Calcium 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:

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 6im0). 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: 6im0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 15 in 6im0

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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:Ca304

b:78.5
occ:1.00
 OD2 C:ASP184 2.4 66.3 1.0
OD2 A:ASP184 2.5 64.5 1.0
OD2 C:ASP182 2.9 78.5 1.0
OD2 A:ASP182 3.1 70.0 1.0
CG C:ASP184 3.6 54.9 1.0
OD1 C:ASP182 3.7 81.8 1.0
CG A:ASP184 3.7 49.9 1.0
CG C:ASP182 3.7 69.3 1.0
OD1 A:ASP182 4.0 62.0 1.0
CG A:ASP182 4.0 60.8 1.0
CB C:ASP184 4.2 47.6 1.0
CB A:ASP184 4.2 47.1 1.0
OD1 C:ASP184 4.6 48.9 1.0
OE2 A:GLU207 4.6 71.3 1.0
OD1 A:ASP184 4.7 48.1 1.0
OE2 C:GLU207 4.8 55.4 1.0

Calcium binding site 2 out of 15 in 6im0

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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:Ca305

b:34.5
occ:1.00
 OD2 C:ASP60 2.2 44.4 1.0
O A:GLU209 2.3 34.2 1.0
OE2 A:GLU208 2.4 35.8 1.0
O C:HOH436 2.5 31.4 1.0
OE2 A:GLU209 2.6 41.9 1.0
CG C:ASP60 3.3 32.9 1.0
C A:GLU209 3.5 32.1 1.0
CD A:GLU208 3.5 33.1 1.0
CD A:GLU209 3.6 37.0 1.0
OD1 C:ASP60 3.8 39.3 1.0
CG A:GLU208 3.9 34.0 1.0
CA A:MET210 4.1 34.9 1.0
N A:MET210 4.2 32.7 1.0
CG A:GLU209 4.2 35.1 1.0
CA A:CA306 4.2 50.4 1.0
CB C:ASP60 4.4 28.4 1.0
OE1 A:GLU209 4.4 37.1 1.0
NZ D:LYS62 4.5 47.6 1.0
CA A:GLU209 4.5 32.2 1.0
N A:GLU209 4.6 28.8 1.0
OE1 A:GLU208 4.6 34.4 1.0
CD D:LYS62 4.7 46.4 1.0
C A:MET210 4.7 35.1 1.0
CE D:LYS62 4.8 47.1 1.0
SD A:MET210 4.9 37.1 1.0
CB A:GLU209 5.0 33.1 1.0

Calcium binding site 3 out of 15 in 6im0

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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


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:Ca306

b:50.4
occ:1.00
 OD1 C:ASP60 2.2 39.3 1.0
OE2 A:GLU208 2.5 35.8 1.0
OE1 A:GLU209 2.5 37.1 1.0
OE1 C:GLU242 2.5 61.3 1.0
OE1 A:GLU208 2.6 34.4 1.0
OE2 A:GLU209 2.6 41.9 1.0
O C:HOH423 2.8 35.6 1.0
CD A:GLU208 2.9 33.1 1.0
CD A:GLU209 2.9 37.0 1.0
CD C:GLU242 3.0 54.2 1.0
OE2 C:GLU242 3.1 58.0 1.0
CG C:ASP60 3.3 32.9 1.0
OD2 C:ASP60 3.6 44.4 1.0
CA A:CA305 4.2 34.5 1.0
CG C:GLU242 4.3 47.1 1.0
CG A:GLU208 4.4 34.0 1.0
CG A:GLU209 4.4 35.1 1.0
O1 C:PG4303 4.5 82.0 1.0
CB C:ASP60 4.6 28.4 1.0
CB C:GLU242 4.7 40.9 1.0
N A:GLU209 4.7 28.8 1.0
O C:HOH419 4.8 32.6 1.0
O A:GLU209 4.9 34.2 1.0
CA C:ASP60 5.0 26.4 1.0

Calcium binding site 4 out of 15 in 6im0

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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


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:Ca307

b:40.5
occ:1.00
 OD2 A:ASP60 2.1 34.5 1.0
OE2 C:GLU208 2.4 43.0 1.0
O C:GLU209 2.5 36.7 1.0
O C:HOH438 2.6 44.5 1.0
OE2 C:GLU209 2.8 36.2 1.0
CG A:ASP60 3.2 30.9 1.0
CD C:GLU208 3.4 37.9 1.0
C C:GLU209 3.6 31.8 1.0
OD1 A:ASP60 3.7 40.7 1.0
CD C:GLU209 3.7 36.9 1.0
CG C:GLU208 3.8 35.0 1.0
CA A:CA308 4.2 44.1 1.0
CA C:MET210 4.3 30.8 1.0
CB A:ASP60 4.4 28.9 1.0
N C:MET210 4.4 29.3 1.0
CG C:GLU209 4.4 37.3 1.0
NZ B:LYS62 4.4 56.8 1.0
OE1 C:GLU209 4.5 36.1 1.0
CD B:LYS62 4.5 48.3 1.0
OE1 C:GLU208 4.5 44.7 1.0
N C:GLU209 4.6 33.0 1.0
CA C:GLU209 4.7 34.7 1.0
CE B:LYS62 4.8 52.3 1.0
O C:HOH435 4.9 22.5 1.0
C C:MET210 4.9 33.0 1.0
SD C:MET210 4.9 34.2 1.0

