Nickel in PDB 6l25: Deoxyribonuclease From Staphylococcus Aureus

The structure of Deoxyribonuclease From Staphylococcus Aureus, PDB code: 6l25 was solved by K.-Y.Lee, D.-G.Kim, B.-J.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.627, 77.832, 77.378, 90.00, 98.81, 90.00
R / Rfree (%)	21.1 / 23.6

The binding sites of Nickel atom in the Deoxyribonuclease From Staphylococcus Aureus (pdb code 6l25). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Deoxyribonuclease From Staphylococcus Aureus, PDB code: 6l25:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Deoxyribonuclease From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Deoxyribonuclease From Staphylococcus Aureus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:23.1 occ:1.00 NE2 A:HIS8 2.1 21.2 1.0 NE2 A:HIS6 2.2 19.4 1.0 OE2 A:GLU92 2.2 21.2 1.0 OD1 A:ASP204 2.2 21.7 1.0 O3 A:PO4303 2.8 34.7 1.0 CE1 A:HIS8 3.1 21.5 1.0 CD2 A:HIS6 3.1 16.6 1.0 CD2 A:HIS8 3.1 19.5 1.0 CD A:GLU92 3.2 17.8 1.0 CG A:ASP204 3.2 21.0 1.0 CE1 A:HIS6 3.2 21.1 1.0 OE1 A:GLU92 3.5 17.4 1.0 OD2 A:ASP204 3.5 25.1 1.0 NI A:NI302 3.5 23.4 1.0 P A:PO4303 3.7 15.9 1.0 O2 A:PO4303 3.9 22.6 1.0 NE2 A:HIS153 3.9 35.3 1.0 CE1 A:HIS153 4.0 28.1 1.0 O4 A:PO4303 4.0 37.0 1.0 ND1 A:HIS8 4.2 20.6 1.0 CG A:HIS8 4.3 19.5 1.0 CG A:HIS6 4.3 16.7 1.0 ND1 A:HIS6 4.3 16.7 1.0 CB A:ASP204 4.5 19.0 1.0 CG A:GLU92 4.5 17.7 1.0 O2 A:PO4304 4.8 32.8 1.0 ND1 A:HIS153 4.9 27.8 1.0 CD2 A:HIS153 4.9 31.8 1.0 CA A:ASP204 4.9 18.0 1.0

Nickel binding site 2 out of 4 in the Deoxyribonuclease From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Deoxyribonuclease From Staphylococcus Aureus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:23.4 occ:1.00 ND1 A:HIS128 2.1 18.6 1.0 OE1 A:GLU92 2.1 17.4 1.0 O2 A:PO4303 2.2 22.6 1.0 O2 A:PO4304 2.4 32.8 1.0 NE2 A:HIS153 2.6 35.3 1.0 CE1 A:HIS128 2.8 21.0 1.0 CD A:GLU92 3.1 17.8 1.0 CG A:HIS128 3.3 16.9 1.0 P A:PO4303 3.3 15.9 1.0 OE2 A:GLU92 3.5 21.2 1.0 P A:PO4304 3.5 35.9 1.0 NI A:NI301 3.5 23.1 1.0 CE1 A:HIS153 3.6 28.1 1.0 O3 A:PO4304 3.6 44.0 1.0 CD2 A:HIS153 3.6 31.8 1.0 O4 A:PO4303 3.7 37.0 1.0 O3 A:PO4303 3.7 34.7 1.0 CB A:HIS128 3.8 16.8 1.0 NE2 A:HIS128 4.0 19.5 1.0 NE2 A:HIS63 4.1 18.5 1.0 OD2 A:ASP204 4.2 25.1 1.0 CD2 A:HIS128 4.2 18.8 1.0 O1 A:PO4304 4.3 55.0 1.0 CG A:GLU92 4.4 17.7 1.0 O1 A:PO4303 4.5 27.7 1.0 O4 A:PO4304 4.5 53.3 1.0 CA A:HIS128 4.6 15.9 1.0 NE2 A:HIS6 4.6 19.4 1.0 ND1 A:HIS153 4.7 27.8 1.0 CG A:HIS153 4.8 27.3 1.0 CD2 A:HIS63 4.8 20.3 1.0 OD1 A:ASP204 4.8 21.7 1.0 CE1 A:HIS6 4.8 21.1 1.0 CG A:ASP204 4.9 21.0 1.0 CB A:GLU92 4.9 17.6 1.0

