Nickel in PDB 7cl2: The Crystal Structure of Kanj

All present enzymatic activity of The Crystal Structure of Kanj:
1.14.11.37;

The structure of The Crystal Structure of Kanj, PDB code: 7cl2 was solved by Y.Kitayama, A.Miyanaga, F.Kudo, T.Eguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.80 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.202, 182.209, 109.228, 90, 93.97, 90
R / Rfree (%)	18.4 / 20.6

The binding sites of Nickel atom in the The Crystal Structure of Kanj (pdb code 7cl2). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the The Crystal Structure of Kanj, PDB code: 7cl2:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the The Crystal Structure of Kanj


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of Kanj within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:51.4 occ:1.00 NE2 A:HIS219 2.2 42.8 1.0 NE2 A:HIS132 2.2 42.4 1.0 OD1 A:ASP134 2.3 41.3 1.0 O A:HOH503 2.3 43.6 1.0 O A:HOH412 2.3 42.9 1.0 O A:HOH406 2.4 46.0 1.0 CE1 A:HIS219 3.1 41.5 1.0 CE1 A:HIS132 3.2 40.5 1.0 CD2 A:HIS132 3.2 39.2 1.0 CG A:ASP134 3.2 41.4 1.0 CD2 A:HIS219 3.2 40.6 1.0 OD2 A:ASP134 3.4 40.7 1.0 ND1 A:HIS219 4.2 41.3 1.0 ND1 A:HIS132 4.2 41.9 1.0 CG A:HIS219 4.3 41.2 1.0 CG A:HIS132 4.3 38.7 1.0 O2 A:SO4302 4.4 63.1 1.0 O A:HOH457 4.6 56.5 1.0 OE1 A:GLN129 4.6 38.1 1.0 CB A:ASP134 4.6 40.0 1.0 NH2 A:ARG213 4.9 45.9 1.0 CA A:ASP134 5.0 40.2 1.0

Nickel binding site 2 out of 6 in the The Crystal Structure of Kanj


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of Kanj within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:41.1 occ:1.00 NE2 B:HIS219 2.2 35.0 1.0 NE2 B:HIS132 2.2 34.9 1.0 OD1 B:ASP134 2.3 36.5 1.0 O B:HOH406 2.3 32.0 1.0 O B:HOH543 2.3 42.9 1.0 O B:HOH438 2.3 36.3 1.0 CE1 B:HIS219 3.1 34.3 1.0 CE1 B:HIS132 3.2 34.5 1.0 CD2 B:HIS132 3.2 34.6 1.0 CG B:ASP134 3.2 35.0 1.0 CD2 B:HIS219 3.2 33.3 1.0 OD2 B:ASP134 3.4 34.1 1.0 ND1 B:HIS219 4.2 33.3 1.0 ND1 B:HIS132 4.3 35.2 1.0 CG B:HIS219 4.3 32.9 1.0 CG B:HIS132 4.3 34.6 1.0 O3 B:SO4302 4.3 49.8 1.0 O B:HOH425 4.4 46.3 1.0 OE1 B:GLN129 4.6 38.4 1.0 CB B:ASP134 4.6 34.4 1.0 NH2 B:ARG213 4.9 43.3 1.0 CA B:ASP134 5.0 35.0 1.0

Nickel binding site 3 out of 6 in the The Crystal Structure of Kanj


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Crystal Structure of Kanj within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni301 b:43.2 occ:1.00 NE2 C:HIS219 2.2 38.1 1.0 NE2 C:HIS132 2.2 34.2 1.0 OD1 C:ASP134 2.3 37.4 1.0 O C:HOH464 2.3 35.1 1.0 O C:HOH508 2.3 39.3 1.0 CE1 C:HIS219 3.0 35.8 1.0 CD2 C:HIS132 3.1 33.1 1.0 CE1 C:HIS132 3.2 33.1 1.0 CG C:ASP134 3.2 36.1 1.0 CD2 C:HIS219 3.2 35.4 1.0 OD2 C:ASP134 3.4 36.6 1.0 ND1 C:HIS219 4.2 35.1 1.0 ND1 C:HIS132 4.3 34.2 1.0 CG C:HIS219 4.3 35.5 1.0 CG C:HIS132 4.3 33.2 1.0 O2 C:SO4302 4.6 50.1 1.0 CB C:ASP134 4.6 35.0 1.0 OE1 C:GLN129 4.7 35.9 1.0 NH2 C:ARG213 4.9 41.4 1.0 CA C:ASP134 4.9 34.4 1.0 N C:ASP134 5.0 33.7 1.0

