Calcium in PDB 4hhr: Crystal Structure of Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana)

The structure of Crystal Structure of Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana), PDB code: 4hhr was solved by C.C.Goulah, G.Zhu, M.Koszelak-Rosenblum, M.G.Malkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.78 / 1.51
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	101.935, 101.935, 137.510, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 18.2

The structure of Crystal Structure of Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana) also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Calcium atom in the Crystal Structure of Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana) (pdb code 4hhr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana), PDB code: 4hhr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana)


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 Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:12.1 occ:1.00 OD1 A:ASP164 2.2 13.3 1.0 O A:THR216 2.3 12.3 1.0 OD1 A:ASP220 2.4 12.1 1.0 O A:ASP164 2.4 13.2 1.0 OG A:SER222 2.4 11.9 1.0 O A:TRP218 2.5 11.9 1.0 OG1 A:THR216 2.5 13.1 1.0 C A:THR216 3.3 12.3 1.0 CG A:ASP220 3.4 13.4 1.0 C A:ASP164 3.4 12.2 1.0 CG A:ASP164 3.5 12.5 1.0 CB A:SER222 3.5 11.5 1.0 CB A:THR216 3.6 12.2 1.0 C A:TRP218 3.7 11.5 1.0 OD2 A:ASP220 3.7 14.2 1.0 CA A:THR216 3.9 12.2 1.0 CA A:ASP164 4.0 9.7 1.0 N A:THR216 4.0 12.6 1.0 N A:ASP220 4.1 12.9 1.0 N A:SER222 4.1 10.6 1.0 CB A:ASP164 4.3 9.7 1.0 N A:TRP218 4.3 12.1 1.0 N A:TRP165 4.4 10.7 1.0 OD2 A:ASP164 4.4 12.8 1.0 N A:PRO217 4.4 12.8 1.0 C A:PRO217 4.4 11.5 1.0 CA A:SER222 4.4 10.9 1.0 O A:HOH810 4.5 12.0 1.0 CA A:TRP218 4.5 12.1 1.0 CB A:ASP220 4.6 11.3 1.0 CA A:TRP165 4.6 11.0 1.0 N A:TRP219 4.7 11.3 1.0 CA A:PRO217 4.7 11.7 1.0 CA A:ASP220 4.8 12.5 1.0 N A:SER221 4.8 11.1 1.0 CA A:TRP219 4.8 12.0 1.0 CG2 A:THR216 4.8 14.4 1.0 O A:PRO217 4.9 12.0 1.0 C A:ARG215 4.9 14.2 1.0 C A:ASP220 4.9 11.7 1.0 C A:TRP219 5.0 12.3 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana)


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 Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:24.2 occ:0.50 O A:HOH1050 2.3 19.9 1.0 OE1 A:GLU521 2.3 23.1 1.0 OE1 A:GLU518 2.4 32.9 1.0 CD A:GLU518 3.5 33.3 1.0 CD A:GLU521 3.5 24.8 1.0 OE2 A:GLU518 3.9 35.9 1.0 O A:HOH1041 4.0 22.3 1.0 CB A:GLU521 4.1 18.2 1.0 O A:HOH1422 4.2 43.0 1.0 OE2 A:GLU521 4.3 24.2 1.0 CG A:GLU521 4.4 22.0 1.0 CG A:GLU518 4.7 29.6 1.0 CB A:GLU518 4.9 27.7 1.0 CA A:GLU518 4.9 23.6 1.0 O A:GLU518 4.9 23.8 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana)


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 Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:33.5 occ:0.70 O A:HOH1068 2.0 23.8 1.0 O A:HOH1334 2.2 34.0 1.0 O A:HOH1381 2.3 45.2 1.0 O A:HOH1576 2.6 43.0 1.0 OD1 A:ASP257 4.1 34.9 1.0 OD2 A:ASP257 4.1 41.0 1.0 OE2 A:GLU256 4.3 53.6 1.0 CG A:ASP257 4.6 31.4 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana)


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 Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:30.2 occ:0.70 OD2 A:ASP294 2.4 30.9 1.0 OD2 A:ASP296 2.5 28.4 1.0 O A:HOH1162 2.7 37.3 1.0 CG A:ASP294 3.2 37.8 1.0 O A:HOH1359 3.3 17.7 1.0 CG A:ASP296 3.5 26.5 1.0 OD1 A:ASP294 3.8 38.8 1.0 CB A:ASP296 3.9 26.6 1.0 CB A:ASP294 4.2 36.5 1.0 CA A:ASP294 4.3 37.5 1.0 O A:HOH1397 4.3 32.0 1.0 N A:ASP296 4.4 30.1 1.0 N A:ASP295 4.5 35.8 1.0 O A:HOH1505 4.5 38.6 1.0 OD2 A:ASP295 4.5 44.6 1.0 C A:ASP294 4.7 36.2 1.0 OD1 A:ASP296 4.7 32.1 1.0 CA A:ASP296 4.8 29.0 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana)


