Nickel in PDB 4xcb: Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel, 2-Oxoglutarate, and Hygromycin B Bound

The structure of Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel, 2-Oxoglutarate, and Hygromycin B Bound, PDB code: 4xcb was solved by K.M.Mcculloch, E.K.Mccranie, M.Sarwar, J.L.Mathieu, B.L.Gitschlag, Y.Du, B.O.Bachmann, T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.35 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.220, 117.431, 185.359, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 25.3

The binding sites of Nickel atom in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel, 2-Oxoglutarate, and Hygromycin B Bound (pdb code 4xcb). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel, 2-Oxoglutarate, and Hygromycin B Bound, PDB code: 4xcb:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel, 2-Oxoglutarate, and Hygromycin B Bound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel, 2-Oxoglutarate, and Hygromycin B Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:15.9 occ:1.00 O A:HOH473 2.0 16.7 1.0 O1 A:AKG302 2.0 19.4 1.0 NE2 A:HIS206 2.1 11.8 1.0 NE2 A:HIS102 2.1 16.3 1.0 O5 A:AKG302 2.1 17.5 1.0 O A:HOH472 2.3 17.5 1.0 C1 A:AKG302 2.7 19.9 1.0 C2 A:AKG302 2.8 19.3 1.0 CD2 A:HIS102 3.0 15.4 1.0 CD2 A:HIS206 3.0 14.3 1.0 CE1 A:HIS206 3.1 15.3 1.0 CE1 A:HIS102 3.2 15.8 1.0 O2 A:AKG302 4.0 19.8 1.0 NZ A:LYS137 4.0 15.2 1.0 O22 A:HY0303 4.1 17.3 1.0 OE1 A:GLU202 4.1 25.5 1.0 CG A:HIS206 4.1 13.9 1.0 OE2 A:GLU202 4.1 19.6 1.0 ND1 A:HIS206 4.1 12.1 1.0 CG A:HIS102 4.2 14.7 1.0 ND1 A:HIS102 4.3 17.1 1.0 C3 A:AKG302 4.3 17.1 1.0 CD A:GLU202 4.6 19.8 1.0 CD2 A:LEU200 4.6 17.3 1.0 O A:HOH474 4.6 18.0 1.0 C17 A:HY0303 4.7 14.5 1.0 C4 A:AKG302 5.0 18.5 1.0 C16 A:HY0303 5.0 15.6 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel, 2-Oxoglutarate, and Hygromycin B Bound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel, 2-Oxoglutarate, and Hygromycin B Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:12.3 occ:1.00 O B:HOH442 2.0 19.2 1.0 O1 B:AKG302 2.0 16.2 1.0 O B:HOH441 2.0 14.0 1.0 NE2 B:HIS206 2.1 10.9 1.0 NE2 B:HIS102 2.1 13.0 1.0 O5 B:AKG302 2.2 15.0 1.0 C1 B:AKG302 2.8 16.0 1.0 C2 B:AKG302 2.8 16.6 1.0 CD2 B:HIS206 3.0 9.8 1.0 CD2 B:HIS102 3.0 11.7 1.0 CE1 B:HIS206 3.1 10.3 1.0 CE1 B:HIS102 3.2 11.9 1.0 O2 B:AKG302 4.0 15.8 1.0 NZ B:LYS137 4.0 14.2 1.0 O22 B:HY0303 4.1 15.7 1.0 OE1 B:GLU202 4.1 21.5 1.0 CG B:HIS206 4.1 10.1 1.0 ND1 B:HIS206 4.1 12.7 1.0 OE2 B:GLU202 4.2 18.6 1.0 CG B:HIS102 4.2 10.3 