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Zinc in PDB 6ive: Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase

Protein crystallography data

The structure of Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase, PDB code: 6ive was solved by W.M.Wang, H.F.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.81 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.687, 69.232, 83.334, 75.22, 74.39, 89.20
R / Rfree (%) 18.1 / 22.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase (pdb code 6ive). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase, PDB code: 6ive:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6ive

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Zinc binding site 1 out of 6 in the Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:23.5
occ:1.00
NE2 A:HIS87 2.0 24.8 1.0
NE2 B:HIS82 2.0 22.2 1.0
O4 A:PO4202 2.0 23.2 1.0
ND1 A:HIS65 2.1 23.1 1.0
CD2 A:HIS87 2.8 21.0 1.0
CD2 B:HIS82 3.0 17.9 1.0
CE1 B:HIS82 3.0 21.2 1.0
CE1 A:HIS65 3.0 25.8 1.0
P A:PO4202 3.1 27.3 1.0
CE1 A:HIS87 3.1 27.6 1.0
CG A:HIS65 3.1 23.4 1.0
O1 A:PO4202 3.1 28.3 1.0
CB A:HIS65 3.5 19.4 1.0
OH B:TYR153 3.7 22.7 1.0
O2 A:PO4202 3.9 27.0 1.0
CG A:HIS87 4.0 21.4 1.0
O A:HOH311 4.1 26.4 1.0
ND1 A:HIS87 4.1 27.7 1.0
ND1 B:HIS82 4.1 21.5 1.0
CG B:HIS82 4.1 23.1 1.0
NE2 A:HIS65 4.2 24.0 1.0
OE1 B:GLN59 4.2 23.0 1.0
CD2 A:HIS65 4.2 20.9 1.0
O3 A:PO4202 4.3 28.3 1.0
OD1 A:ASP67 4.5 29.1 1.0
O A:HOH310 4.8 21.4 1.0
CA A:HIS65 4.8 22.6 1.0
N A:ALA66 4.8 20.1 1.0
CD B:GLN59 4.9 24.1 1.0
O A:ALA66 5.0 25.6 1.0
CZ B:TYR153 5.0 22.6 1.0
C A:HIS65 5.0 24.4 1.0

Zinc binding site 2 out of 6 in 6ive

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Zinc binding site 2 out of 6 in the Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:27.9
occ:1.00
NE2 B:HIS87 1.9 22.2 1.0
NE2 C:HIS82 2.1 25.4 1.0
ND1 B:HIS65 2.2 26.6 1.0
O4 C:PO4202 2.5 31.1 1.0
O2 C:PO4202 2.5 32.3 1.0
CD2 C:HIS82 2.9 22.4 1.0
CE1 B:HIS87 2.9 27.9 1.0
CD2 B:HIS87 2.9 22.1 1.0
P C:PO4202 3.0 39.8 1.0
CE1 B:HIS65 3.1 26.7 1.0
CG B:HIS65 3.2 28.1 1.0
CE1 C:HIS82 3.3 23.2 1.0
CB B:HIS65 3.5 24.1 1.0
O C:HOH312 3.9 23.6 1.0
ND1 B:HIS87 4.0 28.2 1.0
O3 C:PO4202 4.0 42.3 1.0
CG B:HIS87 4.1 23.2 1.0
OH C:TYR153 4.1 31.5 1.0
CG C:HIS82 4.1 24.9 1.0
OE1 C:GLN59 4.1 31.0 1.0
O1 C:PO4202 4.2 38.0 1.0
NE2 B:HIS65 4.3 29.8 1.0
ND1 C:HIS82 4.3 23.2 1.0
CD2 B:HIS65 4.3 25.8 1.0
OD1 B:ASP67 4.4 32.3 1.0
CA B:HIS65 4.8 28.1 1.0
CE C:MET99 4.9 20.8 1.0
N B:ALA66 4.9 27.7 1.0