Nickel binding site 4 out of 6 in the The Crystal Structure of Kanj


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The Crystal Structure of Kanj within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni301 b:47.7 occ:1.00 NE2 D:HIS132 2.2 37.6 1.0 NE2 D:HIS219 2.2 39.0 1.0 OD1 D:ASP134 2.3 38.4 1.0 O D:HOH518 2.3 45.6 1.0 O D:HOH418 2.4 43.8 1.0 O D:HOH419 2.4 33.1 1.0 CE1 D:HIS219 3.1 37.2 1.0 CD2 D:HIS132 3.1 36.0 1.0 CE1 D:HIS132 3.1 36.8 1.0 CG D:ASP134 3.2 36.7 1.0 CD2 D:HIS219 3.2 36.4 1.0 OD2 D:ASP134 3.4 37.9 1.0 O D:HOH500 3.8 60.6 1.0 ND1 D:HIS219 4.2 37.5 1.0 ND1 D:HIS132 4.2 37.4 1.0 O D:HOH434 4.3 46.0 1.0 CG D:HIS132 4.3 37.7 1.0 CG D:HIS219 4.3 36.7 1.0 O4 D:SO4302 4.3 59.4 1.0 OE1 D:GLN129 4.5 40.8 1.0 CB D:ASP134 4.6 35.3 1.0 CA D:ASP134 4.9 34.9 1.0 N D:ASP134 5.0 34.4 1.0 NH2 D:ARG213 5.0 38.8 1.0

Nickel binding site 5 out of 6 in the The Crystal Structure of Kanj


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of The Crystal Structure of Kanj within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni301 b:51.3 occ:1.00 NE2 E:HIS132 2.1 40.0 1.0 NE2 E:HIS219 2.2 42.1 1.0 OD1 E:ASP134 2.3 44.9 1.0 O E:HOH470 2.3 47.1 1.0 O E:HOH424 2.3 41.5 1.0 O E:HOH421 2.3 43.7 1.0 CE1 E:HIS219 3.1 40.8 1.0 CE1 E:HIS132 3.1 39.5 1.0 CD2 E:HIS132 3.1 39.4 1.0 CG E:ASP134 3.2 44.6 1.0 CD2 E:HIS219 3.2 42.5 1.0 OD2 E:ASP134 3.4 46.2 1.0 ND1 E:HIS132 4.2 39.0 1.0 ND1 E:HIS219 4.2 41.1 1.0 CG E:HIS132 4.2 38.6 1.0 CG E:HIS219 4.3 41.6 1.0 O E:HOH447 4.4 55.6 1.0 OE1 E:GLN129 4.6 39.9 1.0 O4 E:SO4302 4.6 64.5 1.0 CB E:ASP134 4.6 44.7 1.0 NH2 E:ARG213 4.9 51.6 1.0 CA E:ASP134 4.9 43.0 1.0 N E:ASP134 5.0 42.5 1.0

Nickel binding site 6 out of 6 in the The Crystal Structure of Kanj


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of The Crystal Structure of Kanj within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni301 b:58.3 occ:1.00 NE2 F:HIS132 2.1 50.9 1.0 NE2 F:HIS219 2.2 50.8 1.0 OD1 F:ASP134 2.3 48.1 1.0 O F:HOH416 2.3 46.0 1.0 O F:HOH431 2.4 47.3 1.0 CE1 F:HIS219 3.1 50.0 1.0 CE1 F:HIS132 3.1 52.1 1.0 CD2 F:HIS132 3.1 51.9 1.0 CD2 F:HIS219 3.2 50.5 1.0 CG F:ASP134 3.3 48.5 1.0 OD2 F:ASP134 3.5 50.1 1.0 ND1 F:HIS132 4.2 52.7 1.0 ND1 F:HIS219 4.2 49.6 1.0 CG F:HIS132 4.2 53.5 1.0 CG F:HIS219 4.3 51.8 1.0 O1 F:SO4302 4.5 75.7 1.0 OE1 F:GLN129 4.6 49.1 1.0 CB F:ASP134 4.6 46.7 1.0 CA F:ASP134 5.0 46.6 1.0 NH2 F:ARG213 5.0 52.2 1.0

T.Eguchi, F.Kudo, Y.Kitayama, A.Miyanaga, M.Numakura. Stepwise Post-Glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis. Chembiochem 2021.
ISSN: ESSN 1439-7633
PubMed: 33403742
DOI: 10.1002/CBIC.202000839