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Zinc in PDB 4h9x: Structure of Geobacillus Kaustophilus Lactonase, Mutant E101G/R230C/D266N with ZN2+ and Bound N-Butyryl-Dl-Homoserine Lactone

Protein crystallography data

The structure of Structure of Geobacillus Kaustophilus Lactonase, Mutant E101G/R230C/D266N with ZN2+ and Bound N-Butyryl-Dl-Homoserine Lactone, PDB code: 4h9x 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) 19.85 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.552, 129.156, 51.637, 90.00, 95.84, 90.00
R / Rfree (%) 17.6 / 21.5

Other elements in 4h9x:

The structure of Structure of Geobacillus Kaustophilus Lactonase, Mutant E101G/R230C/D266N with ZN2+ and Bound N-Butyryl-Dl-Homoserine Lactone also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Geobacillus Kaustophilus Lactonase, Mutant E101G/R230C/D266N with ZN2+ and Bound N-Butyryl-Dl-Homoserine Lactone (pdb code 4h9x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Geobacillus Kaustophilus Lactonase, Mutant E101G/R230C/D266N with ZN2+ and Bound N-Butyryl-Dl-Homoserine Lactone, PDB code: 4h9x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4h9x

Go back to Zinc Binding Sites List in 4h9x
Zinc binding site 1 out of 2 in the Structure of Geobacillus Kaustophilus Lactonase, Mutant E101G/R230C/D266N with ZN2+ and Bound N-Butyryl-Dl-Homoserine Lactone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Geobacillus Kaustophilus Lactonase, Mutant E101G/R230C/D266N with ZN2+ and Bound N-Butyryl-Dl-Homoserine Lactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:36.5
occ:0.67
NE2 A:HIS206 2.3 52.4 1.0
ND1 A:HIS178 2.3 25.1 1.0
O A:OH403 2.3 24.4 1.0
OQ2 A:KCX145 2.3 49.4 1.0
CE1 A:HIS206 3.1 40.9 1.0
CG A:HIS178 3.2 22.1 1.0
CD2 A:HIS206 3.2 50.5 1.0
CE1 A:HIS178 3.3 29.5 1.0
CX A:KCX145 3.3 53.0 1.0
CB A:HIS178 3.4 24.6 1.0
FE A:FE401 3.6 23.9 1.0
OQ1 A:KCX145 3.6 34.7 1.0
ND2 A:ASN266 4.1 39.1 1.0
ND1 A:HIS206 4.2 42.8 1.0
CG A:HIS206 4.3 31.0 1.0
CD2 A:HIS178 4.3 33.9 1.0
NE2 A:HIS178 4.3 37.4 1.0
CE1 A:HIS23 4.4 20.6 1.0
NE2 A:HIS23 4.4 28.4 1.0
OAP A:HL4404 4.4 45.5 0.8
CA A:HIS178 4.5 22.9 1.0
NZ A:KCX145 4.5 38.5 1.0
CE A:KCX145 4.8 31.9 1.0
CG A:ASN266 5.0 37.0 1.0

Zinc binding site 2 out of 2 in 4h9x

Go back to Zinc Binding Sites List in 4h9x
Zinc binding site 2 out of 2 in the Structure of Geobacillus Kaustophilus Lactonase, Mutant E101G/R230C/D266N with ZN2+ and Bound N-Butyryl-Dl-Homoserine Lactone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Geobacillus Kaustophilus Lactonase, Mutant E101G/R230C/D266N with ZN2+ and Bound N-Butyryl-Dl-Homoserine Lactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:36.1
occ:0.65
NE2 B:HIS206 2.3 51.7 1.0
OQ2 B:KCX145 2.3 47.5 1.0
O B:OH403 2.4 25.2 1.0
ND1 B:HIS178 2.4 25.4 1.0
CE1 B:HIS206 3.1 39.6 1.0
CD2 B:HIS206 3.2 49.6 1.0
CG B:HIS178 3.3 24.8 1.0
CX B:KCX145 3.3 49.9 1.0
CE1 B:HIS178 3.4 28.1 1.0
CB B:HIS178 3.4 23.7 1.0
FE B:FE401 3.5 23.7 1.0
OQ1 B:KCX145 3.7 31.5 1.0
ND2 B:ASN266 4.1 41.3 1.0
ND1 B:HIS206 4.2 40.9 1.0
CG B:HIS206 4.3 31.1 1.0
CE1 B:HIS23 4.3 19.5 1.0
NE2 B:HIS23 4.4 28.8 1.0
CD2 B:HIS178 4.4 33.6 1.0
NE2 B:HIS178 4.4 37.3 1.0
CA B:HIS178 4.5 26.8 1.0
NZ B:KCX145 4.5 42.1 1.0
OAP B:HL4404 4.6 44.2 0.8
CE B:KCX145 4.8 32.5 1.0
CG B:ASN266 5.0 34.9 1.0

Reference:

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
Page generated: Wed Dec 16 05:21:54 2020

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