Nickel in PDB 6ksg: Vibrio Cholerae Methionine Aminopeptidase in Holo Form

All present enzymatic activity of Vibrio Cholerae Methionine Aminopeptidase in Holo Form:
3.4.11.18;

The structure of Vibrio Cholerae Methionine Aminopeptidase in Holo Form, PDB code: 6ksg was solved by V.Pillalamarri, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.58 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.508, 49.835, 131.221, 90.00, 97.28, 90.00
R / Rfree (%)	19.6 / 23.9

The structure of Vibrio Cholerae Methionine Aminopeptidase in Holo Form also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Nickel atom in the Vibrio Cholerae Methionine Aminopeptidase in Holo Form (pdb code 6ksg). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Vibrio Cholerae Methionine Aminopeptidase in Holo Form, PDB code: 6ksg:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Vibrio Cholerae Methionine Aminopeptidase in Holo Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Vibrio Cholerae Methionine Aminopeptidase in Holo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:39.2 occ:1.00 O A:HOH474 2.0 32.4 1.0 OD1 A:ASP107 2.1 29.0 1.0 OE1 A:GLU252 2.2 30.3 1.0 OD1 A:ASP118 2.3 34.5 1.0 OD2 A:ASP107 2.4 33.7 1.0 CG A:ASP107 2.5 27.5 1.0 CG A:ASP118 3.1 24.9 1.0 CD A:GLU252 3.2 29.0 1.0 OD2 A:ASP118 3.2 30.7 1.0 NI A:NI302 3.4 59.6 1.0 OE2 A:GLU252 3.5 30.9 1.0 O A:HOH437 3.7 31.6 1.0 OG1 A:THR109 4.0 30.5 1.0 CB A:ASP107 4.1 22.0 1.0 N A:THR119 4.4 17.8 1.0 O A:THR119 4.4 21.1 1.0 CB A:ASP118 4.4 21.9 1.0 O A:ILE108 4.4 23.6 1.0 CG A:GLU252 4.5 24.6 1.0 OE1 A:GLU220 4.6 36.5 1.0 C A:THR119 4.7 20.7 1.0 C A:ASP118 4.8 17.8 1.0 CA A:ASP107 4.8 20.6 1.0 CA A:ASP118 4.8 19.1 1.0 O A:HOH418 4.9 32.5 1.0 N A:ILE108 4.9 21.3 1.0 CB A:GLU252 4.9 22.6 1.0 CA A:THR119 5.0 20.1 1.0

Nickel binding site 2 out of 4 in the Vibrio Cholerae Methionine Aminopeptidase in Holo Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Vibrio Cholerae Methionine Aminopeptidase in Holo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:59.6 occ:1.00 OD2 A:ASP118 2.1 30.7 1.0 OE2 A:GLU252 2.3 30.9 1.0 O A:HOH474 2.5 32.4 1.0 OE2 A:GLU220 2.5 31.8 1.0 NE2 A:HIS188 2.8 35.6 1.0 CG A:ASP118 3.2 24.9 1.0 CD A:GLU252 3.2 29.0 1.0 OE1 A:GLU220 3.2 36.5 1.0 CD A:GLU220 3.2 33.8 1.0 NI A:NI301 3.4 39.2 1.0 OE1 A:GLU252 3.5 30.3 1.0 CD2 A:HIS188 3.7 36.1 1.0 CE1 A:HIS188 3.7 34.1 1.0 OD1 A:ASP118 3.7 34.5 1.0 CZ A:PHE194 3.9 38.3 1.0 OG1 A:THR218 3.9 21.4 1.0 CG2 A:THR218 4.1 23.0 1.0 CE1 A:PHE194 4.2 36.0 1.0 CB A:THR218 4.3 20.8 1.0 CB A:ASP118 4.3 21.9 1.0 CG A:GLU252 4.5 24.6 1.0 CG A:GLU220 4.6 28.5 1.0 O A:HOH418 4.7 32.5 1.0 ND1 A:HIS188 4.8 35.0 1.0 CG A:HIS188 4.8 32.9 1.0 CE2 A:PHE194 4.9 40.0 1.0

