Potassium in PDB 4xqk: Atp-Dependent Type Isp Restriction-Modification Enzyme Llabiii Bound to Dna

The structure of Atp-Dependent Type Isp Restriction-Modification Enzyme Llabiii Bound to Dna, PDB code: 4xqk was solved by M.K.Chand, K.Saikrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.22 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.880, 112.660, 146.210, 103.30, 90.88, 105.79
R / Rfree (%)	21.9 / 26

The binding sites of Potassium atom in the Atp-Dependent Type Isp Restriction-Modification Enzyme Llabiii Bound to Dna (pdb code 4xqk). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Atp-Dependent Type Isp Restriction-Modification Enzyme Llabiii Bound to Dna, PDB code: 4xqk:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Atp-Dependent Type Isp Restriction-Modification Enzyme Llabiii Bound to Dna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Atp-Dependent Type Isp Restriction-Modification Enzyme Llabiii Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:K1601 b:86.0 occ:1.00 O A:ASP447 2.9 0.7 1.0 O A:LEU452 2.9 94.2 1.0 O A:HOH1758 3.0 65.6 1.0 O A:THR444 3.0 88.2 1.0 O A:LEU445 3.1 87.3 1.0 HB2 A:ASN450 3.2 0.2 1.0 HA A:LEU445 3.4 0.2 1.0 C A:LEU445 3.6 92.5 1.0 H A:LEU452 3.7 0.1 1.0 HA A:PRO448 3.7 0.4 1.0 HB2 A:LEU452 3.7 99.8 1.0 C A:ASP447 3.9 95.6 1.0 CA A:LEU445 3.9 95.2 1.0 O A:ASN450 3.9 92.3 1.0 C A:LEU452 3.9 85.1 1.0 C A:THR444 4.1 91.8 1.0 CB A:ASN450 4.2 85.2 1.0 N A:LEU452 4.3 86.7 1.0 HD22 A:ASN450 4.3 0.9 1.0 CA A:LEU452 4.4 89.0 1.0 N A:ALA446 4.5 92.9 1.0 N A:ASP447 4.5 96.1 1.0 CB A:LEU452 4.5 83.1 1.0 N A:LEU445 4.5 90.0 1.0 C A:ALA446 4.5 0.7 1.0 CA A:PRO448 4.5 95.3 1.0 C A:ASN450 4.5 88.6 1.0 HB3 A:ASN450 4.6 0.2 1.0 N A:PRO448 4.6 0.2 1.0 O A:ALA446 4.7 0.8 1.0 H A:ASP447 4.7 0.4 1.0 HA A:ASN453 4.7 89.3 1.0 HG21 A:THR444 4.7 0.8 1.0 CA A:ASP447 4.8 93.7 1.0 H A:ASN450 4.8 0.2 1.0 HB3 A:ASP447 4.8 0.5 1.0 ND2 A:ASN450 4.9 84.9 1.0 CA A:ASN450 4.9 83.3 1.0 HD23 A:LEU445 4.9 0.1 1.0 HB3 A:LEU452 5.0 99.8 1.0 H A:ALA446 5.0 0.5 1.0 CG A:ASN450 5.0 89.7 1.0

