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Calcium 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:

Zinc (Zn) 6 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium 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 Calcium atom.
In total 16 binding sites of Calcium where determined in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1, PDB code: 6im3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 6im3

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Calcium binding site 1 out of 16 in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca303

b:68.7
occ:1.00
 O A:HOH406 2.1 44.2 1.0
O F:HOH427 2.4 42.6 1.0
OE2 A:GLU242 2.5 42.9 1.0
OE2 A:GLU207 2.6 78.7 1.0
OE1 F:GLU208 2.7 45.1 1.0
O F:HOH401 2.7 55.3 1.0
CD A:GLU242 3.2 44.5 1.0
OE1 A:GLU242 3.3 46.4 1.0
CD A:GLU207 3.8 68.5 1.0
OE1 F:GLU209 3.9 63.4 1.0
O F:HOH402 3.9 52.5 1.0
CD F:GLU208 3.9 54.2 1.0
O A:HOH402 4.2 31.2 1.0
OH A:TYR186 4.3 48.9 1.0
OE2 F:GLU208 4.5 51.1 1.0
CG A:GLU207 4.6 57.9 1.0
OE1 A:GLU207 4.6 63.6 1.0
CG A:GLU242 4.6 39.9 1.0
CD F:GLU209 4.7 70.7 1.0
OE2 F:GLU209 4.7 77.9 1.0
CA A:CA304 4.7 62.2 1.0
CA F:GLU208 4.8 38.6 1.0
O F:GLU207 4.8 41.2 1.0

Calcium binding site 2 out of 16 in 6im3

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Calcium binding site 2 out of 16 in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
A:Ca304

b:62.2
occ:1.00
 OD2 F:ASP182 2.3 96.0 1.0
O A:HOH402 2.4 31.2 1.0
O F:HOH401 2.5 55.3 1.0
OD2 A:ASP184 2.5 49.0 1.0
OE1 A:GLU207 2.7 63.6 1.0
O A:HOH407 3.1 65.3 1.0
OE2 A:GLU207 3.2 78.7 1.0
CD A:GLU207 3.3 68.5 1.0
CG A:ASP184 3.5 43.6 1.0
CG F:ASP182 3.6 76.6 1.0
CB A:ASP184 3.9 34.5 1.0
OE2 A:GLU242 4.0 42.9 1.0
OE2 F:GLU207 4.1 80.8 1.0
O A:HOH435 4.2 64.9 1.0
O A:HOH439 4.3 58.0 1.0
OE1 F:GLU208 4.4 45.1 1.0
CB F:ASP182 4.4 57.8 1.0
OD1 F:ASP182 4.4 75.0 1.0
O A:LYS243 4.4 59.4 1.0
OD1 A:ASP184 4.6 45.7 1.0
CA A:CA303 4.7 68.7 1.0
CG A:GLU207 4.8 57.9 1.0

Calcium binding site 3 out of 16 in 6im3

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Calcium binding site 3 out of 16 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 Calcium with other atoms in the Ca 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
A:Ca305

b:69.0
occ:1.00
 O F:HOH411 2.3 81.5 1.0
OE1 A:GLU208 2.4 39.7 1.0
O A:HOH405 2.4 57.3 1.0
OE2 F:GLU242 2.5 55.7 1.0
OE1 F:GLU242 2.7 56.6 1.0
O A:HOH432 2.8 44.0 1.0
OE1 A:GLU209 2.8 57.5 1.0
CD F:GLU242 3.0 56.7 1.0
O A:HOH401 3.4 64.1 1.0
CD A:GLU208 3.5 57.1 1.0
CD A:GLU209 3.6 54.2 1.0
OE2 A:GLU209 3.6 60.5 1.0
OE2 A:GLU208 3.9 56.2 1.0
OE1 F:GLU207 4.0 66.0 1.0
O1 F:PG4303 4.0 68.3 1.0
C1 F:PG4303 4.1 71.2 1.0
O F:HOH404 4.3 45.2 1.0
CG F:GLU242 4.5 48.0 1.0
O A:HOH416 4.6 58.7 1.0
N A:GLU209 4.7 31.2 1.0
CA A:GLU208 4.7 34.4 1.0
CG A:GLU208 4.8 46.6 1.0
CD F:GLU207 5.0 80.5 1.0
O A:GLU207 5.0 32.3 1.0

