Atomistry » Calcium » PDB 6im1-6j42 » 6im3
Atomistry »
  Calcium »
    PDB 6im1-6j42 »
      6im3 »

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

Go back to Calcium Binding Sites List in 6im3
Calcium binding site 1 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 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

Go back to Calcium Binding Sites List in 6im3
Calcium binding site 2 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 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

Go back to Calcium Binding Sites List in 6im3
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

Go back to Calcium Binding Sites List in 6im3
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

Go back to Calcium Binding Sites List in 6im3
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

Go back to Calcium Binding Sites List in 6im3
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

Go back to Calcium Binding Sites List in 6im3
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

Go back to Calcium Binding Sites List in 6im3
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

Go back to Calcium Binding Sites List in 6im3
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

Go back to Calcium Binding Sites List in 6im3
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy