Zinc in PDB 7qef: Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A)

The structure of Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A), PDB code: 7qef 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)	48.08 / 2.41
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.376, 81.675, 93.548, 66.57, 89.39, 89.17
R / Rfree (%)	21.5 / 28.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 38;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A) (pdb code 7qef). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 38 binding sites of Zinc where determined in the Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A), PDB code: 7qef:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 38 in the Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:69.0 occ:1.00 OE1 A:GLN759 2.3 34.5 1.0 O A:THR266 2.4 38.6 1.0 O A:ARG763 2.4 41.8 1.0 O A:ASP760 2.5 37.6 1.0 O A:HOH964 2.6 38.3 1.0 CD A:GLN759 3.4 34.9 1.0 C A:ASP760 3.4 39.8 1.0 C A:ARG763 3.6 43.7 1.0 C A:THR266 3.6 31.4 1.0 CB A:GLN759 3.7 32.7 1.0 O A:GLY765 3.8 44.2 1.0 N A:ASP760 3.9 35.1 1.0 CG A:GLN759 4.0 35.7 1.0 N A:ARG763 4.1 39.4 1.0 C A:GLN759 4.2 33.7 1.0 OE2 A:GLU768 4.2 57.2 1.0 CA A:ASP760 4.3 30.4 1.0 N A:SER761 4.3 37.3 1.0 CA A:ARG763 4.3 40.8 1.0 CA A:SER761 4.3 33.8 1.0 C A:SER761 4.4 35.6 1.0 CA A:THR266 4.4 29.5 1.0 NE2 A:GLN759 4.5 26.6 1.0 CD A:PRO268 4.5 31.9 1.0 O A:SER761 4.5 35.7 1.0 CB A:ARG763 4.5 40.0 1.0 CA A:GLN759 4.5 40.6 1.0 N A:GLU267 4.6 29.8 1.0 CB A:THR266 4.6 35.5 1.0 N A:PRO764 4.6 41.5 1.0 O A:GLN759 4.7 28.8 1.0 CA A:GLU267 4.7 29.7 1.0 N A:GLY765 4.7 37.8 1.0 CA A:PRO764 4.8 42.2 1.0 N A:ASP762 4.8 35.1 1.0 C A:PRO764 4.8 36.8 1.0 CB A:ASP760 5.0 37.5 1.0 C A:GLY765 5.0 36.4 1.0

Zinc binding site 2 out of 38 in the Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:124.5 occ:1.00 OD2 A:ASP470 3.0 69.9 1.0 OE2 A:GLU466 3.2 66.0 1.0 NZ A:LYS94 3.8 49.6 1.0 CG A:ASP470 3.9 60.4 1.0 OD1 A:ASP470 3.9 58.6 1.0 CD A:GLU466 4.1 73.2 1.0 OE1 A:GLU466 4.4 86.7 1.0

Zinc binding site 3 out of 38 in the Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn805 b:104.0 occ:1.00 OD1 A:ASP451 2.6 58.9 1.0 N A:SER453 2.8 44.4 1.0 CB A:SER453 3.1 39.1 1.0 OG A:SER453 3.3 47.9 1.0 N A:VAL452 3.3 42.0 1.0 OE1 A:GLN128 3.3 50.8 1.0 CA A:SER453 3.6 43.7 1.0 C A:ASP451 3.6 43.2 1.0 CA A:ASP451 3.8 48.7 1.0 CG A:ASP451 3.8 66.8 1.0 CG1 A:VAL452 3.8 49.5 1.0 C A:VAL452 3.9 50.1 1.0 NE2 A:GLN128 3.9 47.7 1.0 CA A:VAL452 4.0 43.6 1.0 CD A:GLN128 4.0 52.1 1.0 O A:ASP451 4.3 43.7 1.0 CB A:ASP451 4.4 57.1 1.0 CB A:VAL452 4.5 45.1 1.0 C A:SER453 4.7 49.8 1.0 OD2 A:ASP451 4.8 73.0 1.0 N A:VAL454 4.8 33.8 1.0 O A:SER450 4.9 49.4 1.0

