Zinc in PDB 7qe2: Crystal Structure of D-Glucuronic Acid Bound to SN243

The structure of Crystal Structure of D-Glucuronic Acid Bound to SN243, PDB code: 7qe2 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)	48.31 / 2.15
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.23, 82.18, 93.18, 66.74, 89.26, 89.34
R / Rfree (%)	19.6 / 24

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 33;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of D-Glucuronic Acid Bound to SN243 (pdb code 7qe2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 33 binding sites of Zinc where determined in the Crystal Structure of D-Glucuronic Acid Bound to SN243, PDB code: 7qe2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 33 in the Crystal Structure of D-Glucuronic Acid Bound to SN243


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 D-Glucuronic Acid Bound to SN243 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:74.5 occ:1.00 O A:ARG763 2.3 48.4 1.0 O A:THR266 2.4 44.1 1.0 O A:ASP760 2.5 45.0 1.0 OE1 A:GLN759 2.6 43.5 1.0 O A:HOH969 2.6 43.1 1.0 C A:ASP760 3.5 46.3 1.0 C A:ARG763 3.5 50.6 1.0 C A:THR266 3.6 40.3 1.0 CD A:GLN759 3.6 49.8 1.0 CB A:GLN759 3.9 48.4 1.0 O A:GLY765 4.0 49.5 1.0 N A:ASP760 4.0 50.4 1.0 N A:ARG763 4.0 44.8 1.0 CG A:GLN759 4.1 47.4 1.0 CA A:ARG763 4.2 51.4 1.0 CA A:THR266 4.3 43.2 1.0 CA A:SER761 4.3 49.9 1.0 CA A:ASP760 4.3 49.0 1.0 N A:SER761 4.3 47.9 1.0 O A:HOH966 4.3 44.5 1.0 C A:SER761 4.4 48.6 1.0 CB A:THR266 4.4 47.2 1.0 C A:GLN759 4.5 47.0 1.0 N A:PRO764 4.5 48.7 1.0 CB A:ARG763 4.5 51.6 1.0 N A:GLU267 4.6 43.2 1.0 O A:SER761 4.6 46.9 1.0 CA A:PRO764 4.6 47.8 1.0 CD A:PRO268 4.6 44.3 1.0 N A:ASP762 4.7 43.3 1.0 C A:PRO764 4.7 51.6 1.0 OE2 A:GLU768 4.7 63.0 1.0 CA A:GLU267 4.7 42.1 1.0 N A:GLY765 4.8 53.4 1.0 NE2 A:GLN759 4.8 47.6 1.0 CA A:GLN759 4.8 50.2 1.0 CB A:ASP760 4.9 48.0 1.0

Zinc binding site 2 out of 33 in the Crystal Structure of D-Glucuronic Acid Bound to SN243


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 D-Glucuronic Acid Bound to SN243 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn805 b:75.9 occ:1.00 OE1 A:GLN326 2.3 41.2 1.0 O A:GLY337 2.4 44.6 1.0 O A:ALA339 2.4 45.3 1.0 O A:HOH950 2.5 45.8 1.0 O A:LEU330 2.6 44.5 1.0 C A:GLY337 3.2 46.0 1.0 C A:ALA339 3.3 49.8 1.0 N A:ALA339 3.3 50.9 1.0 CD A:GLN326 3.5 43.3 1.0 C A:LEU330 3.7 45.1 1.0 CB A:GLN326 3.7 42.8 1.0 CA A:GLY337 3.8 46.5 1.0 C A:LYS338 3.8 50.0 1.0 N A:GLU327 3.8 45.2 1.0 CA A:ALA339 3.9 53.5 1.0 CD A:PRO332 4.0 44.2 1.0 CA A:GLN326 4.1 44.9 1.0 N A:LYS338 4.1 43.9 1.0 CG A:GLN326 4.1 41.2 1.0 O A:HOH1023 4.3 45.0 1.0 N A:PRO332 4.3 47.0 1.0 O A:LYS338 4.3 48.1 1.0 N A:GLN340 4.4 43.9 1.0 C A:GLN326 4.4 43.2 1.0 CA A:LYS338 4.4 45.1 1.0 C A:ASP331 4.4 41.0 1.0 O A:GLU327 4.5 48.0 1.0 N A:ASP331 4.5 42.8 1.0 CA A:ASP331 4.5 43.9 1.0 NE2 A:GLN326 4.5 41.4 1.0 CA A:LEU330 4.6 41.6 1.0 CB A:ALA339 4.6 49.8 1.0 CB A:LEU330 4.7 41.0 1.0 CG A:PRO332 4.7 42.7 1.0 N A:LEU330 4.8 45.7 1.0 CB A:PRO332 4.8 43.0 1.0 CA A:GLU327 4.8 47.6 1.0 CA A:PRO332 4.8 41.3 1.0 CA A:GLN340 4.9 42.1 1.0 CG A:GLN340 4.9 40.3 1.0 CB A:GLU327 4.9 46.2 1.0

