Phosphorus in PDB 1ak0: P1 Nuclease in Complex with A Substrate Analog

Enzymatic activity of P1 Nuclease in Complex with A Substrate Analog

All present enzymatic activity of P1 Nuclease in Complex with A Substrate Analog:
3.1.30.1;

Protein crystallography data

The structure of P1 Nuclease in Complex with A Substrate Analog, PDB code: 1ak0 was solved by C.Romier, D.Suck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.980, 74.040, 102.130, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.5

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the P1 Nuclease in Complex with A Substrate Analog (pdb code 1ak0). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 3 binding sites of Phosphorus where determined in the P1 Nuclease in Complex with A Substrate Analog, PDB code: 1ak0:
Jump to Phosphorus binding site number: 1; 2; 3;

Phosphorus binding site 1 out of 3 in 1ak0

Go back to Phosphorus Binding Sites List in 1ak0
Phosphorus binding site 1 out of 3 in the P1 Nuclease in Complex with A Substrate Analog


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of P1 Nuclease in Complex with A Substrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P293

b:48.6
occ:1.00
P A:THS293 0.0 48.6 1.0
O5' A:THS293 1.5 50.7 1.0
O3' A:ADS292 1.6 44.9 1.0
S3P A:THS293 1.9 46.2 1.0
S2P A:THS293 1.9 46.4 1.0
C5' A:THS293 2.4 57.7 1.0
C3' A:ADS292 2.8 40.8 1.0
C4' A:ADS292 3.5 40.6 1.0
C4' A:THS293 3.7 61.6 1.0
C2' A:ADS292 3.9 37.6 1.0
O4' A:THS293 4.1 64.5 1.0
O A:HOH519 4.3 47.0 1.0
O4' A:ADS292 4.3 37.7 1.0
O5' A:ADS292 4.4 46.4 1.0
C1' A:ADS292 4.5 33.7 1.0
C5' A:ADS292 4.6 41.7 1.0
C3' A:THS293 4.9 63.6 1.0

Phosphorus binding site 2 out of 3 in 1ak0

Go back to Phosphorus Binding Sites List in 1ak0
Phosphorus binding site 2 out of 3 in the P1 Nuclease in Complex with A Substrate Analog


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of P1 Nuclease in Complex with A Substrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P294

b:65.6
occ:1.00
P A:THS294 0.0 65.6 1.0
O5' A:THS294 1.6 60.9 1.0
O3' A:THS293 1.7 65.2 1.0
S2P A:THS294 2.0 66.1 1.0
S3P A:THS294 2.0 68.7 1.0
C5' A:THS294 2.6 53.0 1.0
C3' A:THS293 3.0 63.6 1.0
C4' A:THS294 3.7 48.6 1.0
C2' A:THS293 3.9 65.4 1.0
C4' A:THS293 3.9 61.6 1.0
C3' A:THS294 3.9 46.1 1.0
C6 A:THS294 4.2 45.0 1.0
C1' A:THS293 4.2 67.2 1.0
C2' A:THS294 4.3 46.6 1.0
O4' A:THS294 4.3 47.5 1.0
C5M A:THS295 4.5 18.8 1.0
O4' A:THS293 4.5 64.5 1.0
C1' A:THS294 4.7 47.3 1.0
N1 A:THS294 4.9 46.1 1.0
O A:HOH521 4.9 40.5 1.0
C5M A:THS294 5.0 46.2 1.0

Phosphorus binding site 3 out of 3 in 1ak0

Go back to Phosphorus Binding Sites List in 1ak0
Phosphorus binding site 3 out of 3 in the P1 Nuclease in Complex with A Substrate Analog


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of P1 Nuclease in Complex with A Substrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P295

b:42.0
occ:1.00
P A:THS295 0.0 42.0 1.0
O5' A:THS295 1.6 36.1 1.0
O3' A:THS294 1.6 42.5 1.0
S3P A:THS295 1.9 40.8 1.0
S2P A:THS295 2.0 39.0 1.0
C3' A:THS294 2.7 46.1 1.0
C5' A:THS295 2.9 27.9 1.0
C2' A:THS294 3.6 46.6 1.0
C4' A:THS294 3.8 48.6 1.0
C4' A:THS295 3.9 23.4 1.0
C3' A:THS295 4.0 22.9 1.0
C2' A:THS295 4.2 19.4 1.0
C6 A:THS295 4.4 19.9 1.0
O4' A:THS295 4.5 16.0 1.0
C1' A:THS294 4.6 47.3 1.0
O A:HOH437 4.6 21.4 1.0
O4' A:THS294 4.6 47.5 1.0
C5' A:THS294 4.8 53.0 1.0
CZ A:ARG48 4.8 19.0 1.0
O A:HOH553 4.8 54.1 1.0
C1' A:THS295 4.9 17.9 1.0

Reference:

C.Romier, R.Dominguez, A.Lahm, O.Dahl, D.Suck. Recognition of Single-Stranded Dna By Nuclease P1: High Resolution Crystal Structures of Complexes with Substrate Analogs. Proteins V. 32 414 1998.
ISSN: ISSN 0887-3585
PubMed: 9726413
DOI: 10.1002/(SICI)1097-0134(19980901)32:4<414::AID-PROT2>3.3.CO;2-5
Page generated: Fri Sep 25 13:03:39 2020

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