Calcium binding site 5 out of 15 in 6im0

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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:Ca308

b:44.1
occ:1.00
 OD1 A:ASP60 2.4 40.7 1.0
OE2 C:GLU208 2.5 43.0 1.0
OE1 A:GLU242 2.5 64.5 1.0
OE1 C:GLU209 2.5 36.1 1.0
OE2 C:GLU209 2.6 36.2 1.0
OE1 C:GLU208 2.7 44.7 1.0
CD C:GLU209 2.9 36.9 1.0
CD C:GLU208 2.9 37.9 1.0
CD A:GLU242 3.2 56.2 1.0
O1 A:PG4303 3.4 62.4 1.0
CG A:ASP60 3.4 30.9 1.0
OE2 A:GLU242 3.5 74.7 1.0
OD2 A:ASP60 3.7 34.5 1.0
CA A:CA307 4.2 40.5 1.0
CG C:GLU209 4.4 37.3 1.0
CG C:GLU208 4.4 35.0 1.0
CG A:GLU242 4.5 47.7 1.0
C1 A:PG4303 4.7 58.3 1.0
CB A:GLU242 4.8 43.0 1.0
N C:GLU209 4.8 33.0 1.0
CB A:ASP60 4.8 28.9 1.0
O C:GLU209 4.9 36.7 1.0
CG2 A:ILE58 5.0 27.1 1.0

Calcium binding site 6 out of 15 in 6im0

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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
B:Ca304

b:37.8
occ:1.00
 O B:GLU209 2.3 31.0 1.0
OE2 B:GLU208 2.4 35.0 1.0
OE2 B:GLU209 2.7 41.8 1.0
CD B:GLU208 3.4 33.5 1.0
C B:GLU209 3.5 32.4 1.0
CD B:GLU209 3.6 36.2 1.0
CG B:GLU208 3.8 34.2 1.0
CA B:CA308 4.2 44.8 1.0
CA B:MET210 4.2 34.7 1.0
N B:MET210 4.3 32.9 1.0
CG B:GLU209 4.3 36.0 1.0
OE1 B:GLU209 4.4 36.2 1.0
OE1 B:GLU208 4.5 36.2 1.0
N B:GLU209 4.6 33.3 1.0
CA B:GLU209 4.6 33.5 1.0
C B:MET210 4.8 36.4 1.0
SD B:MET210 4.9 37.8 1.0
O B:HOH438 4.9 25.2 1.0

Calcium binding site 7 out of 15 in 6im0

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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:Ca305

b:41.5
occ:1.00
 OD2 B:ASP60 2.2 36.7 1.0
O B:HOH429 2.6 37.9 1.0
CG B:ASP60 3.2 32.9 1.0
OD1 B:ASP60 3.7 41.5 1.0
CA B:CA307 4.1 44.4 1.0
NZ A:LYS62 4.3 50.4 1.0
CB B:ASP60 4.4 30.4 1.0
CD A:LYS62 4.5 45.1 1.0
CE A:LYS62 4.7 47.0 1.0

Calcium binding site 8 out of 15 in 6im0

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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:Ca306

b:84.5
occ:1.00
 OD2 B:ASP184 2.5 63.5 1.0
OD2 B:ASP182 2.9 65.0 1.0
CG B:ASP184 3.6 48.5 1.0
CG B:ASP182 3.8 61.3 1.0
OD1 B:ASP182 3.8 63.3 1.0
CB B:ASP184 4.1 45.0 1.0
OE2 B:GLU207 4.6 70.8 1.0
OD1 B:ASP184 4.7 50.4 1.0

Calcium binding site 9 out of 15 in 6im0

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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:Ca307

b:44.4
occ:1.00
 OD1 B:ASP60 2.5 41.5 1.0
OE1 B:GLU242 2.6 63.9 1.0
CD B:GLU242 3.3 54.1 1.0
CG B:ASP60 3.4 32.9 1.0
OE2 B:GLU242 3.5 72.5 1.0
OD2 B:ASP60 3.7 36.7 1.0
CA B:CA305 4.1 41.5 1.0
CG B:GLU242 4.6 45.1 1.0
CB B:ASP60 4.8 30.4 1.0
CB B:GLU242 4.9 39.9 1.0

Calcium binding site 10 out of 15 in 6im0

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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:Ca308

b:44.8
occ:1.00
 OE2 B:GLU208 2.5 35.0 1.0
OE1 B:GLU209 2.6 36.2 1.0
OE1 B:GLU208 2.6 36.2 1.0
OE2 B:GLU209 2.6 41.8 1.0
CD B:GLU208 2.9 33.5 1.0
CD B:GLU209 3.0 36.2 1.0
CA B:CA304 4.2 37.8 1.0
CG B:GLU208 4.4 34.2 1.0
CG B:GLU209 4.5 36.0 1.0
N B:GLU209 4.8 33.3 1.0
O B:GLU209 4.9 31.0 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: Sat Dec 12 06:11:24 2020

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