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Zinc 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

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the P1 Nuclease in Complex with A Substrate Analog, PDB code: 1ak0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1ak0

Go back to Zinc Binding Sites List in 1ak0
Zinc binding site 1 out of 4 in the P1 Nuclease in Complex with A Substrate Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn271

b:13.6
occ:1.00
OD2 A:ASP120 2.0 10.3 1.0
NE2 A:HIS116 2.3 7.0 1.0
ND1 A:HIS60 2.3 10.0 1.0
OD1 A:ASP45 2.8 11.3 1.0
CG A:ASP120 3.0 10.0 1.0
CD2 A:HIS116 3.1 8.7 1.0
OD1 A:ASP120 3.2 7.8 1.0
CE1 A:HIS60 3.2 11.3 1.0
CG A:HIS60 3.3 11.7 1.0
CE1 A:HIS116 3.4 7.3 1.0
CB A:HIS60 3.6 10.3 1.0
ZN A:ZN273 3.7 13.9 1.0
CG A:ASP45 3.7 13.9 1.0
OD2 A:ASP45 4.0 15.7 1.0
NH1 A:ARG48 4.0 16.6 1.0
CB A:ASP120 4.3 9.5 1.0
CG A:HIS116 4.3 8.8 1.0
NE2 A:HIS60 4.4 9.5 1.0
NE2 A:HIS6 4.4 6.8 1.0
ND1 A:HIS116 4.4 8.6 1.0
CE1 A:HIS126 4.4 8.4 1.0
CD2 A:HIS60 4.4 11.2 1.0
CA A:HIS60 4.7 11.8 1.0
CZ A:ARG48 4.8 19.0 1.0
NH2 A:ARG48 4.9 21.1 1.0
CE1 A:HIS6 4.9 10.6 1.0

Zinc binding site 2 out of 4 in 1ak0

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Zinc binding site 2 out of 4 in the P1 Nuclease in Complex with A Substrate Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn272

b:13.3
occ:1.00
OD2 A:ASP153 2.0 8.1 1.0
O3' A:THS295 2.0 25.6 1.0
NE2 A:HIS149 2.3 6.3 1.0
NE2 A:HIS126 2.3 9.3 1.0
CG A:ASP153 2.7 10.1 1.0
OD1 A:ASP153 2.8 9.6 1.0
CD2 A:HIS149 3.2 7.7 1.0
CE1 A:HIS126 3.2 8.4 1.0
C3' A:THS295 3.3 22.9 1.0
CD2 A:HIS126 3.3 7.5 1.0
CE1 A:HIS149 3.4 4.5 1.0
C2' A:THS295 3.8 19.4 1.0
C4' A:THS295 3.8 23.4 1.0
C1' A:THS295 3.8 17.9 1.0
O4' A:THS295 4.1 16.0 1.0
N A:TRP1 4.2 9.0 1.0
CB A:ASP153 4.2 9.2 1.0
O A:HOH433 4.2 35.8 1.0
O A:HOH510 4.4 40.0 1.0
ND1 A:HIS126 4.4 8.2 1.0
CG A:HIS149 4.4 5.2 1.0
ND1 A:HIS149 4.4 7.9 1.0
CG A:HIS126 4.4 8.3 1.0
NE2 A:GLN123 4.5 7.9 1.0
ZN A:ZN273 4.6 13.9 1.0
O A:TRP1 4.8 10.1 1.0
O2 A:THS295 4.9 22.5 1.0

Zinc binding site 3 out of 4 in 1ak0

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Zinc binding site 3 out of 4 in the P1 Nuclease in Complex with A Substrate Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn273

b:13.9
occ:1.00
OD1 A:ASP120 2.0 7.8 1.0
O A:TRP1 2.0 10.1 1.0
NE2 A:HIS6 2.3 6.8 1.0
N A:TRP1 2.5 9.0 1.0
C A:TRP1 2.9 11.8 1.0
CD2 A:HIS6 3.0 10.8 1.0
CG A:ASP120 3.2 10.0 1.0
CA A:TRP1 3.2 8.9 1.0
CE1 A:HIS6 3.4 10.6 1.0
ZN A:ZN271 3.7 13.6 1.0
OD2 A:ASP120 3.7 10.3 1.0
CB A:TRP1 3.8 9.2 1.0
NE2 A:HIS116 4.2 7.0 1.0
N A:GLY2 4.2 11.8 1.0
CG A:HIS6 4.3 10.5 1.0
CE1 A:HIS116 4.3 7.3 1.0
OD2 A:ASP45 4.3 15.7 1.0
ND1 A:HIS6 4.4 9.5 1.0
CB A:ASP120 4.4 9.5 1.0
CE1 A:HIS126 4.5 8.4 1.0
NE2 A:HIS126 4.5 9.3 1.0
CG A:TRP1 4.5 8.3 1.0
CA A:ASP120 4.6 10.0 1.0
ZN A:ZN272 4.6 13.3 1.0
OD1 A:ASP153 4.6 9.6 1.0
CD1 A:TRP1 4.7 9.1 1.0
O A:HOH510 4.7 40.0 1.0
OD2 A:ASP153 4.9 8.1 1.0
CA A:GLY2 4.9 12.6 1.0
O A:GLY2 4.9 10.4 1.0
CG A:ASP153 4.9 10.1 1.0

Zinc binding site 4 out of 4 in 1ak0

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Zinc binding site 4 out of 4 in the P1 Nuclease in Complex with A Substrate Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of P1 Nuclease in Complex with A Substrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn274

b:19.2
occ:1.00
OE2 A:GLU181 1.8 27.3 1.0
O A:HOH539 2.0 30.9 1.0
NE2 A:HIS15 2.2 15.3 1.0
CD A:GLU181 2.4 21.5 1.0
OE1 A:GLU181 2.5 22.5 1.0
CD2 A:HIS15 3.1 14.5 1.0
CE1 A:HIS15 3.3 15.8 1.0
CG A:GLU181 3.7 24.8 1.0
CG A:HIS15 4.3 16.9 1.0
ND1 A:HIS15 4.3 15.7 1.0
CE1 A:TYR16 4.4 17.9 1.0
OH A:TYR16 4.6 20.6 1.0
CG1 A:VAL177 4.7 18.0 1.0
CZ A:TYR16 4.8 20.1 1.0
CB A:GLU181 4.8 22.9 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: Wed Dec 16 02:44:42 2020

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