Calcium binding site 4 out of 16 in 6im3

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Calcium binding site 4 out of 16 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 Calcium with other atoms in the Ca 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
A:Ca306

b:47.3
occ:1.00
 OD2 F:ASP60 2.3 52.9 1.0
O A:HOH493 2.4 46.3 1.0
O A:HOH410 2.4 42.8 1.0
O A:GLU209 2.4 33.9 1.0
OE2 A:GLU209 2.7 60.5 1.0
OE2 A:GLU208 2.8 56.2 1.0
CG F:ASP60 3.1 49.1 1.0
OD1 F:ASP60 3.2 54.3 1.0
CD A:GLU208 3.6 57.1 1.0
C A:GLU209 3.6 37.9 1.0
O A:HOH405 3.7 57.3 1.0
CD A:GLU209 3.8 54.2 1.0
CG A:GLU208 4.1 46.6 1.0
CA A:MET210 4.2 34.4 1.0
CG A:GLU209 4.2 43.1 1.0
N A:MET210 4.3 38.3 1.0
OE2 A:GLU211 4.4 71.3 1.0
OE1 A:GLU208 4.4 39.7 1.0
CB F:ASP60 4.6 44.1 1.0
N A:GLU209 4.6 31.2 1.0
CA A:GLU209 4.6 32.6 1.0
O A:HOH416 4.6 58.7 1.0
C A:MET210 4.6 30.8 1.0
OE1 A:GLU209 4.8 57.5 1.0
O A:MET210 4.9 30.3 1.0

Calcium binding site 5 out of 16 in 6im3

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Calcium binding site 5 out of 16 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 Calcium with other atoms in the Ca 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
A:Ca307

b:48.0
occ:1.00
 O F:HOH403 2.0 60.4 1.0
O A:HOH512 2.4 47.8 1.0
OE2 F:GLU208 2.4 51.1 1.0
OD2 A:ASP60 2.4 40.8 1.0
O F:HOH422 2.4 41.8 1.0
O F:GLU209 2.6 39.6 1.0
OE2 F:GLU209 3.0 77.9 1.0
OD1 A:ASP60 3.0 44.6 1.0
CG A:ASP60 3.1 41.7 1.0
O F:HOH402 3.3 52.5 1.0
CD F:GLU208 3.5 54.2 1.0
C F:GLU209 3.7 44.8 1.0
CG F:GLU208 4.0 53.8 1.0
CD F:GLU209 4.0 70.7 1.0
CA F:MET210 4.4 41.2 1.0
N F:MET210 4.5 41.0 1.0
OE1 F:GLU208 4.5 45.1 1.0
CG F:GLU209 4.5 65.7 1.0
OE2 F:GLU211 4.6 93.9 1.0
CB A:ASP60 4.6 32.1 1.0
N F:GLU209 4.7 42.4 1.0
CA F:GLU209 4.7 43.0 1.0
NZ B:LYS62 4.8 65.2 1.0
O F:HOH446 4.8 48.4 1.0
C F:MET210 4.8 38.8 1.0

Calcium binding site 6 out of 16 in 6im3

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Calcium binding site 6 out of 16 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 Calcium with other atoms in the Ca 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
A:Ca308

b:71.7
occ:1.00
 O A:HOH407 2.3 65.3 1.0
O F:HOH404 2.4 45.2 1.0
OD2 F:ASP184 2.4 64.1 1.0
O A:HOH401 2.4 64.1 1.0
OD2 A:ASP182 2.6 81.5 1.0
OE1 F:GLU207 2.9 66.0 1.0
OE2 F:GLU207 3.2 80.8 1.0
CG F:ASP184 3.4 55.7 1.0
CD F:GLU207 3.4 80.5 1.0
CG A:ASP182 3.8 78.4 1.0
CB F:ASP184 3.8 51.1 1.0
O A:HOH435 4.1 64.9 1.0
OE2 F:GLU242 4.2 55.7 1.0
OE1 A:GLU207 4.2 63.6 1.0
O F:HOH417 4.2 63.0 1.0
O F:LYS243 4.4 65.1 1.0
CB A:ASP182 4.4 69.0 1.0
OD1 F:ASP184 4.5 53.2 1.0
OE1 A:GLU208 4.5 39.7 1.0
OD1 A:ASP182 4.8 82.9 1.0
CG F:GLU207 4.9 72.7 1.0
CD A:GLU208 4.9 57.1 1.0
O F:HOH411 5.0 81.5 1.0
CB A:GLU208 5.0 36.5 1.0

Calcium binding site 7 out of 16 in 6im3

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Calcium binding site 7 out of 16 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 Calcium with other atoms in the Ca binding site number 7 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:Ca303

b:66.6
occ:1.00
 O E:HOH406 2.0 44.0 1.0
OE2 B:GLU242 2.5 49.3 1.0
O E:HOH429 2.5 44.0 1.0
O E:HOH404 2.6 57.8 1.0
OE1 E:GLU208 2.7 50.0 1.0
OE1 B:GLU207 3.0 88.2 1.0
CD B:GLU242 3.1 41.0 1.0
OE1 B:GLU242 3.2 46.3 1.0
O E:HOH402 3.6 56.9 1.0
CD B:GLU207 3.9 81.0 1.0
CD E:GLU208 3.9 65.9 1.0
OE1 E:GLU209 4.0 50.8 1.0
O B:HOH403 4.1 36.0 1.0
OH B:TYR186 4.4 45.0 1.0
CG B:GLU242 4.5 39.9 1.0
OE2 E:GLU208 4.6 63.2 1.0
CG B:GLU207 4.6 70.2 1.0
CA B:CA304 4.6 67.0 1.0
OE2 B:GLU207 4.7 76.2 1.0
CA E:GLU208 4.7 41.7 1.0
O E:GLU207 4.7 40.4 1.0
CD E:GLU209 4.8 66.8 1.0
OE2 E:GLU209 4.9 72.5 1.0

