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Zinc in PDB 6im3: 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: 6im3 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) 123.92 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 119.040, 120.811, 123.915, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24

Other elements in 6im3:

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

Calcium (Ca) 16 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 6im3). 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: 6im3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6im3

Go back to Zinc Binding Sites List in 6im3
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:33.7
occ:1.00
 N1 A:AZM302 2.0 39.1 1.0
NE2 A:HIS107 2.1 34.1 1.0
ND1 A:HIS126 2.1 28.8 1.0
NE2 A:HIS109 2.2 32.0 1.0
CD2 A:HIS107 2.9 30.2 1.0
CE1 A:HIS126 3.0 29.5 1.0
O2 A:AZM302 3.0 33.7 1.0
S1 A:AZM302 3.0 40.7 1.0
CD2 A:HIS109 3.1 30.9 1.0
CE1 A:HIS107 3.1 33.0 1.0
CE1 A:HIS109 3.2 30.0 1.0
CG A:HIS126 3.2 24.8 1.0
CB A:HIS126 3.7 22.5 1.0
OE1 A:GLU113 3.8 42.3 1.0
OG1 A:THR193 3.9 27.4 1.0
C1 A:AZM302 4.0 51.6 1.0
O1 A:AZM302 4.0 35.0 1.0
CG A:HIS107 4.1 30.4 1.0
NE2 A:HIS126 4.1 27.6 1.0
ND1 A:HIS107 4.1 33.5 1.0
ND1 A:HIS109 4.2 30.8 1.0
CD2 A:HIS126 4.2 30.1 1.0
CG A:HIS109 4.3 28.2 1.0
N3 A:AZM302 4.8 54.6 1.0
CD A:GLU113 4.9 39.7 1.0

Zinc binding site 2 out of 6 in 6im3

Go back to Zinc Binding Sites List in 6im3
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:35.3
occ:1.00
 N1 B:AZM302 2.1 38.9 1.0
ND1 B:HIS126 2.1 32.0 1.0
NE2 B:HIS107 2.1 33.6 1.0
NE2 B:HIS109 2.2 29.9 1.0
CD2 B:HIS107 2.9 33.9 1.0
CE1 B:HIS126 2.9 29.5 1.0
O2 B:AZM302 2.9 30.7 1.0
CD2 B:HIS109 3.1 29.7 1.0
S1 B:AZM302 3.1 41.2 1.0
CE1 B:HIS107 3.2 39.0 1.0
CE1 B:HIS109 3.2 34.9 1.0
CG B:HIS126 3.2 29.9 1.0
O B:HOH480 3.6 55.7 1.0
CB B:HIS126 3.7 27.4 1.0
OE1 B:GLU113 3.8 40.1 1.0
OG1 B:THR193 3.9 27.6 1.0
C1 B:AZM302 4.1 63.4 1.0
NE2 B:HIS126 4.1 29.6 1.0
CG B:HIS107 4.1 31.3 1.0
O1 B:AZM302 4.2 49.6 1.0
ND1 B:HIS107 4.2 29.0 1.0
CG B:HIS109 4.2 30.8 1.0
ND1 B:HIS109 4.2 33.0 1.0
CD2 B:HIS126 4.3 32.7 1.0
CD B:GLU113 4.8 39.7 1.0
N3 B:AZM302 4.9 60.8 1.0

Zinc binding site 3 out of 6 in 6im3

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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:53.7
occ:1.00
 NE2 C:HIS107 2.1 50.9 1.0
N1 C:AZM302 2.1 62.8 1.0
NE2 C:HIS109 2.2 57.5 1.0
ND1 C:HIS126 2.2 47.2 1.0
CD2 C:HIS107 2.9 53.0 1.0
O2 C:AZM302 2.9 68.2 1.0
S1 C:AZM302 3.0 70.5 1.0
CE1 C:HIS126 3.1 46.9 1.0
CD2 C:HIS109 3.1 50.6 1.0
CE1 C:HIS107 3.1 58.3 1.0
CE1 C:HIS109 3.1 47.0 1.0
CG C:HIS126 3.2 45.9 1.0
CB C:HIS126 3.6 49.0 1.0
OE1 C:GLU113 3.9 59.5 1.0
OG1 C:THR193 3.9 46.3 1.0
O1 C:AZM302 4.0 54.2 1.0
CG C:HIS107 4.1 54.7 1.0
ND1 C:HIS107 4.1 55.9 1.0
C1 C:AZM302 4.2 76.0 1.0
NE2 C:HIS126 4.2 44.9 1.0
ND1 C:HIS109 4.2 53.5 1.0
CG C:HIS109 4.2 58.0 1.0
CD2 C:HIS126 4.3 46.0 1.0
N3 C:AZM302 4.8 68.1 1.0
CD C:GLU113 4.9 58.8 1.0