1.0 ND1 B:HIS102 4.3 10.4 1.0 C3 B:AKG302 4.3 16.9 1.0 CD B:GLU202 4.6 15.4 1.0 O B:HOH439 4.6 17.4 1.0 C17 B:HY0303 4.7 14.8 1.0 CD2 B:LEU200 4.7 11.7 1.0 CD2 B:LEU99 5.0 15.7 1.0 C4 B:AKG302 5.0 16.6 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel, 2-Oxoglutarate, and Hygromycin B Bound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel, 2-Oxoglutarate, and Hygromycin B Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni301 b:21.4 occ:1.00 O C:HOH438 1.4 9.7 1.0 NE2 C:HIS102 1.9 19.2 1.0 O2 C:AKG302 2.0 21.8 1.0 O C:HOH437 2.1 21.6 1.0 NE2 C:HIS206 2.3 18.1 1.0 O5 C:AKG302 2.6 24.4 1.0 CD2 C:HIS102 2.7 18.4 1.0 C1 C:AKG302 2.9 27.4 1.0 CE1 C:HIS102 3.0 17.1 1.0 C2 C:AKG302 3.1 28.3 1.0 CD2 C:HIS206 3.1 18.5 1.0 CE1 C:HIS206 3.3 19.1 1.0 O22 C:HY0303 3.9 21.5 1.0 CG C:HIS102 3.9 17.7 1.0 NZ C:LYS137 4.0 27.0 1.0 O1 C:AKG302 4.0 27.8 1.0 ND1 C:HIS102 4.0 16.5 1.0 OE2 C:GLU202 4.2 25.5 1.0 OE1 C:GLU202 4.2 24.4 1.0 CG C:HIS206 4.3 17.6 1.0 ND1 C:HIS206 4.3 19.9 1.0 C17 C:HY0303 4.5 18.3 1.0 C3 C:AKG302 4.6 23.9 1.0 CD C:GLU202 4.7 22.2 1.0 C16 C:HY0303 4.8 19.3 1.0 CD2 C:LEU99 4.8 21.0 1.0 CD2 C:LEU200 4.9 21.4 1.0 CE C:LYS137 4.9 21.9 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel, 2-Oxoglutarate, and Hygromycin B Bound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Hygx From Streptomyces Hygroscopicus with Nickel, 2-Oxoglutarate, and Hygromycin B Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni301 b:20.9 occ:1.00 O D:HOH456 1.5 12.6 1.0 NE2 D:HIS102 2.0 20.5 1.0 NE2 D:HIS206 2.1 15.2 1.0 O D:HOH457 2.1 21.6 1.0 O1 D:AKG302 2.1 19.2 1.0 O5 D:AKG302 2.3 23.1 1.0 C1 D:AKG302 2.9 26.3 1.0 CD2 D:HIS102 2.9 17.7 1.0 CD2 D:HIS206 3.0 22.2 1.0 C2 D:AKG302 3.0 26.7 1.0 CE1 D:HIS102 3.0 17.3 1.0 CE1 D:HIS206 3.0 17.8 1.0 NZ D:LYS137 3.9 23.8 1.0 O22 D:HY0303 4.0 19.1 1.0 CG D:HIS102 4.1 16.0 1.0 ND1 D:HIS102 4.1 17.6 1.0 O2 D:AKG302 4.1 22.7 1.0 ND1 D:HIS206 4.1 18.0 1.0 CG D:HIS206 4.1 14.7 1.0 OE1 D:GLU202 4.1 29.1 1.0 OE2 D:GLU202 4.2 23.9 1.0 C3 D:AKG302 4.5 22.8 1.0 C17 D:HY0303 4.6 20.1 1.0 CD D:GLU202 4.6 24.4 1.0 O D:HOH497 4.7 24.5 1.0 CD2 D:LEU200 4.8 20.7 1.0 C16 D:HY0303 4.9 20.4 1.0 CD2 D:LEU99 4.9 20.9 1.0

K.M.Mcculloch, E.K.Mccranie, J.A.Smith, M.Sarwar, J.L.Mathieu, B.L.Gitschlag, Y.Du, B.O.Bachmann, T.M.Iverson. Oxidative Cyclizations in Orthosomycin Biosynthesis Expand the Known Chemistry of An Oxygenase Superfamily. Proc.Natl.Acad.Sci.Usa V. 112 11547 2015.
ISSN: ESSN 1091-6490
PubMed: 26240321
DOI: 10.1073/PNAS.1500964112