0
O3A C:ADP1300 2.7 0.6 1.0
PA C:ADP1300 2.8 0.6 1.0
O2B C:ADP1300 3.0 0.8 1.0
O1A C:ADP1300 3.2 0.2 1.0
PB C:ADP1300 3.5 0.2 1.0
O3B C:ADP1300 4.3 0.4 1.0
O5' C:ADP1300 4.4 0.1 1.0
O1B C:ADP1300 4.7 0.5 1.0
CA C:GLY251 4.9 62.9 1.0

Magnesium binding site 3 out of 8 in 2buf

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Magnesium binding site 3 out of 8 in the Arginine Feed-Back Inhibitable Acetylglutamate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Arginine Feed-Back Inhibitable Acetylglutamate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1301

b:57.0
occ:1.00
 O3B D:ADP1300 2.2 59.4 1.0
PB D:ADP1300 3.1 57.9 1.0
O2A D:ADP1300 3.1 58.2 1.0
O1B D:ADP1300 3.1 58.8 1.0
O3A D:ADP1300 3.2 55.1 1.0
PA D:ADP1300 3.7 55.7 1.0
O2B D:ADP1300 4.5 54.7 1.0
O1A D:ADP1300 4.5 52.9 1.0
O5' D:ADP1300 5.0 53.2 1.0

Magnesium binding site 4 out of 8 in 2buf

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Magnesium binding site 4 out of 8 in the Arginine Feed-Back Inhibitable Acetylglutamate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Arginine Feed-Back Inhibitable Acetylglutamate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1300

b:69.8
occ:1.00
 O3B E:ADP1299 2.5 76.3 1.0
O2A E:ADP1299 2.8 77.8 1.0
OD1 E:ASN197 3.4 69.7 1.0
OE1 E:NLG1301 3.4 82.3 1.0
PB E:ADP1299 3.8 76.6 1.0
ND2 E:ASN197 3.9 71.9 1.0
PA E:ADP1299 3.9 77.2 1.0
O3A E:ADP1299 3.9 76.7 1.0
CG E:ASN197 4.0 69.7 1.0
NZ E:LYS33 4.2 75.2 1.0
CD E:NLG1301 4.2 83.6 1.0
O1B E:ADP1299 4.2 77.2 1.0
OD1 E:ASP199 4.3 71.4 1.0
OE2 E:NLG1301 4.3 83.4 1.0
CG E:ASP199 4.6 69.3 1.0
O E:GLY88 4.6 86.5 1.0
O E:GLY251 4.7 72.1 1.0
CA E:GLY251 4.7 73.8 1.0
O5' E:ADP1299 4.8 74.7 1.0
NZ E:LYS255 4.9 65.8 1.0
OD2 E:ASP199 4.9 69.3 1.0

Magnesium binding site 5 out of 8 in 2buf

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Magnesium binding site 5 out of 8 in the Arginine Feed-Back Inhibitable Acetylglutamate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Arginine Feed-Back Inhibitable Acetylglutamate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1300

b:85.7
occ:1.00
 O1B G:ADP1299 2.5 0.6 1.0
O3A G:ADP1299 2.6 0.4 1.0
PB G:ADP1299 2.9 0.8 1.0
O2A G:ADP1299 3.1 0.1 1.0
O3B G:ADP1299 3.2 0.9 1.0
PA G:ADP1299 3.3 0.5 1.0
O1A G:ADP1299 3.8 0.2 1.0
OD1 G:ASN37 4.0 0.3 1.0
ND2 G:ASN37 4.0 0.5 1.0
O2B G:ADP1299 4.3 0.8 1.0
CG G:ASN37 4.4 0.7 1.0
O5' G:ADP1299 4.7 0.4 1.0

