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Zinc in PDB 8cc3: Vibrio Cholerae Gbpa (Lpmo Domain)

Protein crystallography data

The structure of Vibrio Cholerae Gbpa (Lpmo Domain), PDB code: 8cc3 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) 47.14 / 1.13
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.911, 89.103, 47.135, 90, 90, 90
R / Rfree (%) 17.4 / 20.1

Other elements in 8cc3:

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 8cc3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Vibrio Cholerae Gbpa (Lpmo Domain), PDB code: 8cc3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8cc3

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Zinc binding site 1 out of 7 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:10.8
occ:0.92
OD1 A:ASP70 1.9 9.7 1.0
OD2 A:ASP185 2.0 8.8 1.0
CG A:ASP185 2.7 8.6 1.0
CG A:ASP70 2.9 8.9 1.0
OD1 A:ASP185 2.9 8.6 1.0
OD2 A:ASP70 3.1 9.8 1.0
NZ A:LYS124 4.1 17.5 1.0
CB A:ASP185 4.2 8.7 1.0
O A:HOH436 4.2 16.9 1.0
CB A:ASP70 4.2 8.7 1.0
O A:HOH489 4.3 15.3 1.0
CD A:LYS124 4.3 11.5 1.0
OG A:SER192 4.4 7.3 0.9
N A:GLY71 4.5 9.6 1.0
CE A:LYS124 4.7 15.4 1.0
CA A:ASP70 4.9 8.8 1.0

Zinc binding site 2 out of 7 in 8cc3

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Zinc binding site 2 out of 7 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:20.7
occ:0.50
OD2 A:ASP147 2.0 16.8 1.0
O A:HOH415 2.1 22.4 1.0
CG A:ASP147 2.8 15.9 1.0
OD1 A:ASP147 3.0 17.0 1.0
ND2 A:ASN149 3.8 18.4 0.4
O A:ASN149 4.1 14.5 0.6
CB A:ASN149 4.1 16.3 0.4
CB A:ASP147 4.2 14.3 1.0
O A:ASN149 4.3 12.3 0.4
CB A:ASN149 4.4 15.6 0.6
CG A:ASN149 4.5 16.2 0.4
O A:HOH521 4.6 113.3 0.5
OD1 A:ASN149 4.7 14.1 0.6

Zinc binding site 3 out of 7 in 8cc3

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Zinc binding site 3 out of 7 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:8.3
occ:0.79
OE1 A:GLU67 2.0 11.1 1.0
OE1 B:GLU62 2.0 9.5 1.0
O A:ACT301 2.1 16.1 1.0
CD B:GLU62 2.8 9.1 1.0
CD A:GLU67 2.8 9.8 1.0
C A:ACT301 2.9 15.8 1.0
OXT A:ACT301 3.0 24.3 1.0
OE2 B:GLU62 3.0 9.8 1.0
OE2 A:GLU67 3.1 12.4 1.0
OG B:SER65 4.1 9.1 1.0
CG B:GLU62 4.2 8.7 1.0
CG A:GLU67 4.2 9.5 1.0
CH3 A:ACT301 4.3 17.1 1.0
CB A:ALA191 4.3 10.9 1.0
O A:HOH433 4.4 12.9 1.0
CB B:GLU62 4.5 8.3 1.0
CZ A:PHE193 4.5 8.3 1.0
OG1 A:THR189 4.7 11.6 1.0
CE1 A:PHE193 4.7 8.4 1.0
CU A:CU303 4.7 8.5 1.0
CE1 A:HIS24 4.8 8.5 1.0
NE2 A:HIS121 4.9 9.7 1.0
CB B:SER65 4.9 8.8 1.0

Zinc binding site 4 out of 7 in 8cc3

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Zinc binding site 4 out of 7 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:12.3
occ:0.33
O A:HOH505 1.8 52.6 1.0
NE2 A:GLN139 2.1 17.9 0.4
OE1 A:GLN139 2.1 12.6 0.6
O A:HOH486 2.2 20.1 1.0
O A:HOH430 2.3 22.6 1.0
OE1 A:GLN139 2.4 16.9 0.4
CD A:GLN139 2.6 16.6 0.4
CD A:GLN139 3.2 12.6 0.6
NE2 A:GLN139 3.6 13.0 0.6
CG A:GLN139 4.0 15.9 0.4
O A:ASN138 4.1 14.6 1.0
CG A:GLN139 4.5 12.1 0.6
O A:HOH471 4.6 23.4 1.0
CB A:GLN139 4.7 13.1 0.6
CA A:GLN139 4.8 14.9 0.4
CA A:GLN139 4.8 12.7 0.6
CB A:GLN139 4.8 15.4 0.4

