Zinc in PDB 7qee: SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide

The structure of SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide, PDB code: 7qee was solved by S.Neun, P.Brear, E.Campbell, K.Omari, O.Wagner, M.Hyvonen, F.Hollfelder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.82 / 2.37
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.499, 82.173, 93.041, 113.69, 90.65, 90.31
R / Rfree (%)	21.7 / 27.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Zinc atom in the SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide (pdb code 7qee). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 26 binding sites of Zinc where determined in the SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide, PDB code: 7qee:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 26 in the SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:68.4 occ:1.00 O A:THR266 2.3 34.6 1.0 O A:ARG763 2.3 31.8 1.0 OE1 A:GLN759 2.5 33.2 1.0 O A:ASP760 2.7 40.7 1.0 C A:ASP760 3.3 43.0 1.0 C A:ARG763 3.5 34.4 1.0 C A:THR266 3.5 31.9 1.0 CD A:GLN759 3.6 30.6 1.0 N A:ASP760 3.8 44.4 1.0 CB A:GLN759 3.9 43.4 1.0 N A:ARG763 4.0 28.1 1.0 O A:GLY765 4.0 38.8 1.0 CA A:ASP760 4.1 43.2 1.0 CG A:GLN759 4.1 36.6 1.0 N A:SER761 4.1 36.6 1.0 CA A:SER761 4.2 38.5 1.0 CA A:ARG763 4.2 41.0 1.0 C A:SER761 4.2 36.2 1.0 CA A:THR266 4.3 32.1 1.0 C A:GLN759 4.3 45.5 1.0 O A:SER761 4.4 40.1 1.0 CD A:PRO268 4.4 33.0 1.0 CB A:ARG763 4.5 41.5 1.0 N A:GLU267 4.5 35.0 1.0 N A:PRO764 4.6 35.9 1.0 OE2 A:GLU768 4.6 67.7 1.0 CB A:THR266 4.6 34.9 1.0 CA A:GLU267 4.7 37.3 1.0 NE2 A:GLN759 4.7 27.0 1.0 CA A:GLN759 4.7 46.8 1.0 CA A:PRO764 4.7 36.7 1.0 N A:ASP762 4.8 33.8 1.0 C A:PRO764 4.8 37.1 1.0 CB A:ASP760 4.8 49.5 1.0 N A:GLY765 5.0 33.7 1.0

Zinc binding site 2 out of 26 in the SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:97.7 occ:1.00 O A:GLY337 2.3 40.5 1.0 O A:LEU330 2.4 33.8 1.0 OE1 A:GLN326 2.5 27.6 1.0 O A:ALA339 2.7 34.6 1.0 C A:GLY337 2.9 41.4 1.0 CA A:GLY337 3.3 41.5 1.0 C A:LEU330 3.3 36.4 1.0 N A:ALA339 3.4 26.7 1.0 C A:ALA339 3.6 34.7 1.0 CD A:GLN326 3.7 33.3 1.0 O A:HOH913 3.7 40.1 1.0 N A:GLU327 3.9 37.2 1.0 N A:LYS338 3.9 41.8 1.0 CB A:GLN326 4.0 33.1 1.0 O A:GLU327 4.0 36.3 1.0 CA A:ALA339 4.0 37.1 1.0 C A:LYS338 4.0 39.0 1.0 CB A:LEU330 4.1 35.5 1.0 CA A:LEU330 4.2 35.0 1.0 N A:ASP331 4.2 38.5 1.0 CA A:GLN326 4.3 30.8 1.0 C A:GLN326 4.4 38.0 1.0 CG A:GLN326 4.4 27.4 1.0 N A:LEU330 4.4 39.6 1.0 C A:ASP331 4.5 36.3 1.0 CA A:LYS338 4.5 39.8 1.0 CA A:ASP331 4.5 33.5 1.0 CB A:ALA339 4.5 33.7 1.0 N A:PRO332 4.5 34.5 1.0 CD A:PRO332 4.6 35.5 1.0 CA A:GLU327 4.6 35.9 1.0 N A:GLY337 4.7 40.9 1.0 CB A:GLU327 4.7 45.9 1.0 O A:LYS338 4.7 37.2 1.0 NE2 A:GLN326 4.7 29.3 1.0 C A:GLU327 4.8 35.8 1.0 N A:GLN340 4.8 36.6 1.0 O A:ASP331 4.9 38.0 1.0 O A:PHE336 5.0 51.7 1.0

