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Zinc in PDB 6eki: Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney

Enzymatic activity of Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney

All present enzymatic activity of Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney:
4.2.1.1;

Protein crystallography data

The structure of Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney, PDB code: 6eki was solved by F.Fredslund, J.-C.N.Poulsen, L.Lo Leggio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.99 / 2.56
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.317, 71.276, 103.344, 88.38, 82.84, 84.22
R / Rfree (%) 16.4 / 23.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney (pdb code 6eki). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney, PDB code: 6eki:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6eki

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Zinc binding site 1 out of 6 in the Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:47.0
occ:1.00
 NE2 A:HIS119 2.1 35.7 1.0
ND1 A:HIS136 2.1 31.7 1.0
NE2 A:HIS117 2.2 37.9 1.0
CD2 A:HIS117 2.9 31.3 1.0
HD2 A:HIS117 2.9 37.6 1.0
O A:HOH411 3.0 37.1 1.0
CE1 A:HIS119 3.0 42.8 1.0
CE1 A:HIS136 3.0 31.7 1.0
HE1 A:HIS136 3.1 38.0 1.0
HE1 A:HIS119 3.1 51.3 1.0
CD2 A:HIS119 3.1 44.7 1.0
CG A:HIS136 3.2 35.0 1.0
HG1 A:THR202 3.2 56.7 1.0
HB2 A:HIS136 3.2 46.3 1.0
CE1 A:HIS117 3.3 48.7 1.0
HD2 A:HIS119 3.4 53.6 1.0
OG1 A:THR202 3.6 47.3 1.0
CB A:HIS136 3.6 38.6 1.0
HE1 A:HIS117 3.6 58.5 1.0
HB3 A:HIS136 3.7 46.3 1.0
OE1 A:GLU123 4.0 38.4 1.0
ND1 A:HIS119 4.1 46.1 1.0
NE2 A:HIS136 4.1 27.2 1.0
CG A:HIS117 4.2 34.7 1.0
CG A:HIS119 4.2 42.9 1.0
CD2 A:HIS136 4.3 32.2 1.0
HH2 A:TRP212 4.3 40.8 1.0
ND1 A:HIS117 4.3 36.6 1.0
HG23 A:THR203 4.7 44.9 1.0
HD1 A:HIS119 4.9 55.3 1.0
HE2 A:HIS136 4.9 32.7 1.0
CD A:GLU123 5.0 35.6 1.0
H A:THR202 5.0 49.1 1.0
CB A:THR202 5.0 33.2 1.0

Zinc binding site 2 out of 6 in 6eki

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Zinc binding site 2 out of 6 in the Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:36.4
occ:1.00
 ND1 B:HIS136 2.0 36.3 1.0
NE2 B:HIS117 2.1 45.2 1.0
NE2 B:HIS119 2.1 40.7 1.0
O B:HOH414 2.8 41.4 1.0
CE1 B:HIS136 2.9 38.8 1.0
CD2 B:HIS119 3.0 37.2 1.0
CD2 B:HIS117 3.0 33.9 1.0
HE1 B:HIS136 3.0 46.6 1.0
HD2 B:HIS119 3.0 44.7 1.0
HD2 B:HIS117 3.1 40.7 1.0
CG B:HIS136 3.1 33.2 1.0
HB2 B:HIS136 3.1 44.6 1.0
CE1 B:HIS117 3.2 38.9 1.0
HG1 B:THR202 3.2 44.3 1.0
CE1 B:HIS119 3.2 39.3 1.0
HE1 B:HIS117 3.5 46.6 1.0
HE1 B:HIS119 3.5 47.1 1.0
CB B:HIS136 3.5 37.2 1.0
OG1 B:THR202 3.7 36.9 1.0
OE1 B:GLU123 3.7 32.6 1.0
HB3 B:HIS136 3.7 44.6 1.0
NE2 B:HIS136 4.1 36.2 1.0
CG B:HIS119 4.2 42.5 1.0
CG B:HIS117 4.2 39.8 1.0
CD2 B:HIS136 4.2 32.1 1.0
HH2 B:TRP212 4.2 47.4 1.0
ND1 B:HIS117 4.3 34.8 1.0
ND1 B:HIS119 4.3 39.0 1.0
HE2 B:HIS136 4.8 43.5 1.0
CD B:GLU123 4.9 37.5 1.0
HG23 B:THR203 4.9 35.1 1.0
CA B:HIS136 5.0 34.1 1.0