Zinc binding site 3 out of 6 in 6ive

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Zinc binding site 3 out of 6 in the Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:23.6
occ:1.00
NE2 C:HIS87 1.9 27.3 1.0
O4 A:PO4203 2.1 24.3 1.0
NE2 A:HIS82 2.1 23.3 1.0
ND1 C:HIS65 2.1 22.4 1.0
O3 A:PO4203 2.9 27.9 1.0
CD2 C:HIS87 2.9 21.6 1.0
CE1 A:HIS82 2.9 22.0 1.0
P A:PO4203 3.0 27.5 1.0
CE1 C:HIS87 3.0 27.3 1.0
CE1 C:HIS65 3.0 24.7 1.0
CG C:HIS65 3.2 22.1 1.0
CD2 A:HIS82 3.2 21.1 1.0
CB C:HIS65 3.6 20.9 1.0
OH A:TYR153 3.8 27.0 1.0
O1 A:PO4203 3.9 31.3 1.0
CG C:HIS87 4.0 22.2 1.0
OD1 C:ASP67 4.0 28.6 1.0
ND1 C:HIS87 4.0 24.9 1.0
O A:HOH323 4.1 25.2 1.0
ND1 A:HIS82 4.1 22.9 1.0
O2 A:PO4203 4.1 22.6 1.0
NE2 C:HIS65 4.1 19.6 1.0
OE1 A:GLN59 4.2 24.6 1.0
CG A:HIS82 4.3 24.4 1.0
CD2 C:HIS65 4.3 20.4 1.0
O A:HOH309 4.7 24.3 1.0
CA C:HIS65 4.9 21.4 1.0
CD A:GLN59 4.9 23.1 1.0
CE A:MET99 4.9 22.2 1.0
CZ A:TYR153 5.0 23.3 1.0
N C:ALA66 5.0 22.4 1.0
CG C:ASP67 5.0 28.8 1.0
C C:HIS65 5.0 21.9 1.0

Zinc binding site 4 out of 6 in 6ive

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Zinc binding site 4 out of 6 in the Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:22.7
occ:1.00
NE2 D:HIS87 2.0 26.4 1.0
ND1 D:HIS65 2.0 25.6 1.0
O2 D:PO4202 2.0 27.4 1.0
NE2 E:HIS82 2.1 23.1 1.0
CD2 D:HIS87 2.9 21.4 1.0
CE1 D:HIS65 2.9 24.6 1.0
CD2 E:HIS82 3.0 18.4 1.0
P D:PO4202 3.1 32.3 1.0
O4 D:PO4202 3.1 29.9 1.0
CE1 E:HIS82 3.1 21.4 1.0
CG D:HIS65 3.1 20.5 1.0
CE1 D:HIS87 3.1 25.1 1.0
CB D:HIS65 3.5 21.7 1.0
OH E:TYR153 3.7 20.6 1.0
O1 D:PO4202 3.9 24.6 1.0
O E:HOH316 4.0 27.8 1.0
CG D:HIS87 4.1 18.7 1.0
NE2 D:HIS65 4.1 19.9 1.0
ND1 D:HIS87 4.2 19.7 1.0
ND1 E:HIS82 4.2 19.6 1.0
CG E:HIS82 4.2 21.1 1.0
CD2 D:HIS65 4.2 19.1 1.0
OE1 E:GLN59 4.2 23.0 1.0
O3 D:PO4202 4.2 27.1 1.0
OD1 D:ASP67 4.3 31.0 1.0
NH2 D:ARG44 4.8 21.9 1.0
CA D:HIS65 4.8 21.5 1.0
N D:ALA66 4.9 19.2 1.0
CD E:GLN59 4.9 22.9 1.0
O D:ALA66 4.9 20.5 1.0
C D:HIS65 4.9 21.7 1.0
CZ E:TYR153 5.0 24.8 1.0

