Nickel in PDB 5i14: Truncated and Mutated T4 Lysozyme

The structure of Truncated and Mutated T4 Lysozyme, PDB code: 5i14 was solved by M.Klima, E.Boura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.02 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.088, 61.206, 69.806, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 24.6

The binding sites of Nickel atom in the Truncated and Mutated T4 Lysozyme (pdb code 5i14). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Truncated and Mutated T4 Lysozyme, PDB code: 5i14:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Truncated and Mutated T4 Lysozyme


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Truncated and Mutated T4 Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:33.4 occ:1.00 O A:HOH335 1.8 35.9 1.0 O A:HOH355 1.8 32.5 1.0 NE2 A:HIS76 2.0 34.8 1.0 O A:HOH338 2.0 37.5 1.0 NE2 A:HIS80 2.1 33.0 1.0 NE2 B:HIS82 2.2 33.3 1.0 CD2 A:HIS76 3.0 33.9 1.0 CE1 A:HIS76 3.0 32.6 1.0 CE1 A:HIS80 3.1 32.3 1.0 CD2 B:HIS82 3.1 35.8 1.0 CD2 A:HIS80 3.1 33.0 1.0 CE1 B:HIS82 3.3 37.7 1.0 O B:HIS80 4.0 32.4 1.0 ND1 A:HIS76 4.1 33.9 1.0 CG A:HIS76 4.1 35.0 1.0 ND1 A:HIS80 4.2 33.6 1.0 CG A:HIS80 4.2 32.4 1.0 OE1 A:GLN79 4.3 47.1 1.0 CG B:HIS82 4.3 33.9 1.0 ND1 B:HIS82 4.3 33.7 1.0 O A:HOH397 4.5 48.5 1.0

Nickel binding site 2 out of 4 in the Truncated and Mutated T4 Lysozyme


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Truncated and Mutated T4 Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:37.1 occ:1.00 NE2 A:HIS89 2.1 38.7 1.0 NE2 A:HIS85 2.1 34.5 1.0 O A:HOH359 2.2 46.1 1.0 O A:HOH354 2.2 41.0 1.0 NE2 A:HIS73 2.2 34.1 1.0 CD2 A:HIS73 2.9 38.0 1.0 CE1 A:HIS89 3.0 40.6 1.0 CE1 A:HIS85 3.0 35.8 1.0 CD2 A:HIS89 3.1 35.1 1.0 O A:HOH383 3.1 58.3 1.0 CD2 A:HIS85 3.1 35.8 1.0 CE1 A:HIS73 3.3 41.0 1.0 ND1 A:HIS89 4.1 42.5 1.0 ND1 A:HIS85 4.2 33.1 1.0 CG A:HIS73 4.2 39.2 1.0 CG A:HIS89 4.2 35.9 1.0 CG A:HIS85 4.2 34.6 1.0 ND1 A:HIS73 4.3 39.5 1.0

Nickel binding site 3 out of 4 in the Truncated and Mutated T4 Lysozyme


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Truncated and Mutated T4 Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni203 b:32.1 occ:1.00 O A:HOH324 2.0 30.6 1.0 O B:HOH311 2.1 27.1 1.0 NE2 B:HIS80 2.1 30.8 1.0 NE2 B:HIS76 2.1 32.8 1.0 O B:HOH342 2.1 37.5 1.0 NE2 A:HIS82 2.2 31.2 1.0 CD2 A:HIS82 2.9 32.9 1.0 CE1 B:HIS80 3.0 31.3 1.0 CD2 B:HIS76 3.1 31.8 1.0 CD2 B:HIS80 3.1 34.2 1.0 CE1 B:HIS76 3.1 35.6 1.0 CE1 A:HIS82 3.3 35.5 1.0 O A:HIS80 3.9 31.5 1.0 ND1 B:HIS80 4.1 35.6 1.0 CG A:HIS82 4.2 31.7 1.0 OE1 B:GLN79 4.2 39.0 1.0 CG B:HIS80 4.2 29.8 1.0 ND1 B:HIS76 4.2 35.4 1.0 CG B:HIS76 4.2 32.3 1.0 ND1 A:HIS82 4.3 33.0 1.0 CD B:GLN79 5.0 36.8 1.0

Nickel binding site 4 out of 4 in the Truncated and Mutated T4 Lysozyme


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Truncated and Mutated T4 Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:36.4 occ:1.00 O B:HOH322 1.8 42.0 1.0 O B:HOH338 2.0 37.3 1.0 NE2 B:HIS85 2.1 34.0 1.0 NE2 B:HIS89 2.1 34.3 1.0 O B:HOH360 2.1 34.7 1.0 NE2 B:HIS73 2.2 31.7 1.0 CD2 B:HIS73 3.0 32.0 1.0 CE1 B:HIS85 3.0 38.8 1.0 CE1 B:HIS89 3.0 38.8 1.0 CD2 B:HIS85 3.1 37.5 1.0 CD2 B:HIS89 3.1 33.9 1.0 CE1 B:HIS73 3.3 38.9 1.0 ND1 B:HIS89 4.1 35.8 1.0 ND1 B:HIS85 4.2 39.0 1.0 CG B:HIS73 4.2 31.4 1.0 CG B:HIS89 4.2 34.5 1.0 CG B:HIS85 4.2 37.1 1.0 ND1 B:HIS73 4.3 36.4 1.0

E.Boura, A.Baumlova, D.Chalupska, A.Dubankova, M.Klima. Metal Ions-Binding T4 Lysozyme As An Intramolecular Protein Purification Tag Compatible with X-Ray Crystallography. Protein Sci. V. 26 1116 2017.
ISSN: ESSN 1469-896X
PubMed: 28342173
DOI: 10.1002/PRO.3162