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Magnesium in PDB 1ao0: Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp

Enzymatic activity of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp

All present enzymatic activity of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp:
2.4.2.14;

Protein crystallography data

The structure of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp, PDB code: 1ao0 was solved by D.R.Tomchick, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 160.300, 70.400, 182.700, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 26.4

Other elements in 1ao0:

The structure of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp also contains other interesting chemical elements:

Iron (Fe) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp (pdb code 1ao0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp, PDB code: 1ao0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1ao0

Go back to Magnesium Binding Sites List in 1ao0
Magnesium binding site 1 out of 4 in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg469

b:10.1
occ:1.00
 OD1 A:ASP346 2.0 19.2 1.0
OD1 A:ASP345 2.1 15.3 1.0
O A:HOH470 2.1 11.7 1.0
O2' A:5GP467 2.1 13.3 1.0
OG A:SER283 2.2 23.6 1.0
CB A:SER283 2.3 13.0 1.0
O3' A:5GP467 2.5 17.5 1.0
CG A:ASP345 3.2 17.9 1.0
CG A:ASP346 3.2 22.0 1.0
C2' A:5GP467 3.3 17.5 1.0
OD2 A:ASP345 3.6 18.3 1.0
C3' A:5GP467 3.6 20.2 1.0
CA A:SER283 3.6 15.3 1.0
C A:SER283 3.9 18.2 1.0
N A:ASP346 3.9 20.9 1.0
OD2 A:ASP346 4.0 11.9 1.0
O1B A:ADP468 4.1 60.0 1.0
N A:SER284 4.1 11.7 1.0
CB A:ASP346 4.2 17.4 1.0
CB A:SER284 4.3 10.0 1.0
C4' A:5GP467 4.3 14.7 1.0
N A:SER283 4.4 15.5 1.0
O A:SER283 4.4 24.9 1.0
C1' A:5GP467 4.5 23.5 1.0
OG A:SER284 4.5 13.5 1.0
CB A:ASP345 4.5 16.3 1.0
CB A:VAL280 4.6 10.1 1.0
CA A:ASP346 4.6 21.6 1.0
CA A:ASP345 4.7 23.3 1.0
C A:ASP345 4.8 23.4 1.0
CA A:SER284 4.8 11.2 1.0
N A:SER347 4.9 12.6 1.0
CG1 A:VAL280 4.9 10.2 1.0
CE1 A:TYR242 4.9 19.5 1.0
CD1 A:TYR242 5.0 19.2 1.0

Magnesium binding site 2 out of 4 in 1ao0

Go back to Magnesium Binding Sites List in 1ao0
Magnesium binding site 2 out of 4 in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg469

b:22.9
occ:1.00
 OD1 B:ASP346 2.0 20.9 1.0
O B:HOH470 2.0 10.1 1.0
OD1 B:ASP345 2.1 18.6 1.0
O2' B:5GP467 2.1 20.3 1.0
OG B:SER283 2.2 24.3 1.0
CB B:SER283 2.3 14.2 1.0
O3' B:5GP467 2.6 16.2 1.0
CG B:ASP345 3.2 23.8 1.0
CG B:ASP346 3.2 15.8 1.0
C2' B:5GP467 3.3 19.7 1.0
C3' B:5GP467 3.6 14.8 1.0
OD2 B:ASP345 3.6 19.6 1.0
CA B:SER283 3.6 20.9 1.0
C B:SER283 3.9 24.8 1.0
N B:ASP346 4.0 27.4 1.0
O1B B:ADP468 4.0 53.6 1.0
OD2 B:ASP346 4.0 18.6 1.0
N B:SER284 4.1 19.8 1.0
CB B:ASP346 4.2 18.2 1.0
C4' B:5GP467 4.3 12.9 1.0
CB B:SER284 4.3 24.0 1.0
N B:SER283 4.4 21.4 1.0
C1' B:5GP467 4.4 20.4 1.0
O B:SER283 4.4 31.2 1.0
OG B:SER284 4.5 24.1 1.0
CB B:ASP345 4.5 26.5 1.0
CB B:VAL280 4.6 15.0 1.0
CA B:ASP346 4.7 22.7 1.0
CA B:ASP345 4.7 29.4 1.0
CA B:SER284 4.8 19.6 1.0
CG1 B:VAL280 4.8 10.2 1.0
C B:ASP345 4.8 30.5 1.0
CE1 B:TYR242 4.9 19.4 1.0
N B:SER347 4.9 21.2 1.0
CD1 B:TYR242 4.9 25.5 1.0
O4' B:5GP467 4.9 12.3 1.0

