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Magnesium in PDB 1ecb: Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with 2 Gmp, 1 Mg Per Subunit

Enzymatic activity of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with 2 Gmp, 1 Mg Per Subunit

All present enzymatic activity of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with 2 Gmp, 1 Mg Per Subunit:
2.4.2.14;

Protein crystallography data

The structure of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with 2 Gmp, 1 Mg Per Subunit, PDB code: 1ecb was solved by J.M.Krahn, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.800, 113.200, 199.600, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 29.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with 2 Gmp, 1 Mg Per Subunit (pdb code 1ecb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with 2 Gmp, 1 Mg Per Subunit, PDB code: 1ecb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1ecb

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Magnesium binding site 1 out of 4 in the Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with 2 Gmp, 1 Mg Per Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with 2 Gmp, 1 Mg Per Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:54.9
occ:1.00
 O3' A:5GP505 1.9 48.6 1.0
O2' A:5GP505 2.0 53.1 1.0
O A:HOH509 2.1 52.9 1.0
OD1 A:ASP367 2.1 47.2 1.0
OD1 A:ASP366 2.3 41.9 1.0
O A:HOH508 2.3 54.4 1.0
C2' A:5GP505 2.8 60.1 1.0
C3' A:5GP505 2.8 55.8 1.0
CG A:ASP367 3.1 41.5 1.0
CG A:ASP366 3.3 30.8 1.0
OD2 A:ASP367 3.6 46.8 1.0
OD2 A:ASP366 3.6 30.0 1.0
C4' A:5GP505 3.6 61.0 1.0
C1' A:5GP505 3.9 67.8 1.0
O3P A:5GP506 4.0 38.2 1.0
N A:ASP367 4.1 32.7 1.0
O4' A:5GP505 4.2 65.3 1.0
CB A:ASP367 4.3 38.9 1.0
O A:ILE301 4.5 29.7 1.0
O2P A:5GP506 4.5 40.0 1.0
CB A:ASP366 4.6 28.4 1.0
CG2 A:ILE301 4.7 13.5 1.0
CA A:ASP367 4.7 33.0 1.0
O A:SER368 4.8 38.3 1.0
N A:SER368 4.8 30.5 1.0
O A:PRO302 4.9 23.2 1.0
CA A:ASP366 4.9 25.3 1.0
CE1 A:TYR258 4.9 24.3 1.0
C A:ASP366 4.9 29.7 1.0
P A:5GP506 4.9 42.7 1.0

Magnesium binding site 2 out of 4 in 1ecb

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Magnesium binding site 2 out of 4 in the Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with 2 Gmp, 1 Mg Per Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with 2 Gmp, 1 Mg Per Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg507

b:46.8
occ:1.00
 O2' B:5GP505 1.9 51.3 1.0
O3' B:5GP505 2.0 53.5 1.0
O B:HOH508 2.1 45.8 1.0
O B:HOH509 2.1 42.8 1.0
OD1 B:ASP367 2.2 40.9 1.0
OD1 B:ASP366 2.3 37.4 1.0
C2' B:5GP505 2.9 62.8 1.0
C3' B:5GP505 2.9 56.4 1.0
CG B:ASP367 3.3 30.5 1.0
CG B:ASP366 3.3 29.3 1.0
C4' B:5GP505 3.7 55.9 1.0
OD2 B:ASP366 3.7 31.1 1.0
OD2 B:ASP367 3.7 33.0 1.0
C1' B:5GP505 3.9 68.9 1.0
O3P B:5GP506 3.9 43.9 1.0
N B:ASP367 4.2 29.1 1.0
O4' B:5GP505 4.2 65.6 1.0
CB B:ASP367 4.5 25.2 1.0
O2P B:5GP506 4.6 47.8 1.0
CB B:ASP366 4.7 31.7 1.0
O B:ILE301 4.7 21.2 1.0
CG2 B:ILE301 4.8 2.0 1.0
O B:SER368 4.8 26.9 1.0
O B:PRO302 4.8 24.8 1.0
N B:SER368 4.9 24.3 1.0
P B:5GP506 4.9 47.4 1.0
CA B:ASP367 4.9 26.2 1.0
CA B:ASP366 4.9 27.0 1.0
CE1 B:TYR258 5.0 27.9 1.0

