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Zinc in PDB 6im0: Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1

Enzymatic activity of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1

All present enzymatic activity of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1, PDB code: 6im0 was solved by M.S.Jin, S.Kim, J.Sung, J.Yeon, S.H.Choi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 123.19 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.885, 109.034, 123.186, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.7

Other elements in 6im0:

The structure of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 also contains other interesting chemical elements:

Calcium (Ca) 15 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 (pdb code 6im0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1, PDB code: 6im0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6im0

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Zinc binding site 1 out of 6 in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:32.0
occ:1.00
 O3 A:BCT302 2.0 47.4 1.0
ND1 A:HIS126 2.0 32.1 1.0
NE2 A:HIS107 2.1 31.3 1.0
NE2 A:HIS109 2.1 28.8 1.0
O1 A:BCT302 2.6 45.0 1.0
C A:BCT302 2.7 47.8 1.0
CE1 A:HIS126 2.9 34.0 1.0
CD2 A:HIS107 3.0 28.7 1.0
CE1 A:HIS109 3.1 30.5 1.0
CD2 A:HIS109 3.1 29.3 1.0
CE1 A:HIS107 3.1 31.9 1.0
CG A:HIS126 3.1 29.9 1.0
CB A:HIS126 3.6 28.8 1.0
OG1 A:THR193 3.6 42.0 1.0
O2 A:BCT302 3.9 45.7 1.0
OE1 A:GLU113 3.9 38.6 1.0
NE2 A:HIS126 4.1 30.9 1.0
ND1 A:HIS107 4.2 29.2 1.0
CG A:HIS107 4.2 30.0 1.0
ND1 A:HIS109 4.2 28.1 1.0
CD2 A:HIS126 4.2 29.9 1.0
CG A:HIS109 4.2 28.9 1.0
CD A:GLU113 4.9 39.9 1.0
CB A:THR193 5.0 39.4 1.0

Zinc binding site 2 out of 6 in 6im0

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Zinc binding site 2 out of 6 in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:31.1
occ:1.00
 ND1 B:HIS126 2.0 30.3 1.0
O3 B:BCT302 2.0 41.1 1.0
NE2 B:HIS107 2.1 31.3 1.0
NE2 B:HIS109 2.1 29.3 1.0
O1 B:BCT302 2.8 44.5 1.0
C B:BCT302 2.8 44.5 1.0
CE1 B:HIS126 2.9 32.0 1.0
CD2 B:HIS107 3.0 29.4 1.0
CD2 B:HIS109 3.1 30.6 1.0
CE1 B:HIS107 3.1 31.6 1.0
CG B:HIS126 3.1 30.1 1.0
CE1 B:HIS109 3.1 29.9 1.0
CB B:HIS126 3.5 29.1 1.0
OG1 B:THR193 3.7 44.4 1.0
OE1 B:GLU113 3.9 32.4 1.0
O2 B:BCT302 4.0 47.7 1.0
NE2 B:HIS126 4.1 29.6 1.0
CG B:HIS107 4.1 29.8 1.0
ND1 B:HIS107 4.2 29.7 1.0
CD2 B:HIS126 4.2 30.9 1.0
ND1 B:HIS109 4.2 26.9 1.0
CG B:HIS109 4.2 28.1 1.0
CD B:GLU113 5.0 34.4 1.0
CA B:HIS126 5.0 28.4 1.0

Zinc binding site 3 out of 6 in 6im0

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Zinc binding site 3 out of 6 in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:34.1
occ:1.00
 O3 C:BCT302 2.1 50.0 1.0
ND1 C:HIS126 2.1 29.4 1.0
NE2 C:HIS107 2.1 35.6 1.0
NE2 C:HIS109 2.2 26.6 1.0
C C:BCT302 2.8 46.1 1.0
O1 C:BCT302 2.9 37.5 1.0
CE1 C:HIS126 3.0 29.8 1.0
CD2 C:HIS107 3.0 35.8 1.0
CE1 C:HIS109 3.1 27.8 1.0
CE1 C:HIS107 3.1 36.8 1.0
CD2 C:HIS109 3.1 25.8 1.0
CG C:HIS126 3.2 28.0 1.0
CB C:HIS126 3.6 29.4 1.0
OG1 C:THR193 3.6 30.4 1.0
OE1 C:GLU113 3.9 26.0 1.0
O2 C:BCT302 3.9 43.3 1.0
NE2 C:HIS126 4.1 27.6 1.0
ND1 C:HIS107 4.2 34.3 1.0
CG C:HIS107 4.2 35.6 1.0
ND1 C:HIS109 4.2 25.7 1.0
CD2 C:HIS126 4.2 28.4 1.0
CG C:HIS109 4.3 25.1 1.0
CD C:GLU113 4.9 27.6 1.0
CB C:THR193 4.9 33.5 1.0

