Zinc in PDB 7y7u: Dimeric Structure of A Quorum-Quenching Metallo-Hydrolase, Lrsl

Protein crystallography data

The structure of Dimeric Structure of A Quorum-Quenching Metallo-Hydrolase, Lrsl, PDB code: 7y7u was solved by A.A.Momin, S.T.Arold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.18 / 1.89
Space group P 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 166.51, 166.51, 166.51, 90, 90, 90
R / Rfree (%) 19.1 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Dimeric Structure of A Quorum-Quenching Metallo-Hydrolase, Lrsl (pdb code 7y7u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Dimeric Structure of A Quorum-Quenching Metallo-Hydrolase, Lrsl, PDB code: 7y7u:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7y7u

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Zinc binding site 1 out of 4 in the Dimeric Structure of A Quorum-Quenching Metallo-Hydrolase, Lrsl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dimeric Structure of A Quorum-Quenching Metallo-Hydrolase, Lrsl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:35.9
occ:1.00
O A:HOH515 2.0 37.1 1.0
NE2 A:HIS236 2.1 29.1 1.0
ND1 A:HIS153 2.1 36.7 1.0
NE2 A:HIS151 2.2 32.6 1.0
OD2 A:ASP257 2.2 35.8 1.0
CD2 A:HIS236 3.0 32.1 1.0
CE1 A:HIS153 3.1 36.7 1.0
O A:HOH636 3.1 53.4 1.0
CE1 A:HIS236 3.1 32.7 1.0
CD2 A:HIS151 3.1 33.3 1.0
CE1 A:HIS151 3.2 30.4 1.0
CG A:HIS153 3.2 36.4 1.0
ZN A:ZN402 3.3 36.8 1.0
CG A:ASP257 3.4 36.6 1.0
CB A:HIS153 3.6 31.8 1.0
NE2 A:HIS156 4.0 37.4 1.0
CB A:ASP257 4.0 34.0 1.0
CG A:HIS236 4.2 30.2 1.0
CD2 A:HIS156 4.2 37.1 1.0
ND1 A:HIS236 4.2 33.3 1.0
NE2 A:HIS153 4.2 34.5 1.0
NE2 A:HIS260 4.3 37.3 1.0
CG A:HIS151 4.3 31.7 1.0
ND1 A:HIS151 4.3 32.3 1.0
CD2 A:HIS153 4.3 36.6 1.0
OD1 A:ASP257 4.4 33.3 1.0
OD1 A:ASP155 4.5 36.8 1.0
OD2 A:ASP155 4.7 33.5 1.0

Zinc binding site 2 out of 4 in 7y7u

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Zinc binding site 2 out of 4 in the Dimeric Structure of A Quorum-Quenching Metallo-Hydrolase, Lrsl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dimeric Structure of A Quorum-Quenching Metallo-Hydrolase, Lrsl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:36.8
occ:1.00
O A:HOH515 2.0 37.1 1.0
NE2 A:HIS304 2.1 29.3 1.0
OD2 A:ASP257 2.1 35.8 1.0
NE2 A:HIS156 2.1 37.4 1.0
OD2 A:ASP155 2.2 33.5 1.0
CG A:ASP257 2.8 36.6 1.0
OD1 A:ASP257 2.9 33.3 1.0
CE1 A:HIS304 3.1 32.3 1.0
CD2 A:HIS156 3.1 37.1 1.0
CD2 A:HIS304 3.1 30.6 1.0
CE1 A:HIS156 3.1 38.3 1.0
CG A:ASP155 3.2 33.8 1.0
ZN A:ZN401 3.3 35.9 1.0
OD1 A:ASP155 3.5 36.8 1.0
O A:HOH636 3.7 53.4 1.0
CE1 A:HIS151 4.1 30.4 1.0
NE2 A:HIS151 4.1 32.6 1.0
ND1 A:HIS304 4.2 33.0 1.0
ND1 A:HIS156 4.2 36.5 1.0
CG A:HIS156 4.2 34.9 1.0
CG A:HIS304 4.2 29.0 1.0
CB A:ASP257 4.3 34.0 1.0
NE2 A:HIS260 4.3 37.3 1.0
CB A:ASP155 4.5 32.3 1.0
CD2 A:HIS260 4.7 34.0 1.0
NE2 A:HIS236 4.8 29.1 1.0
O A:HOH651 4.9 59.8 1.0