Zinc binding site 3 out of 26 in the SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:106.3 occ:1.00 OD1 A:ASP602 1.9 83.4 1.0 O A:HOH901 1.9 65.7 1.0 CG A:ASP602 3.0 81.7 1.0 OD2 A:ASP602 3.6 85.1 1.0 CB A:ASP602 4.0 72.1 1.0 CA A:ASP602 4.4 68.1 1.0

Zinc binding site 4 out of 26 in the SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:64.2 occ:1.00 O A:HOH914 2.2 34.3 1.0 O A:HOH903 2.3 42.3 1.0 O A:HOH909 2.4 47.0 1.0 O A:HOH940 2.4 28.1 1.0 NE2 A:HIS505 2.4 47.0 1.0 CE1 A:HIS505 3.0 47.6 1.0 OD2 A:ASP504 3.5 53.6 1.0 CD2 A:HIS505 3.5 46.6 1.0 OE1 A:GLU247 3.7 76.1 1.0 ND1 A:HIS505 4.1 43.4 1.0 CG A:ASP504 4.3 52.1 1.0 OD1 A:ASP504 4.3 54.6 1.0 CG A:HIS505 4.4 42.9 1.0 CD A:GLU247 4.9 77.6 1.0 CB A:ALA502 4.9 37.7 1.0

Zinc binding site 5 out of 26 in the SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn805 b:99.0 occ:1.00 O A:GLU67 2.1 78.8 1.0 OE1 A:GLU72 2.2 74.7 1.0 OD1 A:ASN63 2.5 78.1 1.0 OE2 A:GLU72 2.6 71.5 1.0 OD1 A:ASN65 2.7 79.8 1.0 CD A:GLU72 2.7 74.6 1.0 OD1 A:ASP61 2.7 72.0 1.0 OD1 A:ASP69 2.8 73.6 1.0 CG A:ASN63 3.1 79.5 1.0 ND2 A:ASN63 3.1 71.4 1.0 C A:GLU67 3.3 79.7 1.0 CG A:ASN65 3.5 77.6 1.0 N A:ASP69 3.5 70.9 1.0 CG A:ASP69 3.7 77.2 1.0 ND2 A:ASN65 3.8 74.8 1.0 CA A:LEU68 3.9 69.0 1.0 CG A:ASP61 3.9 79.8 1.0 N A:LEU68 4.0 75.8 1.0 C A:LEU68 4.1 70.7 1.0 CG A:GLU72 4.2 71.5 1.0 CA A:ASP61 4.2 74.5 1.0 CB A:ASP69 4.2 67.3 1.0 N A:GLU67 4.4 77.5 1.0 CA A:ASP69 4.5 70.0 1.0 CB A:ASP61 4.5 80.0 1.0 CA A:GLU67 4.5 80.9 1.0 CB A:ASN63 4.5 70.2 1.0 C A:ASP61 4.6 76.9 1.0 N A:ASN63 4.6 78.1 1.0 OD2 A:ASP69 4.6 81.6 1.0 N A:LEU62 4.6 70.5 1.0 N A:ASN65 4.7 71.4 1.0 CB A:ASN65 4.7 76.3 1.0 CB A:GLU72 4.8 65.3 1.0 N A:GLY66 4.9 71.7 1.0 OD2 A:ASP61 4.9 79.5 1.0 CD1 A:ILE52 4.9 74.3 1.0

