Phosphorus in PDB 1a82: Dethiobiotin Synthetase From Escherichia Coli, Complex with Substrates Atp and Diaminopelargonic Acid

Enzymatic activity of Dethiobiotin Synthetase From Escherichia Coli, Complex with Substrates Atp and Diaminopelargonic Acid

All present enzymatic activity of Dethiobiotin Synthetase From Escherichia Coli, Complex with Substrates Atp and Diaminopelargonic Acid:
6.3.3.3;

Protein crystallography data

The structure of Dethiobiotin Synthetase From Escherichia Coli, Complex with Substrates Atp and Diaminopelargonic Acid, PDB code: 1a82 was solved by H.Kaeck, K.J.Gibson, Y.Lindqvist, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 72.900, 47.900, 60.900, 90.00, 106.50, 90.00
R / Rfree (%) 19 / 24.6

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Dethiobiotin Synthetase From Escherichia Coli, Complex with Substrates Atp and Diaminopelargonic Acid (pdb code 1a82). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 3 binding sites of Phosphorus where determined in the Dethiobiotin Synthetase From Escherichia Coli, Complex with Substrates Atp and Diaminopelargonic Acid, PDB code: 1a82:
Jump to Phosphorus binding site number: 1; 2; 3;

Phosphorus binding site 1 out of 3 in 1a82

Go back to Phosphorus Binding Sites List in 1a82
Phosphorus binding site 1 out of 3 in the Dethiobiotin Synthetase From Escherichia Coli, Complex with Substrates Atp and Diaminopelargonic Acid


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Dethiobiotin Synthetase From Escherichia Coli, Complex with Substrates Atp and Diaminopelargonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P802

b:23.5
occ:1.00
PG A:ATP802 0.0 23.5 1.0
O1G A:ATP802 1.5 19.6 1.0
O2G A:ATP802 1.5 20.8 1.0
O3G A:ATP802 1.6 16.2 1.0
O3B A:ATP802 1.7 13.3 1.0
O A:HOH716 3.0 13.0 1.0
PB A:ATP802 3.0 8.3 1.0
MG A:MG901 3.3 12.4 1.0
O A:HOH444 3.3 10.8 1.0
O1B A:ATP802 3.3 7.3 1.0
OG1 A:THR11 3.4 8.2 1.0
NZ A:LYS15 3.6 7.8 1.0
O2B A:ATP802 3.7 8.3 1.0
OE1 A:GLU12 3.7 36.0 1.0
N8 A:DNN801 3.9 13.7 1.0
N A:GLU12 3.9 8.8 1.0
OD2 A:ASP54 4.2 4.4 1.0
N7 A:DNN801 4.2 11.7 1.0
O A:HOH717 4.3 15.8 1.0
O3A A:ATP802 4.3 9.6 1.0
CE A:LYS15 4.3 6.4 1.0
CA A:THR11 4.5 9.0 1.0
CB A:THR11 4.5 9.1 1.0
OE2 A:GLU115 4.6 6.4 1.0
N A:GLY118 4.6 7.1 1.0
C A:THR11 4.7 8.4 1.0
CA A:GLU12 4.7 10.9 1.0
C7 A:DNN801 4.8 14.7 1.0
C6 A:DNN801 4.8 14.3 1.0
C8 A:DNN801 4.9 13.0 1.0
NZ A:LYS37 4.9 5.1 1.0
CD A:GLU12 5.0 30.6 1.0

Phosphorus binding site 2 out of 3 in 1a82

Go back to Phosphorus Binding Sites List in 1a82
Phosphorus binding site 2 out of 3 in the Dethiobiotin Synthetase From Escherichia Coli, Complex with Substrates Atp and Diaminopelargonic Acid


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Dethiobiotin Synthetase From Escherichia Coli, Complex with Substrates Atp and Diaminopelargonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P802

b:8.3
occ:1.00
PB A:ATP802 0.0 8.3 1.0
O1B A:ATP802 1.5 7.3 1.0
O2B A:ATP802 1.5 8.3 1.0
O3A A:ATP802 1.6 9.6 1.0
O3B A:ATP802 1.6 13.3 1.0
PA A:ATP802 3.0 11.6 1.0
PG A:ATP802 3.0 23.5 1.0
MG A:MG901 3.2 12.4 1.0
O A:HOH444 3.4 10.8 1.0
O3G A:ATP802 3.4 16.2 1.0
O2A A:ATP802 3.4 10.5 1.0
N A:LYS15 3.5 5.8 1.0
O1A A:ATP802 3.7 11.3 1.0
N A:GLU12 3.7 8.8 1.0
N A:GLY14 3.8 7.7 1.0
NZ A:LYS15 3.8 7.8 1.0
O2G A:ATP802 3.8 20.8 1.0
CA A:GLU12 3.9 10.9 1.0
N A:VAL13 4.0 6.7 1.0
CB A:LYS15 4.0 5.0 1.0
O5' A:ATP802 4.0 11.0 1.0
O1G A:ATP802 4.0 19.6 1.0
N A:THR16 4.1 4.3 1.0
C A:GLY14 4.2 6.9 1.0
CA A:GLY14 4.2 6.3 1.0
CA A:LYS15 4.2 5.4 1.0
C A:GLU12 4.3 9.0 1.0
OE1 A:GLU12 4.4 36.0 1.0
CE A:LYS15 4.4 6.4 1.0
C5' A:ATP802 4.4 9.4 1.0
CG A:LYS15 4.5 7.0 1.0
OE2 A:GLU115 4.5 6.4 1.0
OG1 A:THR16 4.5 4.0 1.0
C A:LYS15 4.7 4.6 1.0
C A:THR11 4.8 8.4 1.0
CB A:THR16 4.9 6.8 1.0
C A:VAL13 4.9 8.7 1.0

Phosphorus binding site 3 out of 3 in 1a82

Go back to Phosphorus Binding Sites List in 1a82
Phosphorus binding site 3 out of 3 in the Dethiobiotin Synthetase From Escherichia Coli, Complex with Substrates Atp and Diaminopelargonic Acid


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Dethiobiotin Synthetase From Escherichia Coli, Complex with Substrates Atp and Diaminopelargonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P802

b:11.6
occ:1.00
PA A:ATP802 0.0 11.6 1.0
O2A A:ATP802 1.5 10.5 1.0
O1A A:ATP802 1.5 11.3 1.0
O5' A:ATP802 1.6 11.0 1.0
O3A A:ATP802 1.6 9.6 1.0
C5' A:ATP802 2.6 9.4 1.0
PB A:ATP802 3.0 8.3 1.0
O1B A:ATP802 3.1 7.3 1.0
O A:HOH444 3.6 10.8 1.0
CA A:GLY14 3.7 6.3 1.0
O A:HOH714 3.7 18.3 1.0
C4' A:ATP802 3.8 11.8 1.0
O3B A:ATP802 3.9 13.3 1.0
N A:GLY14 3.9 7.7 1.0
C3' A:ATP802 4.0 10.9 1.0
O2B A:ATP802 4.0 8.3 1.0
C A:GLY14 4.1 6.9 1.0
CB A:THR16 4.1 6.8 1.0
N A:THR16 4.2 4.3 1.0
C2' A:ATP802 4.2 11.2 1.0
N A:LYS15 4.3 5.8 1.0
C8 A:ATP802 4.3 9.8 1.0
N A:VAL17 4.4 2.0 1.0
O4' A:ATP802 4.5 9.9 1.0
MG A:MG901 4.6 12.4 1.0
OG1 A:THR16 4.6 4.0 1.0
CA A:THR16 4.6 4.8 1.0
CG2 A:VAL17 4.7 4.5 1.0
O A:GLY14 4.8 7.1 1.0
C1' A:ATP802 4.9 10.6 1.0
CA A:GLU12 5.0 10.9 1.0

Reference:

H.Kack, K.J.Gibson, Y.Lindqvist, G.Schneider. Snapshot of A Phosphorylated Substrate Intermediate By Kinetic Crystallography. Proc.Natl.Acad.Sci.Usa V. 95 5495 1998.
ISSN: ISSN 0027-8424
PubMed: 9576910
DOI: 10.1073/PNAS.95.10.5495
Page generated: Fri Sep 25 12:25:47 2020

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