Iron in PDB 6jst: Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl

The structure of Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl, PDB code: 6jst was solved by B.Xue, W.S.Yew, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 1.73
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.991, 51.187, 134.473, 90.99, 91.33, 96.33
R / Rfree (%)	21.9 / 26.4

The structure of Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Iron atom in the Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl (pdb code 6jst). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl, PDB code: 6jst:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:10.6 occ:0.90 O A:OH403 1.9 20.7 1.0 OQ2 A:KCX145 2.0 15.6 1.0 NE2 A:HIS25 2.0 7.8 1.0 NE2 A:HIS23 2.0 15.8 1.0 OD1 A:ASN266 2.1 9.4 1.0 O A:HOH503 2.7 38.0 1.0 CX A:KCX145 2.9 25.4 1.0 CE1 A:HIS25 2.9 5.8 1.0 CD2 A:HIS23 3.0 12.1 1.0 CE1 A:HIS23 3.0 19.5 1.0 CD2 A:HIS25 3.1 8.8 1.0 CG A:ASN266 3.1 16.6 1.0 OQ1 A:KCX145 3.3 20.5 1.0 ZN A:ZN402 3.6 16.5 0.8 ND2 A:ASN266 3.6 17.5 1.0 NZ A:KCX145 4.0 25.6 1.0 ND1 A:HIS25 4.1 12.1 1.0 ND1 A:HIS23 4.1 18.8 1.0 CG A:HIS23 4.1 15.4 1.0 CG A:HIS25 4.2 7.9 1.0 CE1 A:HIS206 4.2 18.2 1.0 C4 A:LAE404 4.2 45.6 0.9 NE2 A:HIS206 4.4 17.2 1.0 CB A:ASN266 4.4 15.1 1.0 CG A:PRO69 4.5 9.9 1.0 O3 A:LAE404 4.9 46.4 0.9 CA A:ASN266 4.9 18.7 1.0

Iron binding site 2 out of 4 in the Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:12.1 occ:1.00 O B:OH403 1.9 20.5 1.0 OQ1 B:KCX145 1.9 18.9 1.0 OD1 B:ASN266 2.0 10.0 1.0 NE2 B:HIS23 2.0 13.4 1.0 NE2 B:HIS25 2.1 11.9 1.0 CX B:KCX145 2.9 29.7 1.0 CD2 B:HIS25 3.0 8.8 1.0 CD2 B:HIS23 3.0 12.8 1.0 CE1 B:HIS23 3.0 19.9 1.0 CG B:ASN266 3.1 16.6 1.0 OQ2 B:KCX145 3.2 38.3 1.0 CE1 B:HIS25 3.2 6.5 1.0 ZN B:ZN402 3.6 21.0 0.8 ND2 B:ASN266 3.6 18.9 1.0 NZ B:KCX145 4.0 21.8 1.0 O B:HOH692 4.0 57.9 1.0 CG B:HIS23 4.1 14.1 1.0 ND1 B:HIS23 4.1 15.1 1.0 CG B:HIS25 4.2 7.7 1.0 CE1 B:HIS206 4.3 21.8 1.0 ND1 B:HIS25 4.3 11.7 1.0 CB B:ASN266 4.3 17.3 1.0 NE2 B:HIS206 4.4 21.3 1.0 CG B:PRO69 4.5 11.1 1.0 CA B:ASN266 4.8 20.1 1.0

Iron binding site 3 out of 4 in the Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:29.2 occ:0.80 NE2 C:HIS25 2.1 35.9 1.0 OD1 C:ASN266 2.1 40.7 1.0 NE2 C:HIS23 2.1 35.3 1.0 OQ2 C:KCX145 2.2 37.3 1.0 O C:OH403 2.4 34.4 1.0 CG C:ASN266 3.0 29.1 1.0 CX C:KCX145 3.0 42.8 1.0 CD2 C:HIS23 3.0 35.3 1.0 CD2 C:HIS25 3.1 35.0 1.0 CE1 C:HIS25 3.1 33.4 1.0 OQ1 C:KCX145 3.2 45.6 1.0 CE1 C:HIS23 3.2 36.6 1.0 ND2 C:ASN266 3.3 25.8 1.0 ZN C:ZN402 3.5 35.5 0.8 NZ C:KCX145 4.1 43.2 1.0 ND1 C:HIS25 4.2 32.6 1.0 CG C:HIS25 4.2 34.9 1.0 CE1 C:HIS206 4.2 43.8 1.0 CG C:HIS23 4.2 34.8 1.0 ND1 C:HIS23 4.3 35.0 1.0 NE2 C:HIS206 4.3 46.3 1.0 CB C:ASN266 4.3 28.6 1.0 CG C:PRO69 4.5 26.2 1.0 CA C:ASN266 4.9 25.1 1.0

Iron binding site 4 out of 4 in the Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:30.0 occ:0.93 NE2 D:HIS25 1.9 42.2 1.0 OQ2 D:KCX145 2.0 38.3 1.0 OD1 D:ASN266 2.0 39.3 1.0 NE2 D:HIS23 2.1 39.0 1.0 CE1 D:HIS25 2.8 39.4 1.0 CX D:KCX145 3.0 38.6 1.0 CD2 D:HIS25 3.0 42.2 1.0 CG D:ASN266 3.0 36.8 1.0 CE1 D:HIS23 3.1 34.0 1.0 CD2 D:HIS23 3.1 33.8 1.0 OQ1 D:KCX145 3.2 46.8 1.0 ND2 D:ASN266 3.4 32.7 1.0 ZN D:ZN402 3.7 31.7 0.7 ND1 D:HIS25 3.9 42.6 1.0 CG D:HIS25 4.1 44.7 1.0 NZ D:KCX145 4.1 34.9 1.0 ND1 D:HIS23 4.2 34.8 1.0 CG D:HIS23 4.2 35.0 1.0 O D:HOH574 4.3 45.1 1.0 CB D:ASN266 4.4 34.2 1.0 CE1 D:HIS206 4.4 33.1 1.0 NE2 D:HIS206 4.6 34.3 1.0 CG D:PRO69 4.6 28.6 1.0 CA D:ASN266 4.9 26.1 1.0

M.K.Go, L.N.Zhao, B.Xue, S.Supekar, R.C.Robinson, H.Fan, W.S.Yew. Directed Computational Evolution of Quorum-Quenching Lactonases From the Amidohydrolase Superfamily Structure 2020.
ISSN: ISSN 0969-2126