Zinc binding site 5 out of 7 in 8cc3

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Zinc binding site 5 out of 7 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
B:Zn302

b:8.5
occ:0.84
OE2 B:GLU67 1.9 9.2 0.6
OE2 B:GLU67 1.9 8.8 0.4
OXT A:ACT302 2.0 14.8 1.0
OE1 A:GLU62 2.0 8.8 1.0
CD A:GLU62 2.8 9.6 1.0
CD B:GLU67 2.8 9.4 0.4
CD B:GLU67 2.8 10.0 0.6
OE2 A:GLU62 2.9 9.3 1.0
C A:ACT302 2.9 16.2 1.0
OE1 B:GLU67 3.1 10.9 0.6
OE1 B:GLU67 3.2 11.4 0.4
CH3 A:ACT302 3.2 18.9 1.0
O A:ACT302 4.1 22.0 1.0
OG A:SER65 4.1 7.9 1.0
CG B:GLU67 4.2 8.8 0.4
CG A:GLU62 4.2 9.4 1.0
CG B:GLU67 4.2 9.0 0.6
CB B:ALA191 4.3 9.7 1.0
CZ B:PHE193 4.4 8.6 1.0
O B:HOH406 4.4 14.5 1.0
CE1 B:PHE193 4.5 8.9 1.0
CD1 A:LEU89 4.6 9.8 0.4
CB A:GLU62 4.6 9.0 1.0
CE1 B:HIS24 4.7 9.5 1.0
OG1 B:THR189 4.7 9.3 1.0
CU B:CU301 4.7 9.0 0.9
CG2 B:THR189 4.8 10.6 1.0
NE2 B:HIS121 4.8 12.2 1.0
CB A:SER65 4.9 8.2 1.0

Zinc binding site 6 out of 7 in 8cc3

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Zinc binding site 6 out of 7 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:Zn303

b:12.5
occ:1.00
OD2 B:ASP70 1.8 14.7 1.0
O B:HOH409 2.0 9.7 1.0
OD1 B:ASP185 2.0 11.1 1.0
CG B:ASP70 2.6 11.5 1.0
OD1 B:ASP70 2.8 11.4 1.0
CG B:ASP185 2.9 9.0 1.0
OD2 B:ASP185 3.2 13.7 1.0
O B:HOH408 3.4 33.5 1.0
O B:VAL186 3.5 10.1 1.0
O B:ALA191 3.8 8.0 1.0
CB B:ASP70 4.1 13.0 1.0
O B:HOH490 4.1 15.0 1.0
O B:THR189 4.1 10.2 1.0
CB B:ASP185 4.2 8.1 1.0
N B:VAL186 4.3 8.1 1.0
OG B:SER192 4.3 8.2 1.0
CA B:ALA190 4.4 9.2 1.0
C B:VAL186 4.4 9.0 1.0
N B:ALA191 4.4 8.7 1.0
C B:ALA190 4.5 9.0 1.0
O B:HOH468 4.5 15.0 1.0
C B:ASP185 4.5 7.6 1.0
CA B:ASP185 4.6 7.6 1.0
C B:ALA191 4.6 8.7 1.0
C B:THR189 4.8 9.4 1.0
O B:ALA190 4.9 9.9 1.0
CD B:LYS124 5.0 18.6 1.0
CA B:VAL186 5.0 9.8 1.0
N B:ALA190 5.0 9.0 1.0
O B:HOH446 5.0 23.2 1.0

Zinc binding site 7 out of 7 in 8cc3

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Zinc binding site 7 out of 7 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:Zn304

b:17.3
occ:0.39
OD2 B:ASP202 2.4 38.7 1.0
OE1 B:GLU175 2.5 28.4 1.0
OE2 B:GLU175 2.6 34.3 1.0
CD B:GLU175 2.9 27.0 1.0
CG B:ASP202 3.2 35.6 1.0
OD1 B:ASP202 3.7 34.7 1.0
CB B:ASP202 4.2 33.0 1.0
CG B:GLU175 4.4 23.7 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: Thu Dec 28 12:54:09 2023

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