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

Protein crystallography data

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

Other elements in 8cc5:

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

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

Zinc Binding Sites:

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 8cc5

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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 8cc5

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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 8cc5

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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 8cc5

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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 8cc5

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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 8cc5

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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 8cc5

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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 8cc5

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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

Reference:

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
Page generated: Wed Oct 30 18:40:28 2024

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