Zinc binding site 5 out of 6 in 6ive

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Zinc binding site 5 out of 6 in the Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:24.4
occ:1.00
NE2 E:HIS87 2.1 27.0 1.0
ND1 E:HIS65 2.1 21.9 1.0
NE2 F:HIS82 2.1 23.8 1.0
O1 E:PO4202 2.2 28.2 1.0
O3 E:PO4202 2.8 32.9 1.0
CD2 E:HIS87 2.8 26.1 1.0
CE1 E:HIS65 2.9 20.1 1.0
P E:PO4202 3.0 34.3 1.0
CD2 F:HIS82 3.0 22.8 1.0
CE1 F:HIS82 3.1 23.2 1.0
CG E:HIS65 3.2 19.3 1.0
CE1 E:HIS87 3.2 25.2 1.0
CB E:HIS65 3.6 19.1 1.0
O E:HOH302 3.8 32.1 1.0
OH F:TYR153 3.9 25.1 1.0
O4 E:PO4202 3.9 33.8 1.0
CG E:HIS87 4.1 23.7 1.0
NE2 E:HIS65 4.1 23.1 1.0
O2 E:PO4202 4.2 27.9 1.0
ND1 E:HIS87 4.2 25.0 1.0
CG F:HIS82 4.2 22.1 1.0
ND1 F:HIS82 4.2 21.5 1.0
CD2 E:HIS65 4.2 23.1 1.0
OE1 F:GLN59 4.3 25.2 1.0
OD1 E:ASP67 4.3 32.2 1.0
CE F:MET99 4.9 23.5 1.0
NH2 E:ARG44 4.9 19.9 1.0
CA E:HIS65 4.9 22.1 1.0
N E:ALA66 5.0 20.6 1.0

Zinc binding site 6 out of 6 in 6ive

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Zinc binding site 6 out of 6 in the Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Molecular Structure of A Thermostable and A Zinc Ion Binding Gamma- Class Carbonic Anhydrase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:22.7
occ:1.00
NE2 F:HIS87 2.0 26.5 1.0
NE2 D:HIS82 2.1 19.2 1.0
O2 D:PO4203 2.1 25.9 1.0
ND1 F:HIS65 2.1 18.5 1.0
CD2 F:HIS87 2.7 19.7 1.0
O3 D:PO4203 2.9 25.1 1.0
CE1 F:HIS65 3.0 23.6 1.0
CD2 D:HIS82 3.0 22.2 1.0
P D:PO4203 3.0 27.6 1.0
CE1 D:HIS82 3.1 21.8 1.0
CE1 F:HIS87 3.1 26.4 1.0
CG F:HIS65 3.2 23.9 1.0
CB F:HIS65 3.6 23.0 1.0
OH D:TYR153 3.7 24.4 1.0
O D:HOH311 3.9 29.3 1.0
O4 D:PO4203 3.9 28.7 1.0
CG F:HIS87 4.0 21.1 1.0
ND1 F:HIS87 4.1 25.3 1.0
OE1 D:GLN59 4.2 23.5 1.0
NE2 F:HIS65 4.2 22.9 1.0
OD1 F:ASP67 4.2 31.4 1.0
CG D:HIS82 4.2 23.9 1.0
ND1 D:HIS82 4.2 20.8 1.0
O1 D:PO4203 4.2 23.1 1.0
CD2 F:HIS65 4.3 22.3 1.0
CA F:HIS65 4.9 21.8 1.0
NH2 F:ARG44 4.9 24.2 1.0
CD D:GLN59 4.9 21.5 1.0
CZ D:TYR153 5.0 18.9 1.0
N F:ALA66 5.0 24.9 1.0

Reference:

W.Wang, Y.Zhang, L.Wang, Q.Jing, X.Wang, X.Xi, X.Zhao, H.Wang. Molecular Structure of Thermostable and Zinc-Ion-Binding Gamma-Class Carbonic Anhydrases. Biometals V. 32 317 2019.
ISSN: ISSN 1572-8773
PubMed: 30895492
DOI: 10.1007/S10534-019-00190-8
Page generated: Wed Dec 16 12:02:01 2020

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