Potassium binding site 2 out of 3 in the Atp-Dependent Type Isp Restriction-Modification Enzyme Llabiii Bound to Dna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Atp-Dependent Type Isp Restriction-Modification Enzyme Llabiii Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:K1602 b:83.0 occ:1.00 O A:GLY966 2.7 76.2 1.0 OD2 A:ASP962 2.7 79.0 1.0 O A:ASP962 2.8 73.8 1.0 O A:HOH1772 2.9 81.2 1.0 O A:GLU969 2.9 79.7 1.0 O A:HOH1731 3.0 49.9 1.0 OD1 A:ASN965 3.1 81.0 1.0 CG A:ASP962 3.2 80.1 1.0 HA2 A:GLY970 3.4 99.7 1.0 OD1 A:ASP962 3.5 77.6 1.0 C A:ASP962 3.9 58.1 1.0 C A:GLY966 3.9 78.7 1.0 HA A:ASP962 3.9 71.1 1.0 HA A:ASP967 4.0 99.1 1.0 C A:GLU969 4.0 87.7 1.0 CA A:GLY970 4.2 83.0 1.0 CA A:ASP962 4.3 59.2 1.0 CG A:ASN965 4.3 65.5 1.0 H A:GLU969 4.3 0.5 1.0 CB A:ASP962 4.3 70.5 1.0 C A:GLY970 4.5 81.5 1.0 O A:GLY970 4.5 94.5 1.0 HD21 A:ASN965 4.5 77.0 1.0 N A:GLY970 4.6 86.4 1.0 HB3 A:ASP962 4.8 84.6 1.0 O A:ASN965 4.8 80.4 1.0 CA A:ASP967 4.8 82.6 1.0 N A:ASP967 4.8 82.8 1.0 ND2 A:ASN965 4.8 64.2 1.0 CA A:GLY966 4.8 76.2 1.0 N A:GLY966 4.9 72.8 1.0 C A:ASN965 4.9 68.9 1.0 HA A:GLU963 4.9 71.2 1.0 HA2 A:GLY966 5.0 91.4 1.0 HA3 A:GLY970 5.0 99.7 1.0

Potassium binding site 3 out of 3 in the Atp-Dependent Type Isp Restriction-Modification Enzyme Llabiii Bound to Dna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Atp-Dependent Type Isp Restriction-Modification Enzyme Llabiii Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:K1601 b:82.7 occ:1.00 O B:ASP962 2.7 63.0 1.0 OD2 B:ASP962 2.7 70.8 1.0 O B:GLY966 2.8 61.0 1.0 O B:GLU969 2.8 86.8 1.0 O B:HOH1740 2.8 62.3 1.0 O B:HOH1728 2.9 51.0 1.0 OD1 B:ASN965 3.2 71.5 1.0 CG B:ASP962 3.2 67.7 1.0 OD1 B:ASP962 3.5 62.4 1.0 HA2 B:GLY970 3.5 0.2 1.0 C B:ASP962 3.8 50.8 1.0 HA B:ASP962 3.9 63.4 1.0 C B:GLY966 3.9 72.4 1.0 C B:GLU969 4.0 87.9 1.0 CA B:ASP962 4.2 52.8 1.0 CG B:ASN965 4.3 64.7 1.0 HA B:ASP967 4.3 97.0 1.0 CB B:ASP962 4.3 60.7 1.0 HD21 B:ASN965 4.3 72.2 1.0 CA B:GLY970 4.3 86.8 1.0 O B:GLY970 4.3 90.5 1.0 H B:GLU969 4.4 0.2 1.0 C B:GLY970 4.4 79.4 1.0 N B:GLY970 4.6 89.3 1.0 HA2 B:GLY966 4.6 76.6 1.0 HB3 B:ASP962 4.6 72.8 1.0 CA B:GLY966 4.7 63.9 1.0 ND2 B:ASN965 4.7 60.2 1.0 N B:GLY966 4.7 58.9 1.0 HA B:GLU963 4.7 65.5 1.0 H B:GLY966 4.8 70.6 1.0 N B:ASP967 4.9 78.4 1.0 N B:GLU963 4.9 55.2 1.0 CA B:ASP967 5.0 80.9 1.0

M.K.Chand, N.Nirwan, F.M.Diffin, K.V.Aelst, M.Kulkarni, C.Pernstich, M.D.Szczelkun, K.Saikrishnan. Translocation-Coupled Dna Cleavage By the Type Isp Restriction-Modification Enzymes Nat.Chem.Biol. V. 11 870 2015.
ISSN: ESSN 1552-4469
PubMed: 26389736
DOI: 10.1038/NCHEMBIO.1926