Magnesium binding site 6 out of 8 in 2buf

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Magnesium binding site 6 out of 8 in the Arginine Feed-Back Inhibitable Acetylglutamate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Arginine Feed-Back Inhibitable Acetylglutamate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1298

b:94.3
occ:1.00
 ND2 H:ASN37 2.5 0.9 1.0
O3A H:ADP1297 2.6 0.0 0.5
O3B H:ADP1297 2.7 0.9 0.5
CG H:ASN37 3.2 0.2 1.0
PA H:ADP1297 3.2 0.9 0.5
O1A H:ADP1297 3.2 0.8 0.5
PB H:ADP1297 3.3 0.1 0.5
O2A H:ADP1297 3.4 0.0 0.5
OD1 H:ASN37 3.4 0.5 1.0
O1B H:ADP1297 4.3 1.0 0.5
CB H:ASN37 4.3 0.6 1.0
O2B H:ADP1297 4.4 0.8 0.5
O5' H:ADP1297 4.7 0.0 0.5

Magnesium binding site 7 out of 8 in 2buf

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Magnesium binding site 7 out of 8 in the Arginine Feed-Back Inhibitable Acetylglutamate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Arginine Feed-Back Inhibitable Acetylglutamate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1299

b:74.1
occ:1.00
 O1B I:ADP1298 2.4 84.0 1.0
O2A I:ADP1298 3.0 72.3 1.0
OD2 I:ASP199 3.2 73.0 1.0
PB I:ADP1298 3.8 82.6 1.0
O3A I:ADP1298 3.9 76.4 1.0
OD1 I:ASN197 4.0 80.2 1.0
PA I:ADP1298 4.0 74.3 1.0
NZ I:LYS33 4.1 66.4 1.0
CG I:ASP199 4.1 70.6 1.0
OE2 I:NLG1300 4.3 94.3 1.0
OE1 I:NLG1300 4.4 93.5 1.0
NZ I:LYS255 4.4 65.1 1.0
O I:GLY251 4.5 68.8 1.0
OD1 I:ASP199 4.5 69.6 1.0
ND2 I:ASN197 4.7 78.1 1.0
CD I:NLG1300 4.7 93.2 1.0
O2B I:ADP1298 4.7 82.5 1.0
O3B I:ADP1298 4.7 83.4 1.0
CG I:ASN197 4.7 78.4 1.0

Magnesium binding site 8 out of 8 in 2buf

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Magnesium binding site 8 out of 8 in the Arginine Feed-Back Inhibitable Acetylglutamate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Arginine Feed-Back Inhibitable Acetylglutamate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1301

b:68.7
occ:1.00
 O2A L:ADP1300 2.3 90.0 1.0
O1B L:ADP1300 3.2 90.9 1.0
ND2 L:ASN197 3.4 87.4 1.0
PA L:ADP1300 3.5 88.3 1.0
O3A L:ADP1300 3.7 90.1 1.0
OD2 L:ASP199 3.7 90.8 1.0
O3B L:ADP1300 3.7 90.6 1.0
OD1 L:ASN197 3.8 87.4 1.0
PB L:ADP1300 3.8 92.2 1.0
O L:GLY251 3.8 78.1 1.0
OE1 L:NLG1302 4.0 0.7 1.0
CG L:ASN197 4.0 87.4 1.0
NZ L:LYS255 4.1 81.5 1.0
OE2 L:NLG1302 4.2 0.1 1.0
CA L:GLY251 4.3 79.0 1.0
CD L:NLG1302 4.3 0.3 1.0
O1A L:ADP1300 4.5 89.0 1.0
O5' L:ADP1300 4.5 86.3 1.0
C L:GLY251 4.5 77.8 1.0
CG L:ASP199 4.8 88.6 1.0
CE L:LYS255 4.8 80.7 1.0
O L:GLY88 5.0 0.4 1.0

Reference:

S.Ramon-Maiques, M.L.Fernandez-Murga, F.Gil-Ortiz, A.Vagin, I.Fita, V.Rubio. Structural Bases of Feed-Back Control of Arginine Biosynthesis, Revealed By the Structure of Two Hexameric N-Acetylglutamate Kinases, From Thermotoga Maritima and Pseudomonas Aeruginosa J.Mol.Biol. V. 356 695 2006.
ISSN: ISSN 0022-2836
PubMed: 16376937
DOI: 10.1016/J.JMB.2005.11.079
Page generated: Tue Aug 13 22:04:27 2024

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