Zinc binding site 3 out of 6 in 6eki

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Zinc binding site 3 out of 6 in the Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:50.1
occ:1.00
 ND1 C:HIS136 2.1 44.2 1.0
NE2 C:HIS117 2.1 38.5 1.0
NE2 C:HIS119 2.2 34.9 1.0
CD2 C:HIS117 3.0 39.7 1.0
CE1 C:HIS136 3.0 36.8 1.0
HD2 C:HIS117 3.1 47.7 1.0
CE1 C:HIS119 3.1 31.8 1.0
HE1 C:HIS136 3.1 44.1 1.0
HG1 C:THR202 3.1 37.2 1.0
O C:HOH411 3.1 31.3 1.0
HE1 C:HIS119 3.2 38.1 1.0
CE1 C:HIS117 3.2 50.1 1.0
CG C:HIS136 3.2 35.8 1.0
HB2 C:HIS136 3.3 33.4 1.0
CD2 C:HIS119 3.3 29.3 1.0
HE1 C:HIS117 3.5 60.1 1.0
HD2 C:HIS119 3.5 35.2 1.0
OG1 C:THR202 3.5 31.0 1.0
CB C:HIS136 3.7 27.9 1.0
HB3 C:HIS136 3.8 33.4 1.0
OE1 C:GLU123 4.0 39.4 1.0
NE2 C:HIS136 4.2 33.2 1.0
CG C:HIS117 4.2 39.7 1.0
ND1 C:HIS119 4.2 24.4 1.0
HH2 C:TRP212 4.2 41.2 1.0
ND1 C:HIS117 4.3 42.7 1.0
CD2 C:HIS136 4.3 34.7 1.0
CG C:HIS119 4.3 32.8 1.0
HG23 C:THR203 4.7 46.3 1.0
CB C:THR202 4.9 27.2 1.0
HE2 C:HIS136 4.9 39.8 1.0
HD1 C:HIS119 4.9 29.3 1.0
HG21 C:THR202 5.0 39.9 1.0
H C:THR202 5.0 38.7 1.0
CD C:GLU123 5.0 36.1 1.0

Zinc binding site 4 out of 6 in 6eki

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Zinc binding site 4 out of 6 in the Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:38.5
occ:1.00
 NE2 D:HIS117 2.0 45.9 1.0
ND1 D:HIS136 2.3 40.6 1.0
NE2 D:HIS119 2.3 27.6 1.0
O D:HOH416 2.9 32.9 1.0
CD2 D:HIS117 3.0 38.3 1.0
CE1 D:HIS117 3.1 41.8 1.0
HD2 D:HIS117 3.1 46.0 1.0
CD2 D:HIS119 3.1 30.2 1.0
HD2 D:HIS119 3.2 36.2 1.0
HB2 D:HIS136 3.2 41.6 1.0
CE1 D:HIS136 3.2 31.7 1.0
HG1 D:THR202 3.2 57.1 1.0
CG D:HIS136 3.3 36.4 1.0
HE1 D:HIS117 3.3 50.1 1.0
HE1 D:HIS136 3.3 38.0 1.0
CE1 D:HIS119 3.4 29.0 1.0
OG1 D:THR202 3.6 47.6 1.0
CB D:HIS136 3.6 34.6 1.0
HE1 D:HIS119 3.6 34.8 1.0
HB3 D:HIS136 3.7 41.6 1.0
OE1 D:GLU123 3.8 42.5 1.0
CG D:HIS117 4.1 35.6 1.0
ND1 D:HIS117 4.2 38.5 1.0
HH2 D:TRP212 4.3 47.1 1.0
CG D:HIS119 4.3 39.8 1.0
NE2 D:HIS136 4.3 30.1 1.0
CD2 D:HIS136 4.4 32.1 1.0
ND1 D:HIS119 4.4 34.1 1.0
HG23 D:THR203 4.7 54.4 1.0
CD D:GLU123 4.9 44.1 1.0
H D:THR202 4.9 43.4 1.0
HD1 D:HIS117 4.9 46.2 1.0
CB D:THR202 4.9 40.7 1.0

