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Calcium 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:

Zinc (Zn) 6 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

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 6im1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 15 binding sites of Calcium where determined in the Crystal Structure of A Highly Thermostable Carbonic Anhydrase From Persephonella Marina Ex-H1, PDB code: 6im1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 15 in 6im1

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Calcium binding site 1 out of 15 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:Ca302

b:40.4
occ:1.00
 OD2 F:ASP60 2.3 49.2 1.0
O A:HOH503 2.4 43.9 1.0
O A:HOH415 2.4 40.2 1.0
O A:GLU209 2.4 28.8 1.0
OE2 A:GLU208 2.5 46.9 1.0
OE2 A:GLU209 2.7 52.0 1.0
CG F:ASP60 3.2 48.9 1.0
OD1 F:ASP60 3.4 49.2 1.0
CD A:GLU208 3.5 48.9 1.0
C A:GLU209 3.6 34.2 1.0
O A:HOH407 3.6 49.0 1.0
CD A:GLU209 3.7 53.1 1.0
CG A:GLU208 4.1 41.2 1.0
CG A:GLU209 4.2 39.8 1.0
CA A:MET210 4.3 32.4 1.0
N A:MET210 4.4 30.6 1.0
OE2 A:GLU211 4.5 63.0 1.0
OE1 A:GLU208 4.6 35.0 1.0
CB F:ASP60 4.6 36.1 1.0
CA A:GLU209 4.6 31.0 1.0
OE1 A:GLU209 4.6 46.1 1.0
N A:GLU209 4.7 24.8 1.0
C A:MET210 4.7 27.3 1.0
O A:MET210 4.9 27.4 1.0
CE A:LYS144 5.0 57.6 1.0

Calcium binding site 2 out of 15 in 6im1

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Calcium binding site 2 out of 15 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:Ca303

b:66.5
occ:1.00
 O A:HOH408 2.4 56.1 1.0
O F:HOH426 2.5 42.0 1.0
OE2 A:GLU242 2.6 39.3 1.0
OE1 F:GLU208 2.7 36.8 1.0
OE1 A:GLU242 2.9 45.8 1.0
CD A:GLU242 3.0 38.0 1.0
OE1 F:GLU209 3.1 55.5 1.0
O F:HOH405 3.2 48.1 1.0
OE2 A:GLU207 3.4 77.6 1.0
O A:HOH402 3.6 52.5 1.0
CD F:GLU208 3.8 49.3 1.0
CD F:GLU209 4.0 66.6 1.0
OE2 F:GLU209 4.1 71.7 1.0
OE2 F:GLU208 4.2 45.1 1.0
O1 A:PG4305 4.2 69.9 1.0
OH A:TYR186 4.4 37.0 1.0
O A:HOH404 4.5 25.3 1.0
CG A:GLU242 4.5 36.6 1.0
CD A:GLU207 4.6 64.5 1.0
O A:HOH520 4.6 58.8 1.0
C1 A:PG4305 4.7 72.3 1.0
CA F:GLU208 4.8 38.2 1.0
O F:GLU207 4.9 36.1 1.0
N F:GLU209 5.0 38.6 1.0

Calcium binding site 3 out of 15 in 6im1

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Calcium binding site 3 out of 15 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 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:Ca304

b:64.1
occ:1.00
 O F:HOH405 2.3 48.1 1.0
O A:HOH404 2.5 25.3 1.0
OD2 F:ASP182 2.6 82.8 1.0
OE1 A:GLU207 2.6 72.9 1.0
OD2 A:ASP184 2.6 54.6 1.0
O F:HOH417 3.0 67.7 1.0
OE2 A:GLU207 3.0 77.6 1.0
CD A:GLU207 3.1 64.5 1.0
CG A:ASP184 3.6 41.5 1.0
CG F:ASP182 3.7 64.5 1.0
CB A:ASP184 3.9 34.0 1.0
OE2 A:GLU242 4.0 39.3 1.0
OE1 F:GLU207 4.2 78.2 1.0
O A:LYS243 4.4 48.2 1.0
OE1 F:GLU208 4.4 36.8 1.0
O A:HOH482 4.4 52.2 1.0
CB F:ASP182 4.5 44.5 1.0
O A:HOH477 4.6 62.9 1.0
OD1 F:ASP182 4.6 51.6 1.0
CG A:GLU207 4.6 53.6 1.0
OD1 A:ASP184 4.8 42.1 1.0
CA A:CA308 4.8 79.0 1.0