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 Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:39.6 occ:0.70 O A:HOH1714 2.5 46.3 1.0 O A:THR592 2.6 17.6 1.0 O A:HOH989 3.1 23.2 1.0 O A:HOH1026 3.3 28.7 1.0 O A:HOH1366 3.5 39.7 1.0 C A:THR592 3.7 15.7 1.0 CB A:THR592 3.9 17.2 1.0 CA A:THR592 4.0 16.5 1.0 O A:HOH1164 4.2 26.2 1.0 O A:HOH1715 4.5 31.7 1.0 O A:HOH1406 4.6 51.5 1.0 CG2 A:THR592 4.6 20.4 1.0 O A:HOH1202 4.7 29.5 1.0 OD2 A:ASP598 4.7 17.2 1.0 OG1 A:THR592 4.9 18.1 1.0 N A:THR593 4.9 14.7 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana)


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 Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca708 b:30.2 occ:0.70 OD2 A:ASP622 2.2 25.2 1.0 O A:HOH901 2.2 14.7 1.0 O A:HOH1365 2.3 39.6 1.0 O A:HOH1008 2.4 24.2 1.0 O A:HOH1420 2.4 38.7 1.0 O A:HOH1171 2.6 30.9 1.0 O A:HOH962 2.7 20.8 1.0 CG A:ASP622 3.4 22.2 1.0 OD1 A:ASP622 4.0 21.8 1.0 O A:HOH1695 4.1 47.0 1.0 O A:HOH1641 4.3 44.4 1.0 CB A:SER410 4.3 20.6 1.0 O A:LEU411 4.3 20.4 1.0 O A:HOH949 4.4 19.3 1.0 CB A:ASP622 4.5 18.1 1.0 ND1 A:HIS445 4.6 17.9 1.0 CA A:SER410 4.7 18.6 1.0 N A:LEU411 4.8 19.1 1.0 O A:HIS445 4.9 15.6 1.0 NZ A:LYS148 4.9 35.2 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana)


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 Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca709 b:43.2 occ:0.50 O A:HOH1342 2.5 37.5 1.0 O A:HOH1378 2.5 33.3 0.5 OD1 A:ASP403 3.1 45.5 1.0 OD2 A:ASP403 3.4 42.9 1.0 CG A:ASP403 3.5 38.5 1.0 O A:HOH1387 3.9 28.1 0.5 O A:HOH1294 4.1 38.7 1.0 CG A:PRO412 4.3 23.2 1.0 OD2 A:ASP400 4.6 31.9 1.0 O A:HOH1318 4.7 29.5 1.0 CB A:ASP403 4.8 28.0 1.0 O A:HOH1190 4.8 41.5 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana)


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 Fatty Acid Alpha-Dioxygenase (Arabidopsis Thaliana) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca710 b:47.9 occ:0.70 O A:HOH1520 2.2 37.0 1.0 O A:HOH1418 2.3 53.0 1.0 O A:HOH1223 2.3 30.3 1.0 OD1 A:ASP606 2.7 28.4 1.0 O A:HOH1502 3.3 39.3 1.0 O A:HOH1405 3.3 38.0 1.0 CG A:ASP606 3.9 27.1 1.0 OD2 A:ASP609 4.3 30.8 1.0 O A:PRO605 4.4 19.4 1.0 O A:HOH1522 4.5 45.3 1.0 OD2 A:ASP606 4.7 39.3 1.0 O A:HOH1656 4.8 36.1 1.0 CB A:ASP606 4.9 21.3 1.0 C A:PRO605 4.9 18.0 1.0 CA A:ASP606 4.9 20.1 1.0

C.C.Goulah, G.Zhu, M.Koszelak-Rosenblum, M.G.Malkowski. The Crystal Structure of Alpha-Dioxygenase Provides Insight Into Diversity in the Cyclooxygenase-Peroxidase Superfamily. Biochemistry V. 52 1364 2013.
ISSN: ISSN 0006-2960
PubMed: 23373518
DOI: 10.1021/BI400013K