Iron in PDB 4h9t: Structure of Geobacillus Kaustophilus Lactonase, Mutant E101N with Bound N-Butyryl-Dl-Homoserine Lactone

The structure of Structure of Geobacillus Kaustophilus Lactonase, Mutant E101N with Bound N-Butyryl-Dl-Homoserine Lactone, PDB code: 4h9t was solved by B.Xue, J.Y.Chow, W.S.Yew, R.C.Robinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.231, 91.419, 95.686, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21

The structure of Structure of Geobacillus Kaustophilus Lactonase, Mutant E101N with Bound N-Butyryl-Dl-Homoserine Lactone also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Iron atom in the Structure of Geobacillus Kaustophilus Lactonase, Mutant E101N with Bound N-Butyryl-Dl-Homoserine Lactone (pdb code 4h9t). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of Geobacillus Kaustophilus Lactonase, Mutant E101N with Bound N-Butyryl-Dl-Homoserine Lactone, PDB code: 4h9t:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Structure of Geobacillus Kaustophilus Lactonase, Mutant E101N with Bound N-Butyryl-Dl-Homoserine Lactone


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, Mutant E101N with Bound N-Butyryl-Dl-Homoserine Lactone within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:20.6 occ:0.92 NE2 A:HIS25 2.3 11.1 1.0 OD1 A:ASN266 2.3 20.3 1.0 O A:HOH670 2.3 34.0 1.0 NE2 A:HIS23 2.4 19.8 1.0 OQ1 A:KCX145 2.5 19.9 1.0 CE1 A:HIS25 3.1 9.6 1.0 CG A:ASN266 3.2 22.1 1.0 CX A:KCX145 3.2 50.0 1.0 OQ2 A:KCX145 3.3 53.1 1.0 CE1 A:HIS23 3.3 15.2 1.0 CD2 A:HIS23 3.3 15.8 1.0 CD2 A:HIS25 3.3 9.4 1.0 MN A:MN402 3.5 34.1 0.6 ND2 A:ASN266 3.6 34.7 1.0 ND1 A:HIS25 4.3 12.1 1.0 ND1 A:HIS23 4.4 23.0 1.0 CG A:HIS25 4.4 9.7 1.0 CG A:HIS23 4.4 15.7 1.0 OAP A:HL4403 4.5 67.8 0.9 NZ A:KCX145 4.5 42.8 1.0 CB A:ASN266 4.6 9.7 1.0 CE1 A:HIS206 4.7 31.1 1.0 C4 A:HL4403 4.7 61.7 0.9 CG A:PRO69 4.8 11.4 1.0 NE2 A:HIS206 4.9 29.5 1.0

Iron binding site 2 out of 2 in the Structure of Geobacillus Kaustophilus Lactonase, Mutant E101N with Bound N-Butyryl-Dl-Homoserine Lactone


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, Mutant E101N with Bound N-Butyryl-Dl-Homoserine Lactone within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:25.4 occ:0.99 OD1 B:ASN266 2.3 22.8 1.0 NE2 B:HIS25 2.3 12.7 1.0 NE2 B:HIS23 2.4 18.6 1.0 OQ1 B:KCX145 2.6 25.1 1.0 MN B:MN402 3.0 40.0 0.7 OAP B:HL4403 3.1 62.2 0.9 OQ2 B:KCX145 3.1 43.2 1.0 CX B:KCX145 3.2 42.9 1.0 CG B:ASN266 3.2 23.8 1.0 CE1 B:HIS25 3.2 10.9 1.0 C4 B:HL4403 3.2 57.1 0.9 CE1 B:HIS23 3.3 17.1 1.0 CD2 B:HIS25 3.3 11.0 1.0 CD2 B:HIS23 3.4 16.1 1.0 ND2 B:ASN266 3.5 35.7 1.0 C5 B:HL4403 4.3 50.4 0.9 C2 B:HL4403 4.3 66.5 0.9 ND1 B:HIS25 4.4 13.0 1.0 NZ B:KCX145 4.4 46.5 1.0 ND1 B:HIS23 4.4 21.9 1.0 CG B:HIS25 4.4 13.9 1.0 CG B:HIS23 4.5 16.6 1.0 CB B:ASN266 4.5 12.4 1.0 CE1 B:HIS206 4.6 30.6 1.0 CG B:PRO69 4.8 13.7 1.0 NE2 B:HIS206 4.9 30.2 1.0

B.Xue, J.Y.Chow, A.Baldansuren, L.L.Yap, Y.H.Gan, S.A.Dikanov, R.C.Robinson, W.S.Yew. Structural Evidence of A Productive Active Site Architecture For An Evolved Quorum-Quenching Gkl Lactonase. Biochemistry V. 52 2359 2013.
ISSN: ISSN 0006-2960
PubMed: 23461395
DOI: 10.1021/BI4000904