Calcium binding site 4 out of 15 in 6im1

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Calcium binding site 4 out of 15 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 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:41.7
occ:1.00
 O F:HOH401 2.1 72.5 1.0
O F:HOH451 2.3 45.5 1.0
OE2 F:GLU208 2.4 45.1 1.0
OD2 A:ASP60 2.4 42.3 1.0
O F:HOH419 2.4 37.0 1.0
O F:GLU209 2.5 34.8 1.0
OE2 F:GLU209 2.9 71.7 1.0
OD1 A:ASP60 3.0 40.6 1.0
O A:HOH402 3.1 52.5 1.0
CG A:ASP60 3.1 38.1 1.0
CD F:GLU208 3.4 49.3 1.0
C F:GLU209 3.7 37.1 1.0
CD F:GLU209 3.9 66.6 1.0
CG F:GLU208 4.0 49.7 1.0
CA F:MET210 4.3 35.4 1.0
N F:MET210 4.4 35.0 1.0
CG F:GLU209 4.4 55.7 1.0
OE1 F:GLU208 4.5 36.8 1.0
OE2 F:GLU211 4.6 65.3 1.0
CB A:ASP60 4.6 27.8 1.0
N F:GLU209 4.7 38.6 1.0
CA F:GLU209 4.7 35.6 1.0
O F:HOH456 4.8 46.4 1.0
C F:MET210 4.8 31.3 1.0
OE1 F:GLU209 4.8 55.5 1.0

Calcium binding site 5 out of 15 in 6im1

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Calcium binding site 5 out of 15 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:60.1
occ:1.00
 O F:HOH404 2.1 48.6 1.0
OE2 F:GLU242 2.3 45.6 1.0
O A:HOH436 2.5 38.5 1.0
O A:HOH407 2.7 49.0 1.0
OE1 A:GLU208 2.7 35.0 1.0
OE1 F:GLU242 2.9 50.7 1.0
CD F:GLU242 2.9 47.9 1.0
OE1 A:GLU209 3.1 46.1 1.0
OE2 F:GLU207 3.2 80.0 1.0
O A:HOH401 3.3 54.0 1.0
CD A:GLU208 3.8 48.9 1.0
O1 F:PG4302 3.9 63.0 1.0
C1 F:PG4302 4.0 65.8 1.0
CD A:GLU209 4.0 53.1 1.0
O F:HOH403 4.1 38.5 1.0
O A:HOH403 4.1 52.7 1.0
OE2 A:GLU209 4.2 52.0 1.0
OE2 A:GLU208 4.3 46.9 1.0
CG F:GLU242 4.4 41.1 1.0
CD F:GLU207 4.4 70.2 1.0
CA A:GLU208 4.8 30.1 1.0
OH F:TYR186 4.8 45.3 1.0
O A:GLU207 4.9 26.5 1.0
N A:GLU209 5.0 24.8 1.0

Calcium binding site 6 out of 15 in 6im1

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Calcium binding site 6 out of 15 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:79.0
occ:1.00
 O A:HOH401 2.2 54.0 1.0
O F:HOH417 2.4 67.7 1.0
OD2 A:ASP182 2.5 65.9 1.0
OD2 F:ASP184 2.5 65.2 1.0
OE1 F:GLU207 2.7 78.2 1.0
O F:HOH403 2.8 38.5 1.0
OE2 F:GLU207 3.3 80.0 1.0
CD F:GLU207 3.4 70.2 1.0
CG F:ASP184 3.6 52.1 1.0
CG A:ASP182 3.6 61.9 1.0
OE1 A:GLU207 3.8 72.9 1.0
CB F:ASP184 4.0 47.6 1.0
O F:HOH412 4.1 58.5 1.0
O A:HOH482 4.1 52.2 1.0
OE1 A:GLU208 4.3 35.0 1.0
OD1 A:ASP182 4.4 51.6 1.0
OE2 F:GLU242 4.5 45.6 1.0
CB A:ASP182 4.5 44.9 1.0
O F:HOH448 4.6 53.8 1.0
OD1 F:ASP184 4.7 48.9 1.0
O F:LYS243 4.7 64.2 1.0
CA A:CA304 4.8 64.1 1.0
CG F:GLU207 4.8 57.9 1.0
CD A:GLU207 4.9 64.5 1.0
CB A:GLU208 4.9 31.0 1.0

Calcium binding site 7 out of 15 in 6im1

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Calcium binding site 7 out of 15 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:Ca302

b:39.6
occ:1.00
 O B:HOH457 2.2 38.2 1.0
OD2 E:ASP60 2.3 42.5 1.0
O B:GLU209 2.3 31.6 1.0
OE2 B:GLU208 2.4 41.7 1.0
O B:HOH443 2.5 36.2 1.0
OE2 B:GLU209 2.8 49.8 1.0
OD1 E:ASP60 3.0 45.6 1.0
CG E:ASP60 3.0 48.6 1.0
CD B:GLU208 3.5 50.7 1.0
C B:GLU209 3.5 33.7 1.0
O B:HOH403 3.6 44.0 1.0
CD B:GLU209 3.8 60.0 1.0
CG B:GLU208 4.0 44.6 1.0
CA B:MET210 4.2 34.0 1.0
N B:MET210 4.3 32.9 1.0
CG B:GLU209 4.3 43.2 1.0
CB E:ASP60 4.4 39.4 1.0
OE1 B:GLU208 4.5 41.1 1.0
CA B:GLU209 4.6 33.2 1.0
N B:GLU209 4.6 27.9 1.0
OE2 B:GLU211 4.6 55.7 1.0
C B:MET210 4.7 32.2 1.0
OE1 B:GLU209 4.7 42.6 1.0
O B:HOH508 4.8 51.3 1.0
O B:MET210 5.0 35.8 1.0

