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Zinc in PDB 4h9y: Structure of Geobacillus Kaustophilus Lactonase, Mutant E101N with ZN2+

Protein crystallography data

The structure of Structure of Geobacillus Kaustophilus Lactonase, Mutant E101N with ZN2+, PDB code: 4h9y 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) 19.76 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.473, 128.507, 51.497, 90.00, 95.80, 90.00
R / Rfree (%) 19 / 22.7

Other elements in 4h9y:

The structure of Structure of Geobacillus Kaustophilus Lactonase, Mutant E101N with ZN2+ 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 E101N with ZN2+ (pdb code 4h9y). 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 E101N with ZN2+, PDB code: 4h9y:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4h9y

Go back to Zinc Binding Sites List in 4h9y
Zinc binding site 1 out of 2 in the Structure of Geobacillus Kaustophilus Lactonase, Mutant E101N with ZN2+


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 E101N with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:35.3
occ:0.92
NE2 A:HIS206 2.3 30.1 1.0
ND1 A:HIS178 2.3 18.1 1.0
OQ2 A:KCX145 2.3 31.9 1.0
O A:OH403 2.6 36.1 1.0
CX A:KCX145 3.1 42.1 1.0
CG A:HIS178 3.1 25.6 1.0
CD2 A:HIS206 3.2 24.5 1.0
CE1 A:HIS206 3.2 37.0 1.0
CB A:HIS178 3.3 26.3 1.0
OQ1 A:KCX145 3.3 25.4 1.0
CE1 A:HIS178 3.3 27.5 1.0
FE A:FE401 3.6 21.5 1.0
NE2 A:HIS23 4.1 20.8 1.0
CE1 A:HIS23 4.1 19.1 1.0
OD2 A:ASP266 4.1 24.1 1.0
CA A:HIS178 4.2 31.2 1.0
NH2 A:ARG230 4.2 64.8 1.0
ND1 A:HIS206 4.3 27.1 1.0
NZ A:KCX145 4.3 29.1 1.0
CG A:HIS206 4.3 34.6 1.0
CD2 A:HIS178 4.3 19.9 1.0
NE2 A:HIS178 4.4 22.1 1.0
CE1 A:TYR99 4.7 47.5 1.0
CE A:KCX145 4.7 28.2 1.0
CZ A:ARG230 4.9 60.6 1.0
CG A:ASP266 4.9 28.9 1.0

Zinc binding site 2 out of 2 in 4h9y

Go back to Zinc Binding Sites List in 4h9y
Zinc binding site 2 out of 2 in the Structure of Geobacillus Kaustophilus Lactonase, Mutant E101N with ZN2+


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 E101N with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:37.5
occ:0.95
ND1 B:HIS178 2.3 18.3 1.0
NE2 B:HIS206 2.3 30.3 1.0
OQ2 B:KCX145 2.3 32.3 1.0
O B:OH403 2.6 37.8 1.0
CG B:HIS178 3.1 25.1 1.0
CX B:KCX145 3.2 45.0 1.0
CD2 B:HIS206 3.2 23.6 1.0
CE1 B:HIS206 3.2 35.8 1.0
CE1 B:HIS178 3.3 28.9 1.0
CB B:HIS178 3.3 26.0 1.0
OQ1 B:KCX145 3.4 25.7 1.0
FE B:FE401 3.6 20.9 1.0
NE2 B:HIS23 4.1 21.4 1.0
OD2 B:ASP266 4.1 23.3 1.0
CE1 B:HIS23 4.1 20.2 1.0
CA B:HIS178 4.2 30.6 1.0
NH2 B:ARG230 4.2 64.7 1.0
ND1 B:HIS206 4.3 26.9 1.0
CG B:HIS206 4.3 33.6 1.0
CD2 B:HIS178 4.3 19.5 1.0
NZ B:KCX145 4.3 35.0 1.0
NE2 B:HIS178 4.4 21.6 1.0
CE1 B:TYR99 4.7 46.5 1.0
CE B:KCX145 4.7 31.7 1.0
CZ B:ARG230 4.9 59.9 1.0
CG B:ASP266 4.9 27.1 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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