Magnesium binding site 3 out of 4 in 1ecb

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Magnesium binding site 3 out of 4 in the Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with 2 Gmp, 1 Mg Per Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with 2 Gmp, 1 Mg Per Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg507

b:36.6
occ:1.00
 O3' C:5GP505 1.8 42.7 1.0
O2' C:5GP505 1.9 39.9 1.0
O C:HOH508 2.0 40.1 1.0
O C:HOH509 2.1 38.8 1.0
OD2 C:ASP367 2.1 36.3 1.0
OD1 C:ASP366 2.2 29.0 1.0
C2' C:5GP505 2.8 50.1 1.0
C3' C:5GP505 2.8 47.2 1.0
CG C:ASP367 3.0 33.5 1.0
CG C:ASP366 3.1 23.9 1.0
OD1 C:ASP367 3.3 35.2 1.0
OD2 C:ASP366 3.4 25.8 1.0
C4' C:5GP505 3.7 48.4 1.0
C1' C:5GP505 3.9 59.7 1.0
O3P C:5GP506 4.0 29.7 1.0
N C:ASP367 4.2 33.6 1.0
O4' C:5GP505 4.3 57.2 1.0
O2P C:5GP506 4.3 38.0 1.0
CB C:ASP367 4.4 33.3 1.0
CB C:ASP366 4.5 29.3 1.0
O C:ILE301 4.6 33.5 1.0
O C:PRO302 4.7 34.3 1.0
CG2 C:ILE301 4.7 18.4 1.0
P C:5GP506 4.8 35.4 1.0
O C:SER368 4.8 18.3 1.0
CA C:ASP367 4.8 31.3 1.0
CA C:ASP366 4.9 28.6 1.0
OG1 C:THR304 4.9 30.8 1.0
N C:SER368 4.9 26.7 1.0
CE1 C:TYR258 4.9 26.2 1.0

Magnesium binding site 4 out of 4 in 1ecb

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Magnesium binding site 4 out of 4 in the Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with 2 Gmp, 1 Mg Per Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with 2 Gmp, 1 Mg Per Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg507

b:45.7
occ:1.00
 O3' D:5GP505 1.7 50.0 1.0
O2' D:5GP505 2.0 51.1 1.0
O D:HOH508 2.1 44.8 1.0
OD1 D:ASP366 2.2 38.1 1.0
O D:HOH509 2.3 45.1 1.0
OD1 D:ASP367 2.6 36.3 1.0
OD2 D:ASP367 2.6 35.0 1.0
C3' D:5GP505 2.7 57.5 1.0
C2' D:5GP505 2.8 61.6 1.0
CG D:ASP367 2.9 30.8 1.0
CG D:ASP366 3.1 31.6 1.0
OD2 D:ASP366 3.3 31.7 1.0
C4' D:5GP505 3.5 58.6 1.0
C1' D:5GP505 3.8 71.8 1.0
N D:ASP367 4.1 23.8 1.0
O4' D:5GP505 4.1 70.7 1.0
O3P D:5GP506 4.2 45.9 1.0
CB D:ASP367 4.3 29.9 1.0
CB D:ASP366 4.5 29.2 1.0
N D:SER368 4.6 20.8 1.0
CA D:ASP367 4.6 26.2 1.0
O2P D:5GP506 4.7 49.3 1.0
O D:SER368 4.7 24.4 1.0
O D:ILE301 4.7 27.8 1.0
CG2 D:ILE301 4.8 7.5 1.0
C D:ASP366 4.9 23.5 1.0
C5' D:5GP505 4.9 51.0 1.0
CA D:ASP366 5.0 24.2 1.0
O D:PRO302 5.0 28.0 1.0

Reference:

J.M.Krahn, J.H.Kim, M.R.Burns, R.J.Parry, H.Zalkin, J.L.Smith. Coupled Formation of An Amidotransferase Interdomain Ammonia Channel and A Phosphoribosyltransferase Active Site. Biochemistry V. 36 11061 1997.
ISSN: ISSN 0006-2960
PubMed: 9333323
DOI: 10.1021/BI9714114
Page generated: Tue Aug 13 02:55:04 2024

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