Zinc binding site 6 out of 26 in the SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn806 b:139.3 occ:1.00 OE1 A:GLU556 2.3 86.1 1.0 CD A:GLU556 3.6 81.2 1.0 O A:HOH925 3.8 59.2 1.0 OE2 A:GLU556 4.4 71.4 1.0 O B:HOH928 4.4 57.0 1.0 CG A:GLU556 4.6 64.5 1.0 OE2 B:GLU45 4.7 67.0 1.0 OE2 B:GLU43 4.8 94.3 1.0 O B:HOH941 5.0 69.7 1.0 CB A:GLU556 5.0 62.3 1.0

Zinc binding site 7 out of 26 in the SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn807 b:68.6 occ:1.00 NE2 A:HIS603 1.9 59.1 1.0 OE2 A:GLU672 2.3 75.8 1.0 CE1 A:HIS603 2.8 56.9 1.0 OE1 A:GLU672 2.9 71.5 1.0 CD A:GLU672 2.9 68.2 1.0 CD2 A:HIS603 3.0 55.9 1.0 ND1 A:HIS603 4.0 52.8 1.0 CG A:HIS603 4.1 55.6 1.0 NE1 A:TRP658 4.1 50.2 1.0 CZ2 A:TRP658 4.4 50.0 1.0 CG A:GLU672 4.4 59.8 1.0 CE2 A:TRP658 4.5 48.0 1.0 O A:SER596 4.8 65.0 1.0 CD2 A:LEU597 4.9 60.6 1.0

Zinc binding site 8 out of 26 in the SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn808 b:115.9 occ:1.00 O A:HOH908 2.2 61.2 1.0 OE1 A:GLU770 3.1 103.0 1.0 OE1 A:GLU754 3.2 87.3 1.0 OE2 A:GLU754 3.6 88.7 1.0 CD A:GLU754 3.6 95.7 1.0 CD A:GLU770 3.7 91.0 1.0 OE2 A:GLU770 3.8 86.8 1.0 OD1 A:ASP771 3.8 65.0 1.0 OD2 A:ASP771 4.5 54.9 1.0 CG A:ASP771 4.6 51.8 1.0 CG A:GLU770 4.9 68.5 1.0

Zinc binding site 9 out of 26 in the SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn809 b:107.0 occ:1.00 OD2 A:ASP55 2.0 81.3 1.0 CG A:ASP55 2.9 83.3 1.0 OD1 A:ASP55 3.1 84.7 1.0 CB A:ASP55 4.3 77.5 1.0 NH2 A:ARG75 4.5 65.9 1.0 NH1 A:ARG75 4.5 76.7 1.0 CZ A:ARG75 5.0 80.5 1.0

Zinc binding site 10 out of 26 in the SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of SN243 Mutant D415N Bound to Para-Nitrophenyl-Beta-D-Glucuronide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn810 b:119.1 occ:1.00 O A:HOH930 2.5 54.3 1.0 OE1 A:GLU289 2.7 68.8 1.0 OE2 A:GLU289 2.9 70.4 1.0 OE2 A:GLU286 3.2 77.4 1.0 CD A:GLU289 3.2 68.3 1.0 CD A:GLU286 4.3 69.4 1.0 CG A:GLU289 4.7 56.4 1.0 O A:HOH927 4.7 53.5 1.0 OE1 A:GLU286 4.9 67.0 1.0

S.Neun, P.Brear, E.Campbell, T.Tryfona, K.El Omari, A.Wagner, P.Dupree, M.Hyvonen, F.Hollfelder. Functional Metagenomic Screening Identifies An Unexpected Beta-Glucuronidase. Nat.Chem.Biol. V. 18 1096 2022.
ISSN: ESSN 1552-4469
PubMed: 35799064
DOI: 10.1038/S41589-022-01071-X