Zinc binding site 4 out of 6 in 6im3

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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:51.0
occ:1.00
 NE2 D:HIS107 2.1 42.4 1.0
N1 D:AZM302 2.1 61.3 1.0
ND1 D:HIS126 2.1 45.3 1.0
NE2 D:HIS109 2.2 58.4 1.0
CD2 D:HIS107 2.9 50.9 1.0
O2 D:AZM302 3.0 55.5 1.0
S1 D:AZM302 3.0 58.5 1.0
CE1 D:HIS126 3.0 41.8 1.0
CE1 D:HIS107 3.1 47.8 1.0
CD2 D:HIS109 3.1 50.3 1.0
CE1 D:HIS109 3.2 58.2 1.0
CG D:HIS126 3.2 38.6 1.0
CB D:HIS126 3.5 45.5 1.0
OE1 D:GLU113 3.9 50.1 1.0
OG1 D:THR193 3.9 43.8 1.0
O1 D:AZM302 4.0 52.9 1.0
C1 D:AZM302 4.1 76.2 1.0
CG D:HIS107 4.1 50.9 1.0
ND1 D:HIS107 4.1 48.0 1.0
NE2 D:HIS126 4.2 44.2 1.0
ND1 D:HIS109 4.2 46.6 1.0
CG D:HIS109 4.2 58.4 1.0
CD2 D:HIS126 4.3 45.2 1.0
N3 D:AZM302 4.8 63.4 1.0
CD D:GLU113 4.9 48.9 1.0
CA D:HIS126 5.0 48.0 1.0

Zinc binding site 5 out of 6 in 6im3

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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:47.2
occ:1.00
 NE2 E:HIS107 2.0 39.6 1.0
N1 E:AZM302 2.1 44.9 1.0
NE2 E:HIS109 2.1 43.8 1.0
ND1 E:HIS126 2.2 36.5 1.0
CD2 E:HIS107 2.9 46.2 1.0
CE1 E:HIS126 3.0 37.4 1.0
CD2 E:HIS109 3.0 44.0 1.0
CE1 E:HIS107 3.1 45.7 1.0
S1 E:AZM302 3.1 49.5 1.0
CE1 E:HIS109 3.1 50.7 1.0
O2 E:AZM302 3.2 45.9 1.0
CG E:HIS126 3.2 39.5 1.0
CB E:HIS126 3.6 38.2 1.0
OE1 E:GLU113 3.9 48.2 1.0
OG1 E:THR193 4.0 38.0 1.0
CG E:HIS107 4.1 41.9 1.0
ND1 E:HIS107 4.1 43.5 1.0
C1 E:AZM302 4.1 60.3 1.0
NE2 E:HIS126 4.2 36.9 1.0
O1 E:AZM302 4.2 55.1 1.0
ND1 E:HIS109 4.2 42.9 1.0
CG E:HIS109 4.2 46.8 1.0
CD2 E:HIS126 4.3 40.0 1.0
N3 E:AZM302 4.8 58.0 1.0
CD E:GLU113 4.9 51.3 1.0

Zinc binding site 6 out of 6 in 6im3

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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:48.0
occ:1.00
 NE2 F:HIS107 2.1 37.8 1.0
NE2 F:HIS109 2.1 43.2 1.0
N1 F:AZM302 2.1 51.1 1.0
ND1 F:HIS126 2.2 40.6 1.0
CD2 F:HIS107 2.9 45.5 1.0
CD2 F:HIS109 3.0 50.3 1.0
CE1 F:HIS126 3.0 41.3 1.0
S1 F:AZM302 3.1 51.7 1.0
CE1 F:HIS107 3.1 41.4 1.0
CE1 F:HIS109 3.1 51.1 1.0
O2 F:AZM302 3.2 43.5 1.0
CG F:HIS126 3.2 32.8 1.0
CB F:HIS126 3.6 37.0 1.0
OG1 F:THR193 3.8 40.9 1.0
OE1 F:GLU113 3.9 47.5 1.0
CG F:HIS107 4.1 42.1 1.0
O1 F:AZM302 4.1 54.5 1.0
ND1 F:HIS107 4.1 42.2 1.0
C1 F:AZM302 4.2 62.2 1.0
NE2 F:HIS126 4.2 43.0 1.0
ND1 F:HIS109 4.2 46.4 1.0
CG F:HIS109 4.2 47.8 1.0
CD2 F:HIS126 4.3 40.1 1.0
N3 F:AZM302 4.9 57.6 1.0
CD F:GLU113 4.9 48.0 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 23:52:58 2024

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