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Zinc in PDB 6im1: 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: 6im1 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) 124.07 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 118.924, 120.068, 124.067, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.6

Other elements in 6im1:

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 6im1). 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: 6im1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6im1

Go back to Zinc Binding Sites List in 6im1
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:32.4
occ:1.00
 O A:HOH406 2.0 37.6 1.0
NE2 A:HIS107 2.1 29.8 1.0
ND1 A:HIS126 2.2 25.4 1.0
NE2 A:HIS109 2.2 27.2 1.0
CD2 A:HIS107 2.9 25.7 1.0
CE1 A:HIS126 3.0 25.4 1.0
CD2 A:HIS109 3.1 27.0 1.0
CE1 A:HIS107 3.1 29.0 1.0
CE1 A:HIS109 3.2 26.2 1.0
CG A:HIS126 3.2 22.5 1.0
CB A:HIS126 3.6 21.9 1.0
O A:HOH513 3.7 37.3 1.0
OG1 A:THR193 3.8 25.4 1.0
OE1 A:GLU113 3.8 32.5 1.0
O A:HOH514 4.0 40.4 1.0
CG A:HIS107 4.1 23.0 1.0
ND1 A:HIS107 4.2 25.9 1.0
NE2 A:HIS126 4.2 23.4 1.0
CG A:HIS109 4.2 24.3 1.0
ND1 A:HIS109 4.3 26.6 1.0
CD2 A:HIS126 4.3 23.2 1.0
CD A:GLU113 4.9 30.3 1.0

Zinc binding site 2 out of 6 in 6im1

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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:34.4
occ:1.00
 O B:HOH402 2.1 36.2 1.0
NE2 B:HIS107 2.1 28.4 1.0
ND1 B:HIS126 2.2 24.1 1.0
NE2 B:HIS109 2.2 28.4 1.0
CD2 B:HIS107 3.0 31.7 1.0
CE1 B:HIS126 3.0 26.5 1.0
CD2 B:HIS109 3.1 25.9 1.0
CE1 B:HIS107 3.2 31.4 1.0
CE1 B:HIS109 3.2 29.0 1.0
CG B:HIS126 3.2 26.5 1.0
CB B:HIS126 3.7 23.8 1.0
O B:HOH494 3.7 42.8 1.0
OG1 B:THR193 3.8 26.2 1.0
OE1 B:GLU113 3.8 30.4 1.0
O B:HOH500 4.0 39.8 1.0
CG B:HIS107 4.2 26.3 1.0
NE2 B:HIS126 4.2 25.8 1.0
ND1 B:HIS107 4.2 23.8 1.0
CG B:HIS109 4.2 25.5 1.0
ND1 B:HIS109 4.3 28.6 1.0
CD2 B:HIS126 4.3 25.6 1.0
CD B:GLU113 4.8 29.9 1.0

Zinc binding site 3 out of 6 in 6im1

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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:51.7
occ:1.00
 NE2 C:HIS107 2.1 46.2 1.0
NE2 C:HIS109 2.1 48.4 1.0
O C:HOH440 2.2 75.6 1.0
ND1 C:HIS126 2.2 45.1 1.0
CD2 C:HIS107 3.0 44.5 1.0
CD2 C:HIS109 3.1 41.8 1.0
CE1 C:HIS126 3.1 45.2 1.0
CE1 C:HIS109 3.1 44.1 1.0
CE1 C:HIS107 3.1 45.5 1.0
CG C:HIS126 3.2 42.3 1.0
CB C:HIS126 3.6 44.0 1.0
OG1 C:THR193 3.8 41.3 1.0
OE1 C:GLU113 3.8 55.4 1.0
CG C:HIS107 4.2 47.2 1.0
ND1 C:HIS107 4.2 49.8 1.0
ND1 C:HIS109 4.2 43.9 1.0
CG C:HIS109 4.2 47.8 1.0
NE2 C:HIS126 4.2 41.7 1.0
CD2 C:HIS126 4.3 44.4 1.0
O C:HOH448 4.4 58.1 1.0
CD C:GLU113 4.9 55.2 1.0