Zinc binding site 4 out of 38 in the Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn806 b:77.5 occ:1.00 O A:GLY337 2.4 40.5 1.0 O A:LEU330 2.4 34.1 1.0 O A:ALA339 2.4 39.1 1.0 OE1 A:GLN326 2.7 30.5 1.0 C A:GLY337 3.1 34.4 1.0 C A:ALA339 3.5 40.9 1.0 C A:LEU330 3.5 32.4 1.0 N A:ALA339 3.5 30.1 1.0 CA A:GLY337 3.5 33.7 1.0 N A:GLU327 3.7 33.9 1.0 CB A:GLN326 3.7 33.4 1.0 CD A:GLN326 3.8 38.3 1.0 CA A:ALA339 4.0 41.5 1.0 C A:LYS338 4.0 36.1 1.0 CA A:GLN326 4.0 30.9 1.0 CD A:PRO332 4.1 31.0 1.0 N A:LYS338 4.1 35.3 1.0 O A:HOH945 4.1 31.6 1.0 C A:GLN326 4.3 36.2 1.0 CG A:GLN326 4.3 33.3 1.0 CA A:LEU330 4.3 32.7 1.0 O A:GLU327 4.4 31.6 1.0 N A:PRO332 4.4 36.2 1.0 N A:ASP331 4.4 37.1 1.0 CB A:LEU330 4.4 34.1 1.0 N A:LEU330 4.5 39.6 1.0 O A:LYS338 4.5 39.0 1.0 C A:ASP331 4.5 34.5 1.0 CA A:ASP331 4.5 33.1 1.0 N A:GLN340 4.6 34.8 1.0 CA A:LYS338 4.6 32.8 1.0 CB A:ALA339 4.6 31.9 1.0 CA A:GLU327 4.7 39.0 1.0 CB A:GLU327 4.8 39.3 1.0 NE2 A:GLN326 4.9 34.6 1.0 CG A:PRO332 4.9 40.4 1.0 CB A:PRO332 4.9 28.4 1.0 N A:GLY337 5.0 36.9 1.0 CA A:PRO332 5.0 32.3 1.0 C A:GLU327 5.0 36.8 1.0

Zinc binding site 5 out of 38 in the Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn807 b:120.5 occ:1.00 O A:PRO617 3.6 49.0 1.0 OD2 A:ASP614 4.0 78.2 1.0 O A:GLU616 4.1 57.9 1.0 C A:PRO617 4.3 47.6 1.0 OE2 A:GLU637 4.3 66.5 1.0 CA A:LEU618 4.4 39.7 1.0 OE1 A:GLU637 4.4 70.2 1.0 CD A:PRO619 4.5 43.0 1.0 OD1 A:ASP614 4.6 67.5 1.0 CD2 A:LEU618 4.6 48.9 1.0 N A:LEU618 4.6 46.7 1.0 C A:GLU616 4.7 62.1 1.0 CB A:GLU616 4.7 70.0 1.0 CG A:ASP614 4.7 67.6 1.0 CD A:GLU637 4.8 63.5 1.0 N A:PRO619 5.0 39.0 1.0

Zinc binding site 6 out of 38 in the Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn808 b:116.9 occ:1.00 OD1 A:ASP64 3.4 49.5 1.0 CG A:ASP64 4.2 62.9 1.0 OD2 A:ASP64 4.4 67.6 1.0

Zinc binding site 7 out of 38 in the Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn809 b:77.6 occ:1.00 OD1 A:ASP602 2.9 52.8 1.0 OD2 A:ASP602 2.9 50.5 1.0 CG A:ASP602 3.3 41.2 1.0 CB A:ASP602 4.8 34.0 1.0

Zinc binding site 8 out of 38 in the Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn810 b:112.9 occ:1.00 ND1 A:HIS639 2.3 73.4 1.0 CE1 A:HIS639 3.1 66.6 1.0 CG A:HIS639 3.4 67.1 1.0 CB A:HIS639 3.8 60.2 1.0 NE2 A:HIS639 4.3 66.4 1.0 CD2 A:HIS639 4.5 59.9 1.0 CA A:HIS639 4.7 71.3 1.0 O A:HIS639 4.9 85.1 1.0

Zinc binding site 9 out of 38 in the Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn811 b:123.3 occ:1.00 CD A:ARG703 2.9 29.1 1.0 O A:HOH968 3.3 37.4 1.0 CG A:ARG703 3.5 34.2 1.0 CD2 A:HIS274 3.5 34.1 1.0 CG A:HIS274 3.5 41.0 1.0 CB A:HIS274 3.8 33.0 1.0 O A:HOH955 4.0 28.7 1.0 NE2 A:HIS274 4.1 35.4 1.0 ND1 A:HIS274 4.2 40.9 1.0 NE A:ARG703 4.3 62.8 1.0 NH2 A:ARG703 4.3 60.6 1.0 O A:TYR271 4.4 32.9 1.0 CE1 A:HIS274 4.5 30.8 1.0 CZ A:ARG703 4.8 59.0 1.0 CB A:ARG703 5.0 35.2 1.0

Zinc binding site 10 out of 38 in the Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Para-Nitrophenyl-Beta-D-Glucuronide Bound to A Mutant of SN243 (D415A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn812 b:100.3 occ:1.00 NE2 A:HIS129 2.5 60.1 1.0 CE1 A:HIS129 3.4 61.7 1.0 CD2 A:HIS129 3.5 59.0 1.0 O A:ASN126 3.6 69.0 1.0 ND1 A:HIS129 4.6 59.4 1.0 CG A:HIS129 4.7 64.2 1.0 C A:ASN126 4.8 57.3 1.0 O A:THR127 4.8 63.6 1.0 CG1 A:VAL92 4.9 40.8 1.0

S.Neun, P.Brear, E.Campbell, K.Omari, O.Wagner, M.Hyvonen, F.Hollfelder. Functional Metagenomic Screening in Microfluidic Droplets Identifies A Beta-Glucuronidase in An Unprecedented Sequence Neighbourhood To Be Published.