Atomistry » Magnesium » PDB 1e9a-1en9 » 1ecb
Atomistry »
  Magnesium »
    PDB 1e9a-1en9 »
      1ecb »

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

Go back to Magnesium Binding Sites List in 1ecb
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

Go back to Magnesium Binding Sites List in 1ecb
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

Go back to Magnesium Binding Sites List in 1ecb
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

Go back to Magnesium Binding Sites List in 1ecb
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: Mon Dec 14 05:51:52 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy