Phosphorus in PDB 1a0i: Atp-Dependent Dna Ligase From Bacteriophage T7 Complex with Atp

Enzymatic activity of Atp-Dependent Dna Ligase From Bacteriophage T7 Complex with Atp

All present enzymatic activity of Atp-Dependent Dna Ligase From Bacteriophage T7 Complex with Atp:
6.5.1.1;

Protein crystallography data

The structure of Atp-Dependent Dna Ligase From Bacteriophage T7 Complex with Atp, PDB code: 1a0i was solved by H.S.Subramanya, A.J.Doherty, S.R.Ashford, D.B.Wigley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 64.700, 85.200, 79.100, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 34.1

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Atp-Dependent Dna Ligase From Bacteriophage T7 Complex with Atp (pdb code 1a0i). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 3 binding sites of Phosphorus where determined in the Atp-Dependent Dna Ligase From Bacteriophage T7 Complex with Atp, PDB code: 1a0i:
Jump to Phosphorus binding site number: 1; 2; 3;

Phosphorus binding site 1 out of 3 in 1a0i

Go back to Phosphorus Binding Sites List in 1a0i
Phosphorus binding site 1 out of 3 in the Atp-Dependent Dna Ligase From Bacteriophage T7 Complex with Atp


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Atp-Dependent Dna Ligase From Bacteriophage T7 Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P1

b:98.6
occ:1.00
PG A:ATP1 0.0 98.6 1.0
O3G A:ATP1 1.5 97.7 1.0
O1G A:ATP1 1.5 0.1 1.0
O2G A:ATP1 1.5 0.3 1.0
O3B A:ATP1 1.6 90.4 1.0
PB A:ATP1 2.9 84.1 1.0
O3A A:ATP1 3.3 77.6 1.0
O1B A:ATP1 3.5 85.6 1.0
O2B A:ATP1 4.1 81.9 1.0
O A:HOH434 4.1 29.9 1.0
O1A A:ATP1 4.3 65.0 1.0
PA A:ATP1 4.4 48.9 1.0
O2A A:ATP1 4.8 52.4 1.0

Phosphorus binding site 2 out of 3 in 1a0i

Go back to Phosphorus Binding Sites List in 1a0i
Phosphorus binding site 2 out of 3 in the Atp-Dependent Dna Ligase From Bacteriophage T7 Complex with Atp


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Atp-Dependent Dna Ligase From Bacteriophage T7 Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P1

b:84.1
occ:1.00
PB A:ATP1 0.0 84.1 1.0
O1B A:ATP1 1.5 85.6 1.0
O2B A:ATP1 1.5 81.9 1.0
O3A A:ATP1 1.5 77.6 1.0
O3B A:ATP1 1.6 90.4 1.0
PA A:ATP1 2.7 48.9 1.0
PG A:ATP1 2.9 98.6 1.0
O1A A:ATP1 3.1 65.0 1.0
O2G A:ATP1 3.2 0.3 1.0
O5' A:ATP1 3.6 59.2 1.0
O3G A:ATP1 3.7 97.7 1.0
O2A A:ATP1 3.9 52.4 1.0
O1G A:ATP1 4.0 0.1 1.0
C4' A:ATP1 4.4 38.5 1.0
C5' A:ATP1 4.4 45.0 1.0
NZ A:LYS34 4.5 15.9 1.0
O4' A:ATP1 4.5 35.8 1.0
O A:HOH458 4.7 20.5 1.0
O A:HOH434 4.8 29.9 1.0
NH2 A:ARG55 4.8 49.4 1.0
O A:HOH459 5.0 24.3 1.0

Phosphorus binding site 3 out of 3 in 1a0i

Go back to Phosphorus Binding Sites List in 1a0i
Phosphorus binding site 3 out of 3 in the Atp-Dependent Dna Ligase From Bacteriophage T7 Complex with Atp


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Atp-Dependent Dna Ligase From Bacteriophage T7 Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P1

b:48.9
occ:1.00
PA A:ATP1 0.0 48.9 1.0
O1A A:ATP1 1.5 65.0 1.0
O3A A:ATP1 1.5 77.6 1.0
O2A A:ATP1 1.5 52.4 1.0
O5' A:ATP1 1.6 59.2 1.0
C5' A:ATP1 2.6 45.0 1.0
PB A:ATP1 2.7 84.1 1.0
O2B A:ATP1 3.0 81.9 1.0
CE A:LYS238 3.5 2.0 1.0
C4' A:ATP1 3.6 38.5 1.0
O3B A:ATP1 3.6 90.4 1.0
O1B A:ATP1 3.8 85.6 1.0
O2G A:ATP1 3.9 0.3 1.0
O A:HOH434 3.9 29.9 1.0
O4' A:ATP1 4.1 35.8 1.0
NZ A:LYS238 4.4 12.0 1.0
PG A:ATP1 4.4 98.6 1.0
NZ A:LYS232 4.5 32.1 1.0
CD A:LYS238 4.5 18.0 1.0
C3' A:ATP1 4.8 45.1 1.0
CE A:LYS34 4.8 24.4 1.0
CG A:LYS238 5.0 11.3 1.0
O3' A:ATP1 5.0 39.5 1.0

Reference:

H.S.Subramanya, A.J.Doherty, S.R.Ashford, D.B.Wigley. Crystal Structure of An Atp-Dependent Dna Ligase From Bacteriophage T7. Cell(Cambridge,Mass.) V. 85 607 1996.
ISSN: ISSN 0092-8674
PubMed: 8653795
DOI: 10.1016/S0092-8674(00)81260-X
Page generated: Fri Sep 25 11:56:21 2020

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