Calcium binding site 8 out of 15 in 6im1

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Calcium binding site 8 out of 15 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:Ca303

b:54.0
occ:1.00
 O E:HOH402 2.2 66.8 1.0
O B:HOH403 2.3 44.0 1.0
OE1 B:GLU208 2.4 41.1 1.0
OE2 E:GLU242 2.5 47.4 1.0
O B:HOH425 2.6 36.7 1.0
O E:HOH409 2.6 55.4 1.0
OE1 E:GLU242 2.7 47.9 1.0
OE1 B:GLU209 2.8 42.6 1.0
CD E:GLU242 2.9 42.9 1.0
O B:HOH405 3.0 51.2 1.0
CD B:GLU208 3.5 50.7 1.0
CD B:GLU209 3.7 60.0 1.0
OE2 E:GLU207 3.8 87.7 1.0
OE2 B:GLU209 3.8 49.8 1.0
OE2 B:GLU208 3.9 41.7 1.0
O B:HOH401 4.0 48.9 1.0
O5 E:PG4302 4.3 64.6 1.0
C8 E:PG4302 4.4 68.2 1.0
CG E:GLU242 4.4 42.1 1.0
O E:HOH403 4.5 36.9 1.0
CA B:GLU208 4.6 29.2 1.0
N B:GLU209 4.7 27.9 1.0
CG B:GLU208 4.7 44.6 1.0
O B:GLU207 4.8 31.6 1.0
OH E:TYR186 4.9 42.5 1.0
CB B:GLU208 4.9 33.4 1.0
CD E:GLU207 5.0 85.6 1.0

Calcium binding site 9 out of 15 in 6im1

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Calcium binding site 9 out of 15 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:Ca304

b:60.0
occ:1.00
 O E:HOH425 2.5 44.9 1.0
O B:HOH408 2.5 55.0 1.0
OE1 E:GLU208 2.6 40.0 1.0
OE2 B:GLU242 2.6 40.6 1.0
OE1 B:GLU242 2.8 40.5 1.0
O E:HOH401 3.0 51.0 1.0
CD B:GLU242 3.0 34.5 1.0
O E:HOH404 3.0 54.4 1.0
OE1 E:GLU209 3.1 46.9 1.0
OE2 B:GLU207 3.6 92.0 1.0
CD E:GLU208 3.7 61.6 1.0
CD E:GLU209 4.0 65.6 1.0
OE2 E:GLU208 4.2 53.9 1.0
OE2 E:GLU209 4.2 80.5 1.0
O1 B:PG4306 4.3 72.1 1.0
CG B:GLU242 4.5 37.1 1.0
O B:HOH407 4.6 34.7 1.0
OH B:TYR186 4.6 35.0 1.0
CA E:GLU208 4.7 36.2 1.0
C1 B:PG4306 4.8 66.4 1.0
CD B:GLU207 4.8 74.9 1.0
O E:GLU207 4.9 36.1 1.0
N E:GLU209 4.9 34.9 1.0
CG E:GLU208 4.9 50.8 1.0

Calcium binding site 10 out of 15 in 6im1

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Calcium binding site 10 out of 15 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:Ca305

b:65.7
occ:1.00
 OD2 E:ASP182 2.3 67.5 1.0
OE1 B:GLU207 2.6 68.8 1.0
O E:HOH404 2.6 54.4 1.0
O B:HOH407 2.6 34.7 1.0
OD2 B:ASP184 2.7 49.4 1.0
O E:HOH417 3.0 62.8 1.0
OE2 B:GLU207 3.2 92.0 1.0
CD B:GLU207 3.2 74.9 1.0
CG E:ASP182 3.5 56.4 1.0
OE1 E:GLU207 3.5 95.9 1.0
O B:HOH404 3.6 65.3 1.0
CG B:ASP184 3.8 47.6 1.0
CB B:ASP184 4.1 37.1 1.0
OD1 E:ASP182 4.2 48.8 1.0
OE2 B:GLU242 4.2 40.6 1.0
O B:HOH409 4.2 45.9 1.0
CA B:CA308 4.4 78.2 1.0
CB E:ASP182 4.5 48.0 1.0
O B:LYS243 4.6 50.9 1.0
OE1 E:GLU208 4.7 40.0 1.0
CD E:GLU207 4.7 85.6 1.0
CG B:GLU207 4.7 61.1 1.0
O B:HOH460 4.8 58.8 1.0
OD1 B:ASP184 4.9 41.5 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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