Iron in PDB 6jss: Structure of Geobacillus Kaustophilus Lactonase, Y99P Mutant

The structure of Structure of Geobacillus Kaustophilus Lactonase, Y99P Mutant, PDB code: 6jss 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)	19.71 / 2.16
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.491, 51.648, 135.291, 91.83, 91.49, 95.78
R / Rfree (%)	17.5 / 22.9

The structure of Structure of Geobacillus Kaustophilus Lactonase, Y99P Mutant also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Iron atom in the Structure of Geobacillus Kaustophilus Lactonase, Y99P Mutant (pdb code 6jss). 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 Mutant, PDB code: 6jss:
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 Mutant


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 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:15.4 occ:1.00 NE2 A:HIS23 2.1 23.2 1.0 OQ2 A:KCX145 2.1 15.9 1.0 O A:OH403 2.1 19.6 1.0 OD1 A:ASP266 2.2 19.4 1.0 NE2 A:HIS25 2.2 19.4 1.0 CX A:KCX145 3.0 21.4 1.0 CE1 A:HIS23 3.0 20.3 1.0 CD2 A:HIS23 3.1 22.9 1.0 CG A:ASP266 3.1 22.8 1.0 CD2 A:HIS25 3.1 12.4 1.0 CE1 A:HIS25 3.2 13.8 1.0 OQ1 A:KCX145 3.3 21.7 1.0 OD2 A:ASP266 3.3 16.6 1.0 ZN A:ZN402 3.3 24.0 1.0 ND1 A:HIS23 4.1 20.5 1.0 NZ A:KCX145 4.2 14.6 1.0 CG A:HIS23 4.2 18.6 1.0 CE1 A:HIS206 4.2 26.3 1.0 CG A:HIS25 4.2 17.6 1.0 ND1 A:HIS25 4.3 16.4 1.0 NE2 A:HIS206 4.3 27.9 1.0 CB A:ASP266 4.4 22.6 1.0 CG A:PRO69 4.7 14.5 1.0 CA A:ASP266 4.9 19.7 1.0

Iron binding site 2 out of 4 in the Structure of Geobacillus Kaustophilus Lactonase, Y99P Mutant


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 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:18.3 occ:1.00 NE2 B:HIS23 1.9 25.8 1.0 NE2 B:HIS25 2.1 20.1 1.0 OD1 B:ASP266 2.2 18.0 1.0 OQ1 B:KCX145 2.3 17.3 1.0 O B:OH403 2.3 21.4 1.0 CE1 B:HIS23 2.8 21.8 1.0 CD2 B:HIS23 3.0 22.7 1.0 CE1 B:HIS25 3.0 14.1 1.0 CD2 B:HIS25 3.0 14.1 1.0 CG B:ASP266 3.1 26.3 1.0 CX B:KCX145 3.1 25.6 1.0 ZN B:ZN402 3.3 25.1 1.0 OD2 B:ASP266 3.3 18.4 1.0 OQ2 B:KCX145 3.4 20.3 1.0 O B:HOH508 3.5 33.6 1.0 ND1 B:HIS23 4.0 18.3 1.0 O B:HOH656 4.0 48.0 1.0 CG B:HIS23 4.1 22.2 1.0 ND1 B:HIS25 4.1 18.6 1.0 CG B:HIS25 4.2 16.4 1.0 CE1 B:HIS206 4.3 29.6 1.0 NZ B:KCX145 4.3 25.0 1.0 NE2 B:HIS206 4.4 30.0 1.0 CB B:ASP266 4.5 21.1 1.0 CG B:PRO69 4.7 13.7 1.0 O B:HOH624 4.9 56.6 1.0 CA B:ASP266 5.0 23.2 1.0

Iron binding site 3 out of 4 in the Structure of Geobacillus Kaustophilus Lactonase, Y99P Mutant


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 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:20.4 occ:1.00 NE2 C:HIS25 2.0 18.9 1.0 O C:OH403 2.1 15.5 1.0 NE2 C:HIS23 2.1 24.2 1.0 OQ1 C:KCX145 2.1 26.4 1.0 OD1 C:ASP266 2.2 26.4 1.0 CD2 C:HIS25 3.0 19.1 1.0 CE1 C:HIS25 3.0 19.1 1.0 CG C:ASP266 3.0 25.6 1.0 CD2 C:HIS23 3.1 22.6 1.0 CE1 C:HIS23 3.1 31.5 1.0 CX C:KCX145 3.1 30.5 1.0 OD2 C:ASP266 3.2 26.7 1.0 OQ2 C:KCX145 3.3 32.3 1.0 O C:HOH514 3.4 40.3 1.0 ZN C:ZN402 3.5 28.3 1.0 ND1 C:HIS25 4.1 21.4 1.0 CG C:HIS25 4.1 19.0 1.0 ND1 C:HIS23 4.1 29.1 1.0 CG C:HIS23 4.2 24.4 1.0 NZ C:KCX145 4.2 28.0 1.0 CE1 C:HIS206 4.3 20.8 1.0 CB C:ASP266 4.4 15.6 1.0 CG C:PRO69 4.4 18.4 1.0 NE2 C:HIS206 4.5 20.8 1.0 CA C:ASP266 4.9 18.5 1.0

Iron binding site 4 out of 4 in the Structure of Geobacillus Kaustophilus Lactonase, Y99P Mutant


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 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:25.0 occ:1.00 NE2 D:HIS23 2.0 24.1 1.0 NE2 D:HIS25 2.1 24.1 1.0 OQ1 D:KCX145 2.2 27.5 1.0 OD1 D:ASP266 2.2 34.7 1.0 O D:OH403 2.2 40.0 1.0 CE1 D:HIS23 2.9 24.2 1.0 CD2 D:HIS23 3.0 20.0 1.0 CD2 D:HIS25 3.0 22.1 1.0 CX D:KCX145 3.0 23.8 1.0 CG D:ASP266 3.1 26.3 1.0 CE1 D:HIS25 3.2 20.5 1.0 OQ2 D:KCX145 3.2 29.0 1.0 O D:HOH560 3.3 34.8 1.0 OD2 D:ASP266 3.4 23.7 1.0 ZN D:ZN402 3.5 49.6 1.0 ND1 D:HIS23 4.0 20.5 1.0 CG D:HIS23 4.1 21.0 1.0 NZ D:KCX145 4.2 28.8 1.0 CG D:HIS25 4.2 20.7 1.0 ND1 D:HIS25 4.2 21.2 1.0 CE1 D:HIS206 4.3 31.3 1.0 CB D:ASP266 4.4 17.8 1.0 NE2 D:HIS206 4.5 39.4 1.0 CG D:PRO69 4.5 22.9 1.0 CA D:ASP266 4.9 24.9 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