Zinc binding site 4 out of 6 in 6im1

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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:48.4
occ:1.00
 O D:HOH407 2.0 52.6 1.0
NE2 D:HIS107 2.1 44.2 1.0
ND1 D:HIS126 2.2 36.7 1.0
NE2 D:HIS109 2.2 46.4 1.0
CD2 D:HIS107 3.0 46.4 1.0
CE1 D:HIS126 3.0 38.0 1.0
CE1 D:HIS107 3.1 48.4 1.0
CD2 D:HIS109 3.1 42.6 1.0
CE1 D:HIS109 3.2 43.8 1.0
CG D:HIS126 3.2 34.5 1.0
CB D:HIS126 3.6 37.4 1.0
OG1 D:THR193 3.8 40.4 1.0
OE1 D:GLU113 3.8 46.0 1.0
CG D:HIS107 4.1 43.1 1.0
ND1 D:HIS107 4.1 43.0 1.0
NE2 D:HIS126 4.2 38.0 1.0
O D:HOH440 4.2 49.4 1.0
ND1 D:HIS109 4.3 39.0 1.0
CD2 D:HIS126 4.3 36.0 1.0
CG D:HIS109 4.3 44.6 1.0
CD D:GLU113 4.9 43.6 1.0

Zinc binding site 5 out of 6 in 6im1

Go back to Zinc Binding Sites List in 6im1
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:44.6
occ:1.00
 NE2 E:HIS107 2.1 35.3 1.0
O E:HOH406 2.1 47.8 1.0
NE2 E:HIS109 2.1 37.0 1.0
ND1 E:HIS126 2.1 33.1 1.0
CD2 E:HIS107 2.9 37.1 1.0
CE1 E:HIS126 3.0 30.1 1.0
CD2 E:HIS109 3.0 37.6 1.0
CE1 E:HIS107 3.1 36.5 1.0
CE1 E:HIS109 3.1 40.3 1.0
CG E:HIS126 3.2 35.1 1.0
CB E:HIS126 3.6 34.9 1.0
OE1 E:GLU113 3.8 37.3 1.0
OG1 E:THR193 3.9 36.1 1.0
O E:HOH457 4.1 48.2 1.0
CG E:HIS107 4.1 34.3 1.0
ND1 E:HIS107 4.1 34.8 1.0
NE2 E:HIS126 4.1 31.4 1.0
ND1 E:HIS109 4.2 34.6 1.0
CG E:HIS109 4.2 35.4 1.0
CD2 E:HIS126 4.3 36.5 1.0
CD E:GLU113 4.9 39.9 1.0

Zinc binding site 6 out of 6 in 6im1

Go back to Zinc Binding Sites List in 6im1
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:46.2
occ:1.00
 NE2 F:HIS107 2.1 39.7 1.0
NE2 F:HIS109 2.1 38.1 1.0
O F:HOH402 2.2 54.8 1.0
ND1 F:HIS126 2.2 33.4 1.0
CD2 F:HIS107 3.0 39.8 1.0
CD2 F:HIS109 3.0 40.0 1.0
CE1 F:HIS126 3.0 35.8 1.0
CE1 F:HIS109 3.1 44.4 1.0
CE1 F:HIS107 3.1 36.5 1.0
CG F:HIS126 3.3 30.8 1.0
CB F:HIS126 3.7 34.6 1.0
OE1 F:GLU113 3.8 42.5 1.0
OG1 F:THR193 3.8 38.3 1.0
O F:HOH462 3.9 56.1 1.0
CG F:HIS107 4.1 36.5 1.0
ND1 F:HIS107 4.2 42.0 1.0
CG F:HIS109 4.2 38.7 1.0
ND1 F:HIS109 4.2 38.9 1.0
NE2 F:HIS126 4.2 33.9 1.0
CD2 F:HIS126 4.3 33.3 1.0
CD F:GLU113 4.9 41.4 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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