Nickel binding site 3 out of 4 in the Vibrio Cholerae Methionine Aminopeptidase in Holo Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Vibrio Cholerae Methionine Aminopeptidase in Holo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:59.7 occ:1.00 OD1 B:ASP118 2.2 37.0 1.0 OD1 B:ASP107 2.2 30.5 1.0 OE1 B:GLU252 2.2 31.2 1.0 O B:HOH427 2.3 46.5 1.0 CG B:ASP118 2.8 29.4 1.0 OD2 B:ASP118 2.8 33.9 1.0 CG B:ASP107 3.0 28.6 1.0 CD B:GLU252 3.1 27.9 1.0 OD2 B:ASP107 3.1 36.2 1.0 NI B:NI302 3.3 70.7 1.0 OE2 B:GLU252 3.4 34.9 1.0 O B:HOH434 3.8 27.2 0.6 OG1 B:THR109 3.9 34.4 1.0 CB B:ASP118 4.3 25.8 1.0 N B:THR119 4.3 18.7 1.0 CB B:ASP107 4.4 23.8 1.0 O B:THR119 4.4 23.2 1.0 O B:ILE108 4.5 21.5 1.0 CG B:GLU252 4.5 24.9 1.0 OE1 B:GLU220 4.6 34.2 1.0 O B:HOH406 4.6 26.9 0.5 C B:ASP118 4.7 20.2 1.0 C B:THR119 4.7 20.4 1.0 CA B:ASP118 4.8 22.7 1.0 CB B:GLU252 4.9 23.2 1.0 CA B:ASP107 5.0 21.7 1.0

Nickel binding site 4 out of 4 in the Vibrio Cholerae Methionine Aminopeptidase in Holo Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Vibrio Cholerae Methionine Aminopeptidase in Holo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:70.7 occ:1.00 O B:HOH427 2.4 46.5 1.0 OD2 B:ASP118 2.4 33.9 1.0 OE2 B:GLU220 2.7 31.0 1.0 OE2 B:GLU252 3.0 34.9 1.0 OE1 B:GLU220 3.1 34.2 1.0 NE2 B:HIS188 3.1 35.8 1.0 CD B:GLU220 3.2 34.0 1.0 NI B:NI301 3.3 59.7 1.0 CG B:ASP118 3.5 29.4 1.0 CZ B:PHE194 3.7 42.0 1.0 CD B:GLU252 3.7 27.9 1.0 OE1 B:GLU252 3.9 31.2 1.0 CE1 B:HIS188 3.9 35.4 1.0 CD2 B:HIS188 4.0 34.6 1.0 OD1 B:ASP118 4.1 37.0 1.0 CE1 B:PHE194 4.3 39.9 1.0 OG1 B:THR218 4.5 21.1 1.0 O B:HOH402 4.5 30.1 1.0 CE2 B:PHE194 4.6 46.0 1.0 CB B:ASP118 4.7 25.8 1.0 CG2 B:THR218 4.7 24.1 1.0 CG B:GLU220 4.7 29.8 1.0 CB B:THR218 4.9 21.6 1.0 CG B:GLU252 5.0 24.9 1.0

V.Pillalamarri, C.G.Reddy, S.C.Bala, A.Jangam, V.V.Kutty, A.Addlagatta. Methionine Aminopeptidases with Short Sequence Inserts Within the Catalytic Domain Are Differentially Inhibited: Structural and Biochemical Studies of Three Proteins From Vibrio Spp. Eur.J.Med.Chem. V. 209 12883 2020.
ISSN: ISSN 0223-5234
PubMed: 33035924
DOI: 10.1016/J.EJMECH.2020.112883