Calcium binding site 8 out of 16 in 6im3

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Calcium binding site 8 out of 16 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 Calcium with other atoms in the Ca binding site number 8 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:Ca304

b:67.0
occ:1.00
 OD2 E:ASP182 2.3 63.3 1.0
O E:HOH404 2.4 57.8 1.0
O B:HOH403 2.5 36.0 1.0
OD2 B:ASP184 2.6 54.0 1.0
OE1 B:GLU207 2.8 88.2 1.0
O E:HOH410 2.9 69.5 1.0
OE2 B:GLU207 3.0 76.2 1.0
CD B:GLU207 3.3 81.0 1.0
CG E:ASP182 3.5 61.0 1.0
OE2 E:GLU207 3.6 72.9 1.0
CG B:ASP184 3.7 51.1 1.0
O B:HOH402 3.8 63.0 1.0
CB B:ASP184 4.0 39.3 1.0
OE2 B:GLU242 4.1 49.3 1.0
OD1 E:ASP182 4.3 56.5 1.0
CB E:ASP182 4.4 53.8 1.0
O B:HOH422 4.4 53.0 1.0
OE1 E:GLU208 4.5 50.0 1.0
CA B:CA303 4.6 66.6 1.0
O B:LYS243 4.6 53.7 1.0
O B:HOH429 4.6 62.9 1.0
CA B:CA307 4.7 73.7 1.0
CG B:GLU207 4.8 70.2 1.0
OD1 B:ASP184 4.8 45.5 1.0
CD E:GLU207 4.8 83.9 1.0

Calcium binding site 9 out of 16 in 6im3

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Calcium binding site 9 out of 16 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 Calcium with other atoms in the Ca binding site number 9 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:Ca305

b:46.2
occ:1.00
 O B:HOH404 2.0 67.1 1.0
OD2 E:ASP60 2.3 48.5 1.0
O B:HOH482 2.3 43.2 1.0
O B:GLU209 2.3 35.9 1.0
OE2 B:GLU208 2.4 46.2 1.0
O B:HOH427 2.5 38.7 1.0
CG E:ASP60 3.0 50.0 1.0
OD1 E:ASP60 3.0 54.4 1.0
OE2 B:GLU209 3.1 61.4 1.0
CD B:GLU208 3.4 57.2 1.0
C B:GLU209 3.5 35.2 1.0
O E:HOH401 3.7 54.1 1.0
CG B:GLU208 3.8 45.5 1.0
CD B:GLU209 4.0 66.1 1.0
CA B:MET210 4.2 33.5 1.0
N B:MET210 4.3 36.0 1.0
CG B:GLU209 4.5 50.2 1.0
OE1 B:GLU208 4.5 44.5 1.0
CB E:ASP60 4.5 44.3 1.0
CA B:GLU209 4.6 37.5 1.0
N B:GLU209 4.6 35.0 1.0
OE2 B:GLU211 4.7 63.1 1.0
C B:MET210 4.7 33.5 1.0
O B:HOH496 4.8 51.0 1.0
SD B:MET210 4.9 43.9 1.0
O B:HOH497 5.0 46.6 1.0

Calcium binding site 10 out of 16 in 6im3

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Calcium binding site 10 out of 16 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 Calcium with other atoms in the Ca binding site number 10 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:Ca306

b:51.3
occ:1.00
 OE2 E:GLU208 2.2 63.2 1.0
OD2 B:ASP60 2.4 45.6 1.0
O E:HOH443 2.4 53.3 1.0
O E:HOH437 2.6 45.9 1.0
O E:GLU209 2.6 42.4 1.0
OE2 E:GLU209 2.9 72.5 1.0
OD1 B:ASP60 3.0 41.0 1.0
CG B:ASP60 3.1 40.4 1.0
CD E:GLU208 3.3 65.9 1.0
O E:HOH402 3.4 56.9 1.0
C E:GLU209 3.7 50.1 1.0
CG E:GLU208 3.8 56.8 1.0
CD E:GLU209 3.9 66.8 1.0
OE1 E:GLU208 4.3 50.0 1.0
CG E:GLU209 4.5 58.7 1.0
CA E:MET210 4.5 51.4 1.0
CB B:ASP60 4.6 32.1 1.0
N E:MET210 4.6 45.3 1.0
O E:HOH455 4.6 53.2 1.0
N E:GLU209 4.7 39.3 1.0
CA E:GLU209 4.7 43.3 1.0
NZ A:LYS62 4.8 60.6 1.0
OE1 E:GLU209 4.9 50.8 1.0
OE2 E:GLU211 4.9 81.8 1.0
C E:MET210 5.0 48.8 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: Tue Jul 16 09:31:10 2024

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