Zinc binding site 3 out of 33 in the Crystal Structure of D-Glucuronic Acid Bound to SN243


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 D-Glucuronic Acid Bound to SN243 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn807 b:133.8 occ:1.00 O A:HOH1083 2.3 82.9 1.0 O A:HOH1110 2.5 95.6 1.0 OD2 A:ASP64 3.3 80.4 1.0 CG A:ASP64 4.0 75.7 1.0 OD1 A:ASP64 4.1 74.8 1.0

Zinc binding site 4 out of 33 in the Crystal Structure of D-Glucuronic Acid Bound to SN243


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 D-Glucuronic Acid Bound to SN243 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn808 b:64.3 occ:1.00 OD1 A:ASP602 2.2 58.0 1.0 CG A:ASP602 3.1 60.6 1.0 OD2 A:ASP602 3.5 63.4 1.0 O A:HOH1050 3.6 70.9 1.0 CB A:ASP602 4.4 56.5 1.0 CA A:ASP602 4.8 55.2 1.0

Zinc binding site 5 out of 33 in the Crystal Structure of D-Glucuronic Acid Bound to SN243


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 D-Glucuronic Acid Bound to SN243 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn809 b:118.5 occ:1.00 ND1 A:HIS639 2.2 75.8 1.0 CE1 A:HIS639 3.1 69.2 1.0 CG A:HIS639 3.2 76.5 1.0 CB A:HIS639 3.5 84.8 1.0 NE2 A:HIS639 4.2 74.6 1.0 CA A:HIS639 4.3 88.0 1.0 CD2 A:HIS639 4.3 71.0 1.0 O A:HIS639 4.4 97.8 1.0 C A:HIS639 4.8 93.7 1.0

Zinc binding site 6 out of 33 in the Crystal Structure of D-Glucuronic Acid Bound to SN243


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 D-Glucuronic Acid Bound to SN243 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn810 b:104.9 occ:1.00 CG A:HIS274 3.1 55.9 1.0 ND1 A:HIS274 3.2 59.0 1.0 CD2 A:HIS274 3.3 53.6 1.0 CE1 A:HIS274 3.4 58.1 1.0 NE2 A:HIS274 3.5 61.7 1.0 CB A:HIS274 3.7 45.9 1.0 CG A:ARG703 4.0 56.1 1.0 CD A:ARG703 4.1 61.1 1.0 OH A:TYR701 4.1 58.6 1.0 NH2 A:ARG703 4.4 61.7 1.0 CE A:LYS211 4.8 51.6 1.0 NZ A:LYS211 4.8 60.0 1.0 NE A:ARG703 4.9 62.3 1.0

Zinc binding site 7 out of 33 in the Crystal Structure of D-Glucuronic Acid Bound to SN243


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 D-Glucuronic Acid Bound to SN243 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn811 b:95.2 occ:1.00 NE2 A:HIS129 2.2 70.6 1.0 CE1 A:HIS129 3.0 65.8 1.0 CD2 A:HIS129 3.4 62.9 1.0 O A:ASN126 3.8 64.4 1.0 ND1 A:HIS129 4.2 64.6 1.0 O A:HOH1034 4.3 63.9 1.0 CG A:HIS129 4.4 61.8 1.0 O A:THR127 4.4 58.0 1.0 CG1 A:VAL92 4.7 53.6 1.0 C A:ASN126 4.9 61.8 1.0

Zinc binding site 8 out of 33 in the Crystal Structure of D-Glucuronic Acid Bound to SN243


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 D-Glucuronic Acid Bound to SN243 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn812 b:57.0 occ:1.00 NE2 A:HIS505 2.0 52.1 1.0 O A:HOH1017 2.1 49.6 1.0 O B:HOH1042 2.5 60.5 1.0 O A:HOH1064 2.6 61.9 1.0 O A:HOH1109 2.6 57.2 1.0 O A:HOH1099 2.6 55.1 1.0 CE1 A:HIS505 2.7 46.6 1.0 CD2 A:HIS505 3.1 46.8 1.0 OD2 A:ASP504 3.6 61.2 1.0 ND1 A:HIS505 3.9 45.7 1.0 CG A:HIS505 4.0 49.6 1.0 OD1 A:ASP504 4.1 59.8 1.0 CG A:ASP504 4.3 53.6 1.0 CB A:ALA502 4.4 49.6 1.0

Zinc binding site 9 out of 33 in the Crystal Structure of D-Glucuronic Acid Bound to SN243


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 D-Glucuronic Acid Bound to SN243 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn813 b:83.4 occ:1.00 OD1 A:ASN63 2.3 67.0 1.0 OD1 A:ASP61 2.4 67.5 1.0 OD1 A:ASP69 2.4 66.7 1.0 OE1 A:GLU72 2.5 64.5 1.0 OD1 A:ASN65 2.6 74.0 1.0 OE2 A:GLU72 2.6 60.8 1.0 O A:GLU67 2.7 76.6 1.0 CD A:GLU72 2.9 64.2 1.0 CG A:ASN63 3.0 60.5 1.0 ND2 A:ASN63 3.1 59.6 1.0 CG A:ASN65 3.1 68.9 1.0 ND2 A:ASN65 3.3 67.6 1.0 CG A:ASP69 3.5 60.4 1.0 CG A:ASP61 3.7 70.0 1.0 C A:GLU67 3.8 73.1 1.0 N A:ASP69 3.9 67.0 1.0 CB A:ASP69 4.1 65.8 1.0 N A:GLU67 4.3 76.9 1.0 N A:ASN63 4.3 61.7 1.0 CB A:ASN63 4.3 65.9 1.0 OD2 A:ASP69 4.3 64.3 1.0 CA A:ASP61 4.4 66.4 1.0 CB A:ASN65 4.4 67.2 1.0 CG A:GLU72 4.4 58.4 1.0 OD2 A:ASP61 4.5 69.6 1.0 N A:ASN65 4.5 70.4 1.0 CB A:ASP61 4.6 65.7 1.0 N A:LEU62 4.6 62.7 1.0 C A:ASP61 4.6 62.4 1.0 CA A:GLU67 4.6 78.6 1.0 CA A:ASP69 4.6 65.1 1.0 N A:LEU68 4.6 70.3 1.0 CA A:LEU68 4.7 66.3 1.0 C A:LEU68 4.7 69.7 1.0 CA A:ASN63 4.7 68.4 1.0 N A:ASP64 4.8 62.9 1.0 N A:GLY66 4.9 72.9 1.0 CA A:ASN65 5.0 69.0 1.0 C A:ASN63 5.0 65.8 1.0

Zinc binding site 10 out of 33 in the Crystal Structure of D-Glucuronic Acid Bound to SN243


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 D-Glucuronic Acid Bound to SN243 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn814 b:66.6 occ:1.00 OD2 A:ASP492 2.0 67.8 1.0 O A:HOH974 2.2 53.8 1.0 O B:HOH1010 2.5 65.3 1.0 O B:HOH919 2.5 62.6 1.0 CG A:ASP492 2.8 62.2 1.0 O A:HOH1108 2.8 65.7 1.0 OD1 A:ASP492 2.9 62.5 1.0 OE1 B:GLU551 3.7 51.7 1.0 OE2 B:GLU551 3.9 63.5 1.0 CB A:ASP492 4.2 54.6 1.0 CD B:GLU551 4.2 61.2 1.0 OD2 A:ASP494 4.2 68.0 1.0 O A:HOH1104 4.6 64.9 1.0 CB A:ASP494 4.8 55.3 1.0 CG A:ASP494 5.0 59.6 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.