Zinc binding site 5 out of 6 in 6eki

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Zinc binding site 5 out of 6 in the Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:42.0
occ:1.00
 NE2 E:HIS117 1.9 46.2 1.0
ND1 E:HIS136 2.0 35.2 1.0
NE2 E:HIS119 2.3 42.2 1.0
CE1 E:HIS117 2.8 48.8 1.0
CE1 E:HIS136 2.9 41.2 1.0
CD2 E:HIS117 2.9 36.5 1.0
HG1 E:THR202 2.9 54.9 1.0
HE1 E:HIS136 3.0 49.4 1.0
HE1 E:HIS117 3.1 58.6 1.0
HD2 E:HIS117 3.1 43.9 1.0
CG E:HIS136 3.1 42.6 1.0
CD2 E:HIS119 3.2 48.4 1.0
HB2 E:HIS136 3.2 47.4 1.0
O E:HOH412 3.2 38.0 1.0
CE1 E:HIS119 3.3 45.3 1.0
HD2 E:HIS119 3.3 58.0 1.0
OG1 E:THR202 3.4 45.8 1.0
HE1 E:HIS119 3.4 54.3 1.0
CB E:HIS136 3.6 39.5 1.0
HB3 E:HIS136 3.7 47.4 1.0
ND1 E:HIS117 3.9 40.8 1.0
CG E:HIS117 4.0 32.5 1.0
NE2 E:HIS136 4.0 40.2 1.0
OE1 E:GLU123 4.2 44.8 1.0
CD2 E:HIS136 4.2 34.8 1.0
HH2 E:TRP212 4.3 49.2 1.0
CG E:HIS119 4.4 40.6 1.0
ND1 E:HIS119 4.4 39.9 1.0
HG23 E:THR203 4.7 36.5 1.0
HD1 E:HIS117 4.7 48.9 1.0
CB E:THR202 4.8 43.3 1.0
HE2 E:HIS136 4.8 48.2 1.0
HG21 E:THR202 4.9 46.2 1.0
CD E:GLU123 4.9 40.4 1.0
H E:THR202 5.0 45.8 1.0

Zinc binding site 6 out of 6 in 6eki

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Zinc binding site 6 out of 6 in the Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:45.4
occ:1.00
 ND1 F:HIS136 2.0 43.4 1.0
NE2 F:HIS117 2.1 51.0 1.0
NE2 F:HIS119 2.1 36.2 1.0
CE1 F:HIS136 2.8 43.6 1.0
CD2 F:HIS117 2.9 38.3 1.0
HD2 F:HIS117 2.9 46.0 1.0
HE1 F:HIS136 2.9 52.4 1.0
O F:HOH412 3.0 33.7 1.0
CD2 F:HIS119 3.0 33.7 1.0
CG F:HIS136 3.1 49.9 1.0
CE1 F:HIS119 3.1 30.7 1.0
HD2 F:HIS119 3.2 40.4 1.0
HB2 F:HIS136 3.2 49.9 1.0
CE1 F:HIS117 3.3 42.3 1.0
HE1 F:HIS119 3.4 36.9 1.0
HG1 F:THR202 3.4 46.0 1.0
HE1 F:HIS117 3.6 50.7 1.0
CB F:HIS136 3.6 41.6 1.0
OG1 F:THR202 3.6 38.4 1.0
HB3 F:HIS136 3.8 49.9 1.0
NE2 F:HIS136 4.0 41.5 1.0
CG F:HIS117 4.1 42.9 1.0
CD2 F:HIS136 4.2 33.8 1.0
CG F:HIS119 4.2 30.0 1.0
ND1 F:HIS119 4.2 33.7 1.0
ND1 F:HIS117 4.3 47.8 1.0
OE1 F:GLU123 4.3 37.1 1.0
HH2 F:TRP212 4.4 52.6 1.0
HG23 F:THR203 4.5 42.8 1.0
HE2 F:HIS136 4.8 49.8 1.0
H F:THR202 4.8 36.5 1.0
H F:HIS136 4.9 38.5 1.0
CB F:THR202 4.9 42.7 1.0

Reference:

F.Fredslund, M.S.Borchert, J.N.Poulsen, S.B.Mortensen, M.Perner, W.R.Streit, L.Lo Leggio. Structure of A Hyperthermostable Carbonic Anhydrase Identified From An Active Hydrothermal Vent Chimney. Enzyme Microb. Technol. V. 114 48 2018.
ISSN: ISSN 1879-0909
PubMed: 29685353
DOI: 10.1016/J.ENZMICTEC.2018.03.009
Page generated: Mon Oct 28 20:11:08 2024

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