Magnesium binding site 3 out of 4 in 1ao0

Go back to Magnesium Binding Sites List in 1ao0
Magnesium binding site 3 out of 4 in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg469

b:12.9
occ:1.00
 OD1 C:ASP346 2.0 22.5 1.0
O2' C:5GP467 2.0 20.4 1.0
O C:HOH470 2.1 10.0 1.0
OD1 C:ASP345 2.2 16.3 1.0
OG C:SER283 2.2 26.2 1.0
CB C:SER283 2.3 13.9 1.0
O3' C:5GP467 2.5 18.1 1.0
CG C:ASP345 3.2 21.3 1.0
CG C:ASP346 3.2 17.0 1.0
C2' C:5GP467 3.2 25.9 1.0
C3' C:5GP467 3.5 22.7 1.0
OD2 C:ASP345 3.6 17.7 1.0
CA C:SER283 3.6 17.3 1.0
O3B C:ADP468 3.9 65.3 1.0
C C:SER283 3.9 22.7 1.0
N C:ASP346 4.0 26.1 1.0
OD2 C:ASP346 4.0 18.4 1.0
N C:SER284 4.2 19.4 1.0
CB C:ASP346 4.2 12.6 1.0
C4' C:5GP467 4.2 14.5 1.0
C1' C:5GP467 4.3 26.5 1.0
N C:SER283 4.4 18.7 1.0
CB C:SER284 4.4 13.8 1.0
O C:SER283 4.4 31.9 1.0
CB C:ASP345 4.5 18.2 1.0
OG C:SER284 4.6 16.2 1.0
CB C:VAL280 4.7 18.0 1.0
CA C:ASP346 4.7 20.7 1.0
CA C:ASP345 4.8 26.8 1.0
C C:ASP345 4.8 29.9 1.0
CG1 C:VAL280 4.9 10.1 1.0
CA C:SER284 4.9 12.0 1.0
N C:SER347 4.9 17.9 1.0
O4' C:5GP467 4.9 26.5 1.0
CE1 C:TYR242 4.9 22.1 1.0
CD1 C:TYR242 4.9 19.1 1.0

Magnesium binding site 4 out of 4 in 1ao0

Go back to Magnesium Binding Sites List in 1ao0
Magnesium binding site 4 out of 4 in the Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase From B. Subtilis Complexed with Adp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg469

b:10.3
occ:1.00
 OD1 D:ASP346 1.9 17.3 1.0
O2' D:5GP467 2.0 13.4 1.0
OD1 D:ASP345 2.1 13.7 1.0
O D:HOH470 2.1 13.9 1.0
CB D:SER283 2.2 14.8 1.0
OG D:SER283 2.2 18.5 1.0
O3' D:5GP467 2.5 12.0 1.0
CG D:ASP346 3.2 19.5 1.0
CG D:ASP345 3.2 23.8 1.0
C2' D:5GP467 3.3 17.2 1.0
CA D:SER283 3.5 10.6 1.0
C3' D:5GP467 3.6 10.1 1.0
OD2 D:ASP345 3.6 21.3 1.0
C D:SER283 3.8 13.9 1.0
N D:ASP346 3.9 28.0 1.0
O3B D:ADP468 4.0 57.7 1.0
OD2 D:ASP346 4.0 13.9 1.0
N D:SER284 4.0 14.1 1.0
CB D:ASP346 4.1 21.2 1.0
CB D:SER284 4.3 16.3 1.0
C4' D:5GP467 4.3 10.0 1.0
O D:SER283 4.3 17.8 1.0
C1' D:5GP467 4.3 25.0 1.0
N D:SER283 4.3 18.7 1.0
OG D:SER284 4.4 14.7 1.0
CB D:ASP345 4.5 25.1 1.0
CA D:ASP346 4.6 24.7 1.0
CB D:VAL280 4.7 10.3 1.0
CA D:ASP345 4.7 28.1 1.0
CA D:SER284 4.8 17.9 1.0
C D:ASP345 4.8 29.4 1.0
CD1 D:TYR242 4.9 23.2 1.0
N D:SER347 4.9 17.1 1.0
CE1 D:TYR242 4.9 25.2 1.0
O4' D:5GP467 4.9 14.2 1.0
CG1 D:VAL280 4.9 10.0 1.0

Reference:

S.Chen, D.R.Tomchick, D.Wolle, P.Hu, J.L.Smith, R.L.Switzer, H.Zalkin. Mechanism of the Synergistic End-Product Regulation of Bacillus Subtilis Glutamine Phosphoribosylpyrophosphate Amidotransferase By Nucleotides. Biochemistry V. 36 10718 1997.
ISSN: ISSN 0006-2960
PubMed: 9271502
DOI: 10.1021/BI9711893
Page generated: Tue Aug 13 02:07:24 2024

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