Zinc binding site 3 out of 4 in 7y7u

Go back to Zinc Binding Sites List in 7y7u
Zinc binding site 3 out of 4 in the Dimeric Structure of A Quorum-Quenching Metallo-Hydrolase, Lrsl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dimeric Structure of A Quorum-Quenching Metallo-Hydrolase, Lrsl within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:42.7
occ:1.00
OD2 B:ASP257 2.0 37.7 1.0
OD2 B:ASP155 2.1 41.5 1.0
NE2 B:HIS156 2.1 39.8 1.0
NE2 B:HIS304 2.1 32.5 1.0
O B:HOH518 2.3 43.7 1.0
CG B:ASP257 2.8 38.5 1.0
OD1 B:ASP257 2.9 39.0 1.0
CE1 B:HIS304 3.1 31.9 1.0
CE1 B:HIS156 3.1 43.2 1.0
CD2 B:HIS156 3.1 39.1 1.0
CG B:ASP155 3.1 45.9 1.0
CD2 B:HIS304 3.2 30.8 1.0
ZN B:ZN402 3.2 43.3 1.0
OD1 B:ASP155 3.5 40.1 1.0
O B:HOH615 3.7 55.5 1.0
CE1 B:HIS151 4.2 45.4 1.0
NE2 B:HIS151 4.2 47.0 1.0
ND1 B:HIS304 4.2 33.3 1.0
ND1 B:HIS156 4.2 40.5 1.0
CB B:ASP257 4.3 38.5 1.0
CG B:HIS156 4.3 39.4 1.0
CG B:HIS304 4.3 31.0 1.0
CB B:ASP155 4.5 43.4 1.0
NE2 B:HIS260 4.5 40.9 1.0
CD2 B:HIS260 4.6 34.6 1.0
NE2 B:HIS236 4.7 39.5 1.0

Zinc binding site 4 out of 4 in 7y7u

Go back to Zinc Binding Sites List in 7y7u
Zinc binding site 4 out of 4 in the Dimeric Structure of A Quorum-Quenching Metallo-Hydrolase, Lrsl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dimeric Structure of A Quorum-Quenching Metallo-Hydrolase, Lrsl within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:43.3
occ:1.00
NE2 B:HIS236 2.0 39.5 1.0
O B:HOH518 2.0 43.7 1.0
NE2 B:HIS151 2.1 47.0 1.0
ND1 B:HIS153 2.2 39.5 1.0
OD2 B:ASP257 2.2 37.7 1.0
CD2 B:HIS236 3.0 45.5 1.0
CE1 B:HIS236 3.0 41.6 1.0
O B:HOH615 3.0 55.5 1.0
CD2 B:HIS151 3.1 43.3 1.0
CE1 B:HIS151 3.1 45.4 1.0
CE1 B:HIS153 3.2 39.1 1.0
CG B:HIS153 3.2 40.3 1.0
ZN B:ZN401 3.2 42.7 1.0
CG B:ASP257 3.3 38.5 1.0
CB B:HIS153 3.6 39.8 1.0
NE2 B:HIS156 4.0 39.8 1.0
CB B:ASP257 4.0 38.5 1.0
ND1 B:HIS236 4.1 37.1 1.0
CG B:HIS236 4.1 38.3 1.0
CD2 B:HIS156 4.2 39.1 1.0
ND1 B:HIS151 4.3 44.6 1.0
NE2 B:HIS260 4.3 40.9 1.0
CG B:HIS151 4.3 46.4 1.0
NE2 B:HIS153 4.3 40.9 1.0
OD1 B:ASP257 4.3 39.0 1.0
CD2 B:HIS153 4.4 43.2 1.0
OD1 B:ASP155 4.5 40.1 1.0
OD2 B:ASP155 4.7 41.5 1.0
CE1 B:HIS156 4.9 43.2 1.0

Reference:

Z.U.Rehman, A.A.Momin, A.Aldehaiman, T.Irum, R.Grunberg, S.T.Arold. The Exceptionally Efficient Quorum Quenching Enzyme Lrsl Suppresses Pseudomonas Aeruginosa Biofilm Production. Front Microbiol V. 13 77673 2022.
ISSN: ESSN 1664-302X
PubMed: 36071959
DOI: 10.3389/FMICB.2022.977673
Page generated: Sat Apr 8 06:12:08 2023

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