Zinc in PDB 8cc5: Vibrio Cholerae Gbpa (Lpmo Domain)

The structure of Vibrio Cholerae Gbpa (Lpmo Domain), PDB code: 8cc5 was solved by M.Montserrat-Canals, H.V.Sorensen, G.Cordara, U.Krengel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.54 / 1.62
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	75.333, 89.374, 47.497, 90, 90, 90
R / Rfree (%)	17.6 / 21.3

The structure of Vibrio Cholerae Gbpa (Lpmo Domain) also contains other interesting chemical elements:

Copper	(Cu)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Vibrio Cholerae Gbpa (Lpmo Domain) (pdb code 8cc5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Vibrio Cholerae Gbpa (Lpmo Domain), PDB code: 8cc5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Vibrio Cholerae Gbpa (Lpmo Domain)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Vibrio Cholerae Gbpa (Lpmo Domain) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:24.5 occ:0.72 OE1 B:GLU62 1.9 24.9 1.0 OE2 A:GLU67 1.9 25.1 1.0 OXT A:ACT302 2.0 37.3 1.0 CD B:GLU62 2.7 31.6 1.0 CD A:GLU67 2.8 28.1 1.0 C A:ACT302 2.9 54.9 1.0 OE2 B:GLU62 3.0 26.2 1.0 OE1 A:GLU67 3.1 37.8 1.0 O A:ACT302 3.2 58.6 1.0 OG B:SER65 4.1 24.1 1.0 CG B:GLU62 4.1 24.5 1.0 CG A:GLU67 4.2 26.7 1.0 CH3 A:ACT302 4.3 44.1 1.0 CB A:ALA191 4.3 21.3 1.0 CZ A:PHE193 4.5 20.1 1.0 O A:HOH411 4.5 33.1 1.0 OG1 A:THR189 4.6 23.2 1.0 CB B:GLU62 4.6 19.7 1.0 CE1 A:HIS24 4.7 25.3 1.0 CE1 A:PHE193 4.7 22.7 1.0 CG2 A:THR189 4.7 27.4 1.0 CU A:CU303 4.9 25.8 0.9 CD1 B:LEU89 4.9 33.2 1.0 CB B:SER65 4.9 23.5 1.0

Zinc binding site 2 out of 8 in the Vibrio Cholerae Gbpa (Lpmo Domain)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Vibrio Cholerae Gbpa (Lpmo Domain) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:25.0 occ:0.68 OXT A:ACT301 1.8 35.0 1.0 OE2 B:GLU67 1.8 30.4 1.0 OE1 A:GLU62 2.0 27.6 1.0 C A:ACT301 2.7 45.0 1.0 CD B:GLU67 2.7 30.4 1.0 CD A:GLU62 2.9 39.5 1.0 O A:ACT301 2.9 45.2 1.0 OE1 B:GLU67 3.0 34.8 1.0 OE2 A:GLU62 3.1 28.2 1.0 OG A:SER65 4.1 22.8 1.0 CH3 A:ACT301 4.1 46.1 1.0 CG B:GLU67 4.1 27.5 1.0 CG A:GLU62 4.2 29.7 1.0 CB B:ALA191 4.3 24.0 1.0 O B:HOH411 4.3 36.4 1.0 OG1 B:THR189 4.6 26.3 1.0 CB A:GLU62 4.6 22.5 1.0 CZ B:PHE193 4.6 21.2 1.0 CE1 B:HIS24 4.7 24.6 1.0 CE1 B:PHE193 4.8 22.1 1.0 CB A:SER65 4.9 23.7 1.0 CU B:CU301 4.9 26.9 1.0

Zinc binding site 3 out of 8 in the Vibrio Cholerae Gbpa (Lpmo Domain)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Vibrio Cholerae Gbpa (Lpmo Domain) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:26.7 occ:1.00 O A:HOH405 1.9 26.6 1.0 OD2 A:ASP70 2.0 27.0 1.0 OD1 A:ASP185 2.0 22.4 1.0 CG A:ASP70 2.7 22.9 1.0 OD1 A:ASP70 2.8 24.1 1.0 CG A:ASP185 2.9 23.9 1.0 OD2 A:ASP185 3.2 30.1 1.0 O A:HOH403 3.4 41.6 1.0 O A:VAL186 3.5 24.8 1.0 O A:ALA191 4.0 20.0 1.0 O A:HOH438 4.0 29.0 1.0 CB A:ASP70 4.1 31.7 1.0 O A:THR189 4.1 26.9 1.0 CB A:ASP185 4.3 18.2 1.0 N A:VAL186 4.3 21.0 1.0 OG A:SER192 4.4 19.2 1.0 CA A:ALA190 4.5 23.1 1.0 N A:ALA191 4.5 22.1 1.0 C A:VAL186 4.5 22.1 1.0 C A:ALA190 4.5 21.0 1.0 C A:ASP185 4.6 22.7 1.0 CA A:ASP185 4.6 16.9 1.0 C A:ALA191 4.7 19.2 1.0 O A:HOH491 4.7 35.2 1.0 C A:THR189 4.8 25.4 1.0 O A:HOH440 4.9 35.9 1.0 O A:ALA190 5.0 23.4 1.0

