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Zinc in PDB 4ha0: Structure of Geobacillus Kaustophilus Lactonase, Mutant R230D with ZN2+

Protein crystallography data

The structure of Structure of Geobacillus Kaustophilus Lactonase, Mutant R230D with ZN2+, PDB code: 4ha0 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) 19.98 / 1.90
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.974, 76.218, 134.765, 90.00, 90.00, 90.00
R / Rfree (%) 25.9 / 30.3

Other elements in 4ha0:

The structure of Structure of Geobacillus Kaustophilus Lactonase, Mutant R230D 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 R230D with ZN2+ (pdb code 4ha0). 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 R230D with ZN2+, PDB code: 4ha0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4ha0

Go back to Zinc Binding Sites List in 4ha0
Zinc binding site 1 out of 2 in the Structure of Geobacillus Kaustophilus Lactonase, Mutant R230D 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 R230D with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:33.1
occ:0.80
OQ2 A:KCX145 2.2 44.1 1.0
NE2 A:HIS206 2.3 55.4 1.0
ND1 A:HIS178 2.4 44.2 1.0
O A:OH403 2.4 41.3 1.0
CD2 A:HIS206 3.1 46.3 1.0
CG A:HIS178 3.2 43.3 1.0
CB A:HIS178 3.3 42.8 1.0
CX A:KCX145 3.3 46.0 1.0
CE1 A:HIS206 3.4 47.0 1.0
FE A:FE401 3.4 29.7 0.9
CE1 A:HIS178 3.4 44.4 1.0
OH A:TYR99 3.5 59.1 1.0
OQ1 A:KCX145 3.6 34.9 1.0
CE1 A:TYR99 4.0 40.6 1.0
NE2 A:HIS23 4.2 46.6 1.0
OD2 A:ASP266 4.2 61.2 1.0
CZ A:TYR99 4.2 34.7 1.0
CE1 A:HIS23 4.2 44.1 1.0
CA A:HIS178 4.3 43.0 1.0
CG A:HIS206 4.3 47.1 1.0
O A:HOH631 4.3 49.0 1.0
NZ A:KCX145 4.4 33.7 1.0
ND1 A:HIS206 4.4 53.2 1.0
CD2 A:HIS178 4.4 49.2 1.0
NE2 A:HIS178 4.5 50.9 1.0
CE A:KCX145 4.6 33.4 1.0
O A:HOH627 4.8 61.4 1.0
OD1 A:ASP266 4.9 61.3 1.0
CG A:ASP266 4.9 61.5 1.0

Zinc binding site 2 out of 2 in 4ha0

Go back to Zinc Binding Sites List in 4ha0
Zinc binding site 2 out of 2 in the Structure of Geobacillus Kaustophilus Lactonase, Mutant R230D 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 R230D with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:30.1
occ:0.88
ND1 B:HIS178 2.0 26.3 1.0
OQ2 B:KCX145 2.2 30.4 1.0
NE2 B:HIS206 2.3 44.3 1.0
O B:OH403 2.4 34.1 1.0
CE1 B:HIS178 3.0 23.9 1.0
CG B:HIS178 3.0 26.2 1.0
CD2 B:HIS206 3.1 28.9 1.0
CX B:KCX145 3.1 39.3 1.0
CB B:HIS178 3.3 25.6 1.0
CE1 B:HIS206 3.3 20.2 1.0
OH B:TYR99 3.4 53.6 1.0
OQ1 B:KCX145 3.4 20.2 1.0
FE B:FE401 3.4 23.4 0.9
CE1 B:TYR99 4.0 36.5 1.0
NE2 B:HIS178 4.1 43.0 1.0
CD2 B:HIS178 4.1 40.4 1.0
NE2 B:HIS23 4.2 30.7 1.0
CZ B:TYR99 4.2 37.5 1.0
CE1 B:HIS23 4.2 27.2 1.0
OD2 B:ASP266 4.3 33.2 1.0
NZ B:KCX145 4.3 23.0 1.0
CG B:HIS206 4.3 41.2 1.0
CA B:HIS178 4.3 34.5 1.0
O B:HOH578 4.3 39.2 1.0
ND1 B:HIS206 4.4 30.3 1.0
CE B:KCX145 4.7 23.7 1.0
OD1 B:ASP266 4.8 13.6 1.0
CG B:ASP266 4.9 44.4 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 05:21:56 2020

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