Nickel binding site 3 out of 4 in the Deoxyribonuclease From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Deoxyribonuclease From Staphylococcus Aureus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:19.5 occ:1.00 NE2 B:HIS6 2.1 16.0 1.0 OE2 B:GLU92 2.1 15.5 1.0 OD1 B:ASP204 2.1 16.3 1.0 NE2 B:HIS8 2.1 15.1 1.0 O1 B:PO4303 2.8 28.2 1.0 CD2 B:HIS6 3.1 14.5 1.0 CE1 B:HIS8 3.1 16.7 1.0 CD B:GLU92 3.1 18.3 1.0 CD2 B:HIS8 3.1 14.2 1.0 CE1 B:HIS6 3.1 18.2 1.0 CG B:ASP204 3.2 18.0 1.0 OE1 B:GLU92 3.4 16.5 1.0 NI B:NI302 3.5 24.0 1.0 OD2 B:ASP204 3.5 19.1 1.0 P B:PO4303 3.7 14.2 1.0 CE1 B:HIS153 3.9 25.6 1.0 O2 B:PO4303 3.9 22.6 1.0 NE2 B:HIS153 4.0 26.5 1.0 O3 B:PO4303 4.1 32.5 1.0 ND1 B:HIS8 4.2 15.4 1.0 CG B:HIS6 4.2 14.4 1.0 ND1 B:HIS6 4.2 15.4 1.0 CG B:HIS8 4.3 14.1 1.0 CG B:GLU92 4.4 16.3 1.0 CB B:ASP204 4.4 16.1 1.0 ND1 B:HIS153 4.8 24.9 1.0 O2 B:PO4304 4.9 30.8 1.0 CA B:ASP204 4.9 16.5 1.0 CG1 B:VAL36 4.9 18.1 1.0 CD2 B:HIS153 4.9 22.7 1.0

Nickel binding site 4 out of 4 in the Deoxyribonuclease From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Deoxyribonuclease From Staphylococcus Aureus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:24.0 occ:1.00 O2 B:PO4303 2.0 22.6 1.0 OE1 B:GLU92 2.1 16.5 1.0 ND1 B:HIS128 2.2 22.3 1.0 O2 B:PO4304 2.3 30.8 1.0 NE2 B:HIS153 2.6 26.5 1.0 CE1 B:HIS128 3.0 19.5 1.0 CD B:GLU92 3.1 18.3 1.0 P B:PO4303 3.2 14.2 1.0 CG B:HIS128 3.4 20.3 1.0 OE2 B:GLU92 3.4 15.5 1.0 CE1 B:HIS153 3.5 25.6 1.0 NI B:NI301 3.5 19.5 1.0 O1 B:PO4303 3.6 28.2 1.0 P B:PO4304 3.7 29.7 1.0 O3 B:PO4303 3.7 32.5 1.0 CD2 B:HIS153 3.7 22.7 1.0 CB B:HIS128 3.8 18.3 1.0 O4 B:PO4304 3.9 45.0 1.0 NE2 B:HIS63 4.1 17.3 1.0 NE2 B:HIS128 4.2 22.1 1.0 OD2 B:ASP204 4.3 19.1 1.0 CG B:GLU92 4.3 16.3 1.0 CD2 B:HIS128 4.4 21.2 1.0 O4 B:PO4303 4.4 26.1 1.0 O3 B:PO4304 4.6 52.4 1.0 NE2 B:HIS6 4.6 16.0 1.0 CA B:HIS128 4.6 18.0 1.0 O1 B:PO4304 4.7 47.2 1.0 ND1 B:HIS153 4.7 24.9 1.0 OD1 B:ASP204 4.7 16.3 1.0 CD2 B:HIS63 4.7 18.6 1.0 CG B:HIS153 4.8 22.9 1.0 CE1 B:HIS6 4.9 18.2 1.0 CG B:ASP204 4.9 18.0 1.0 CB B:GLU92 4.9 16.6 1.0

K.-Y.Lee, S.-H.Cheon, D.-G.Kim, S.J.Lee, B.-J.Lee. A Structural Study of Tatd From Staphylococcus Aureus Elucidates A Putative Dna-Binding Mode of A MG2+-Dependent Nuclease. Iucrj V. 7 509 2020.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252520003917