Calcium in PDB 4b9b: The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa

Enzymatic activity of The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa

All present enzymatic activity of The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa:
2.6.1.18;

Protein crystallography data

The structure of The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa, PDB code: 4b9b was solved by C.Sayer, M.N.Isupov, A.Westlake, J.A.Littlechild, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.58 / 1.64
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.380, 133.160, 161.960, 90.00, 91.75, 90.00
R / Rfree (%) 17.45 / 21.887

Other elements in 4b9b:

The structure of The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa (pdb code 4b9b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa, PDB code: 4b9b:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4b9b

Go back to Calcium Binding Sites List in 4b9b
Calcium binding site 1 out of 4 in the The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca503

b:17.1
occ:1.00
 OD1 E:ASP180 2.1 7.2 1.0
O C:HOH2399 2.1 8.8 1.0
O C:HOH2717 2.1 6.7 1.0
O C:HOH2398 2.1 6.7 1.0
OD1 C:ASP180 2.2 5.7 1.0
O C:HOH2400 2.2 7.9 1.0
CG E:ASP180 3.1 8.4 1.0
CG C:ASP180 3.1 8.9 1.0
OD2 E:ASP180 3.3 9.3 1.0
OD2 C:ASP180 3.4 11.7 1.0
O2 E:GOL504 4.0 12.9 1.0
O2 C:GOL504 4.0 13.7 1.0
O3 C:GOL504 4.2 19.7 1.0
O E:HIS181 4.2 8.1 1.0
O C:HIS181 4.2 5.3 1.0
N E:HIS181 4.2 5.7 1.0
N C:HIS181 4.3 5.5 1.0
O1 E:GOL504 4.3 19.0 1.0
C3 C:GOL504 4.4 17.7 1.0
CB E:ASP180 4.5 9.2 1.0
CB C:ASP180 4.5 7.2 1.0
C1 E:GOL504 4.5 17.4 1.0
O C:HOH2401 4.6 9.1 1.0
O C:HOH2396 4.6 8.0 1.0
CD2 E:LEU211 4.7 14.0 1.0
CD2 C:LEU211 4.7 13.5 0.6
C2 C:GOL504 4.8 28.6 1.0
CA E:ASP180 4.8 6.1 1.0
CA C:ASP180 4.8 6.5 1.0
C2 E:GOL504 4.9 28.1 1.0

Calcium binding site 2 out of 4 in 4b9b

Go back to Calcium Binding Sites List in 4b9b
Calcium binding site 2 out of 4 in the The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca503

b:18.4
occ:1.00
 O D:HOH2298 2.1 7.8 1.0
O D:HOH2300 2.1 9.2 1.0
O F:HOH2251 2.1 8.7 1.0
OD1 D:ASP180 2.1 7.6 1.0
OD1 F:ASP180 2.1 7.5 1.0
O D:HOH2299 2.2 8.9 1.0
CG F:ASP180 3.1 12.8 1.0
CG D:ASP180 3.1 10.9 1.0
OD2 F:ASP180 3.4 13.2 1.0
OD2 D:ASP180 3.4 11.4 1.0
O F:HOH2252 4.2 15.3 1.0
O D:HOH2303 4.2 17.2 1.0
O F:HIS181 4.2 8.1 1.0
N F:HIS181 4.2 8.3 1.0
O D:HIS181 4.2 10.0 1.0
N D:HIS181 4.2 6.6 1.0
O D:HOH2090 4.3 16.1 1.0
O D:HOH2093 4.3 22.3 1.0
CB F:ASP180 4.5 10.7 1.0
O D:HOH2297 4.5 8.7 1.0
CB D:ASP180 4.5 7.9 1.0
CD2 F:LEU211 4.5 7.9 0.5
O D:HOH2301 4.6 9.7 1.0
CD2 D:LEU211 4.7 14.0 1.0
CA F:ASP180 4.8 9.4 1.0
CA D:ASP180 4.9 7.9 1.0