Zinc binding site 4 out of 8 in the Vibrio Cholerae Gbpa (Lpmo Domain)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Vibrio Cholerae Gbpa (Lpmo Domain) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn307 b:33.1 occ:0.50 ZN A:ZN308 1.9 46.5 0.2 OD2 A:ASP202 2.1 88.8 1.0 OE1 A:GLU175 2.8 64.4 1.0 CG A:ASP202 3.1 82.2 1.0 OE2 A:GLU175 3.2 64.7 1.0 CD A:GLU175 3.4 62.7 1.0 OD1 A:ASP202 3.5 61.9 1.0 CB A:ASP202 4.4 67.3 1.0 CG A:GLU175 4.9 49.5 1.0

Zinc binding site 5 out of 8 in the Vibrio Cholerae Gbpa (Lpmo Domain)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Vibrio Cholerae Gbpa (Lpmo Domain) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn308 b:46.5 occ:0.25 OE2 A:GLU175 1.8 64.7 1.0 ZN A:ZN307 1.9 33.1 0.5 OD2 A:ASP202 2.5 88.8 1.0 CD A:GLU175 2.6 62.7 1.0 OE1 A:GLU175 2.9 64.4 1.0 CG A:ASP202 3.0 82.2 1.0 OD1 A:ASP202 3.3 61.9 1.0 CB A:ASP202 4.0 67.3 1.0 CG A:GLU175 4.1 49.5 1.0

Zinc binding site 6 out of 8 in the Vibrio Cholerae Gbpa (Lpmo Domain)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Vibrio Cholerae Gbpa (Lpmo Domain) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:24.6 occ:0.91 OD2 B:ASP185 2.0 19.6 1.0 OD1 B:ASP70 2.1 28.3 1.0 O B:HOH471 2.2 29.1 1.0 CG B:ASP185 2.7 18.5 1.0 CG B:ASP70 2.7 24.3 1.0 OD1 B:ASP185 2.7 19.2 1.0 OD2 B:ASP70 2.8 29.9 1.0 NA B:NA305 3.4 20.8 1.0 NZ B:LYS124 4.0 45.6 1.0 O B:HOH412 4.1 31.6 1.0 CB B:ASP70 4.1 21.2 1.0 CB B:ASP185 4.2 16.1 1.0 CD B:LYS124 4.2 22.7 1.0 O B:HOH441 4.4 28.5 1.0 OG B:SER192 4.5 17.0 0.8 CE B:LYS124 4.6 32.9 1.0 N B:GLY71 4.7 22.9 1.0 O B:VAL186 4.9 17.7 0.6 CA B:ASP70 4.9 19.6 1.0

Zinc binding site 7 out of 8 in the Vibrio Cholerae Gbpa (Lpmo Domain)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Vibrio Cholerae Gbpa (Lpmo Domain) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:31.6 occ:0.49 OD2 B:ASP147 2.0 29.5 1.0 O B:HOH449 2.2 34.0 1.0 CG B:ASP147 2.8 29.6 1.0 OD1 B:ASP147 3.0 25.0 1.0 CB B:ASP147 4.2 26.9 1.0 O B:ASN149 4.3 23.8 1.0 CB B:ASN149 4.5 24.4 1.0 ND2 B:ASN149 4.7 28.6 1.0

Zinc binding site 8 out of 8 in the Vibrio Cholerae Gbpa (Lpmo Domain)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Vibrio Cholerae Gbpa (Lpmo Domain) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:32.3 occ:0.28 NE2 B:GLN139 2.3 72.8 1.0 OE1 B:GLN139 2.4 51.1 1.0 CD B:GLN139 2.6 58.5 1.0 CG B:GLN139 4.0 53.6 1.0 O B:ASN138 4.0 28.9 1.0 CA B:GLN139 4.7 33.4 1.0 CB B:GLN139 4.8 33.5 1.0 CD B:PRO140 4.9 41.6 1.0 C B:ASN138 5.0 33.9 1.0

H.V.Sorensen, M.Montserrat-Canals, J.S.M.Loose, S.Z.Fisher, M.Moulin, M.P.Blakeley, G.Cordara, K.Bjerregaard-Andersen, U.Krengel. Perdeuterated Gbpa Enables Neutron Scattering Experiments of A Lytic Polysaccharide Monooxygenase. Acs Omega V. 8 29101 2023.
ISSN: ESSN 2470-1343
PubMed: 37599915
DOI: 10.1021/ACSOMEGA.3C02168