Zinc binding site 4 out of 6 in 6im0

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Zinc binding site 4 out of 6 in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:31.8
occ:1.00
 ND1 D:HIS126 2.1 27.8 1.0
O1 D:BCT302 2.1 50.0 1.0
NE2 D:HIS107 2.1 29.0 1.0
NE2 D:HIS109 2.1 25.5 1.0
O3 D:BCT302 2.7 50.1 1.0
C D:BCT302 2.7 52.6 1.0
CE1 D:HIS126 3.0 29.6 1.0
CD2 D:HIS107 3.0 29.2 1.0
CE1 D:HIS107 3.1 31.4 1.0
CD2 D:HIS109 3.1 25.6 1.0
CE1 D:HIS109 3.1 24.6 1.0
CG D:HIS126 3.1 27.6 1.0
CB D:HIS126 3.5 28.5 1.0
OG1 D:THR193 3.7 44.4 1.0
O2 D:BCT302 3.9 53.2 1.0
OE1 D:GLU113 4.0 27.4 1.0
NE2 D:HIS126 4.1 29.8 1.0
ND1 D:HIS107 4.1 29.5 1.0
CG D:HIS107 4.2 29.0 1.0
ND1 D:HIS109 4.2 23.9 1.0
CD2 D:HIS126 4.2 26.7 1.0
CG D:HIS109 4.2 24.5 1.0
CD D:GLU113 5.0 27.3 1.0
CA D:HIS126 5.0 26.7 1.0

Zinc binding site 5 out of 6 in 6im0

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Zinc binding site 5 out of 6 in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:35.3
occ:1.00
 ND1 E:HIS126 2.0 30.1 1.0
O1 E:BCT302 2.1 43.9 1.0
NE2 E:HIS107 2.1 34.5 1.0
NE2 E:HIS109 2.1 32.3 1.0
C E:BCT302 2.9 39.6 1.0
O3 E:BCT302 2.9 35.9 1.0
CE1 E:HIS126 2.9 29.7 1.0
CD2 E:HIS107 3.0 33.3 1.0
CD2 E:HIS109 3.1 31.9 1.0
CE1 E:HIS109 3.1 31.9 1.0
CG E:HIS126 3.1 30.3 1.0
CE1 E:HIS107 3.1 36.9 1.0
CB E:HIS126 3.5 31.4 1.0
OG1 E:THR193 3.7 35.9 1.0
OE1 E:GLU113 3.9 28.7 1.0
O2 E:BCT302 4.0 38.9 1.0
NE2 E:HIS126 4.1 29.5 1.0
CG E:HIS107 4.2 33.1 1.0
ND1 E:HIS109 4.2 30.6 1.0
ND1 E:HIS107 4.2 32.6 1.0
CD2 E:HIS126 4.2 29.8 1.0
CG E:HIS109 4.2 30.4 1.0
CD E:GLU113 4.9 29.6 1.0
CB E:THR193 5.0 34.6 1.0
CA E:HIS126 5.0 31.7 1.0

Zinc binding site 6 out of 6 in 6im0

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Zinc binding site 6 out of 6 in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:35.3
occ:1.00
 ND1 F:HIS126 2.0 27.7 1.0
O3 F:BCT302 2.1 50.6 1.0
NE2 F:HIS107 2.1 35.1 1.0
NE2 F:HIS109 2.1 31.1 1.0
O1 F:BCT302 2.8 54.5 1.0
C F:BCT302 2.8 53.5 1.0
CE1 F:HIS126 3.0 27.6 1.0
CD2 F:HIS107 3.0 34.9 1.0
CE1 F:HIS107 3.1 37.4 1.0
CD2 F:HIS109 3.1 30.9 1.0
CE1 F:HIS109 3.1 31.2 1.0
CG F:HIS126 3.1 26.4 1.0
CB F:HIS126 3.5 26.5 1.0
OG1 F:THR193 3.7 45.6 1.0
OE1 F:GLU113 3.9 27.8 1.0
O2 F:BCT302 4.0 52.0 1.0
NE2 F:HIS126 4.1 26.8 1.0
ND1 F:HIS107 4.1 35.4 1.0
CG F:HIS107 4.2 33.0 1.0
ND1 F:HIS109 4.2 29.2 1.0
CD2 F:HIS126 4.2 24.6 1.0
CG F:HIS109 4.2 28.9 1.0
CD F:GLU113 5.0 27.0 1.0

Reference:

S.Kim, J.Sung, J.Yeon, S.H.Choi, M.S.Jin. Crystal Structure of A Highly Thermostable Alpha-Carbonic Anhydrase From Persephonella Marina Ex-H1. Mol.Cells V. 42 460 2019.
ISSN: ISSN 1016-8478
PubMed: 31250619
DOI: 10.14348/MOLCELLS.2019.0029
Page generated: Mon Oct 28 23:52:59 2024

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