Calcium binding site 3 out of 4 in 4b9b

Go back to Calcium Binding Sites List in 4b9b
Calcium binding site 3 out of 4 in the The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca503

b:20.9
occ:1.00
 OD1 A:ASP180 2.1 8.5 1.0
O A:HOH2346 2.2 6.6 1.0
OD1 G:ASP180 2.2 8.9 1.0
O G:HOH2265 2.2 7.8 1.0
O A:HOH2348 2.2 11.8 1.0
O A:HOH2347 2.2 10.3 1.0
CG A:ASP180 3.1 14.8 1.0
CG G:ASP180 3.2 14.3 1.0
OD2 A:ASP180 3.4 13.4 1.0
OD2 G:ASP180 3.4 15.7 1.0
O3 G:GOL504 4.0 18.3 1.0
O3 A:GOL504 4.1 18.3 1.0
C3 G:GOL504 4.1 38.2 1.0
O A:HIS181 4.2 11.2 1.0
O G:HIS181 4.2 8.5 1.0
N A:HIS181 4.2 7.5 1.0
O G:HOH2532 4.2 20.3 1.0
O A:HOH2654 4.3 18.9 1.0
N G:HIS181 4.3 9.4 1.0
CB A:ASP180 4.5 10.9 1.0
O A:HOH2349 4.5 11.4 1.0
C3 A:GOL504 4.5 43.6 1.0
O A:HOH2345 4.5 9.0 1.0
CB G:ASP180 4.5 11.1 1.0
CD2 A:LEU211 4.7 11.5 0.6
CD2 G:LEU211 4.7 16.6 1.0
CA A:ASP180 4.8 9.8 1.0
CA G:ASP180 4.8 9.5 1.0

Calcium binding site 4 out of 4 in 4b9b

Go back to Calcium Binding Sites List in 4b9b
Calcium binding site 4 out of 4 in the The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of the Omega Aminotransferase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca503

b:19.6
occ:1.00
 OD1 B:ASP180 2.1 8.0 1.0
O B:HOH2275 2.1 8.5 1.0
O B:HOH2274 2.1 7.4 1.0
OD1 H:ASP180 2.2 9.2 1.0
O H:HOH2209 2.2 9.7 1.0
O B:HOH2276 2.2 9.7 1.0
CG B:ASP180 3.1 10.0 1.0
CG H:ASP180 3.1 9.7 1.0
OD2 H:ASP180 3.4 10.6 1.0
OD2 B:ASP180 3.4 15.6 1.0
O1 H:GOL504 3.9 29.6 1.0
O3 B:GOL504 4.1 15.8 1.0
O H:HIS181 4.2 8.7 1.0
N H:HIS181 4.2 8.2 1.0
N B:HIS181 4.2 10.4 1.0
O B:HIS181 4.2 8.8 1.0
C1 H:GOL504 4.2 14.6 1.0
O B:HOH2536 4.3 21.0 1.0
O H:HOH2439 4.4 19.5 1.0
CB B:ASP180 4.5 11.0 1.0
CB H:ASP180 4.5 9.1 1.0
C3 B:GOL504 4.5 37.3 1.0
O B:HOH2273 4.5 8.3 1.0
O B:HOH2277 4.6 12.6 1.0
CD2 H:LEU211 4.7 12.8 0.6
CD2 B:LEU211 4.7 13.0 0.5
CA B:ASP180 4.8 8.4 1.0
CA H:ASP180 4.8 8.6 1.0

Reference:

C.Sayer, M.N.Isupov, A.Westlake, J.A.Littlechild. Structural Studies with Pseudomonas and Chromobacterium [Omega]-Aminotransferases Provide Insights Into Their Differing Substrate Specificity. Acta Crystallogr.,Sect.D V. 69 564 2013.
ISSN: ISSN 0907-4449
PubMed: 23519665
DOI: 10.1107/S0907444912051670
Page generated: Sat Dec 12 04:40:55 2020

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