Calcium in PDB 3l19: Crystal Structure of Calcium Binding Domain of CPCDPK3, CGD5_820

The structure of Crystal Structure of Calcium Binding Domain of CPCDPK3, CGD5_820, PDB code: 3l19 was solved by W.Qiu, A.Hutchinson, A.Wernimont, J.R.Walker, H.Sullivan, Y.-H.Lin, F.Mackenzie, I.Kozieradzki, D.Cossar, M.Schapira, G.Senisterra, M.Vedadi, C.H.Arrowsmith, C.Bountra, J.Weigelt, A.M.Edwards, A.Bochkarev, R.Hui, M.Amani, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.35 / 2.14
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.570, 64.187, 72.807, 90.00, 97.86, 90.00
R / Rfree (%)	21.5 / 25.7

The binding sites of Calcium atom in the Crystal Structure of Calcium Binding Domain of CPCDPK3, CGD5_820 (pdb code 3l19). 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 Calcium Binding Domain of CPCDPK3, CGD5_820, PDB code: 3l19:
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 Calcium Binding Domain of CPCDPK3, CGD5_820


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 Calcium Binding Domain of CPCDPK3, CGD5_820 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:41.4 occ:1.00 OD1 A:ASP423 2.1 44.4 1.0 OD1 A:ASP425 2.2 47.7 1.0 O A:TYR429 2.3 43.0 1.0 OE2 A:GLU434 2.4 33.0 1.0 OD1 A:ASN427 2.5 49.7 1.0 OE1 A:GLU434 2.6 38.6 1.0 CD A:GLU434 2.9 44.8 1.0 CG A:ASP423 3.3 47.2 1.0 CG A:ASP425 3.3 48.6 1.0 CG A:ASN427 3.5 53.6 1.0 C A:TYR429 3.5 44.4 1.0 OD2 A:ASP425 3.8 53.8 1.0 OD2 A:ASP423 4.0 51.8 1.0 ND2 A:ASN427 4.0 38.4 1.0 CB A:ASP423 4.2 40.2 1.0 CA A:ASP423 4.2 37.1 1.0 N A:TYR429 4.3 45.7 1.0 N A:ASN427 4.3 47.5 1.0 N A:ASP425 4.4 40.1 1.0 CG A:GLU434 4.4 35.8 1.0 CA A:TYR429 4.4 45.3 1.0 N A:ILE430 4.4 39.0 1.0 CA A:ILE430 4.5 36.2 1.0 C A:ASP423 4.5 42.0 1.0 N A:ASP431 4.5 34.7 1.0 CB A:ASP425 4.6 42.1 1.0 N A:PHE424 4.6 39.2 1.0 CB A:ASN427 4.6 44.6 1.0 N A:ARG426 4.7 46.6 1.0 CB A:TYR429 4.8 48.6 1.0 OD2 A:ASP431 4.8 53.0 1.0 CA A:ASP425 4.8 41.5 1.0 O A:HOH44 4.9 53.7 1.0 C A:ASP425 4.9 49.6 1.0 CA A:ASN427 4.9 47.5 1.0 N A:GLY428 5.0 47.4 1.0 C A:ILE430 5.0 38.9 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Calcium Binding Domain of CPCDPK3, CGD5_820


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 Calcium Binding Domain of CPCDPK3, CGD5_820 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:56.1 occ:1.00 OD1 A:ASP459 2.2 53.1 1.0 OE2 A:GLU470 2.3 66.3 1.0 OE1 A:GLU470 2.3 64.1 1.0 OD1 A:ASN463 2.4 62.0 1.0 OD2 A:ASP461 2.4 79.0 1.0 O A:LYS465 2.4 53.5 1.0 CD A:GLU470 2.6 64.9 1.0 O A:HOH146 2.7 70.3 1.0 CG A:ASP461 3.2 76.8 1.0 CG A:ASN463 3.3 71.8 1.0 CG A:ASP459 3.5 53.5 1.0 C A:LYS465 3.6 52.1 1.0 OD1 A:ASP461 3.6 80.2 1.0 ND2 A:ASN463 3.9 61.0 1.0 CA A:ASP459 4.1 44.3 1.0 CG A:GLU470 4.1 65.7 1.0 N A:ASN463 4.2 58.0 1.0 CB A:ASP459 4.2 45.3 1.0 N A:ASP461 4.3 60.6 1.0 C A:ASP459 4.3 52.4 1.0 N A:LYS465 4.4 49.9 1.0 OD2 A:ASP459 4.4 57.1 1.0 CB A:ASP461 4.5 66.8 1.0 CB A:ASN463 4.5 58.1 1.0 OG A:SER467 4.5 54.6 1.0 CA A:ILE466 4.5 43.0 1.0 N A:ILE466 4.5 45.1 1.0 N A:GLN460 4.5 52.4 1.0 CA A:LYS465 4.5 48.9 1.0 N A:GLY462 4.6 59.9 1.0 N A:SER467 4.7 47.2 1.0 CA A:ASP461 4.8 62.9 1.0 CA A:ASN463 4.8 58.4 1.0 CG A:LYS465 4.8 72.6 1.0 C A:ASP461 4.9 66.5 1.0 O A:ASP459 4.9 52.5 1.0 N A:GLY464 5.0 55.3 1.0 CB A:GLU470 5.0 61.3 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Calcium Binding Domain of CPCDPK3, CGD5_820


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 Calcium Binding Domain of CPCDPK3, CGD5_820 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3 b:58.9 occ:1.00 OD2 A:ASP493 2.1 62.7 1.0 O A:HOH98 2.2 49.5 1.0 O A:ASP499 2.3 59.0 1.0 OE1 A:GLU504 2.4 52.8 1.0 OE2 A:GLU504 2.6 68.9 1.0 OD1 A:ASN495 2.6 64.3 1.0 OD1 A:ASP497 2.7 70.3 1.0 CD A:GLU504 2.8 66.5 1.0 CG A:ASP493 3.3 58.9 1.0 CG A:ASP497 3.4 73.2 1.0 C A:ASP499 3.5 58.1 1.0 CG A:ASN495 3.6 74.0 1.0 OD2 A:ASP497 3.6 79.8 1.0 CA A:ASP493 4.0 57.3 1.0 ND2 A:ASN495 4.0 61.4 1.0 CB A:ASP493 4.1 58.9 1.0 N A:ASP499 4.2 57.9 1.0 OD1 A:ASP493 4.2 57.9 1.0 N A:ASP497 4.3 64.6 1.0 CG A:GLU504 4.3 54.2 1.0 N A:VAL500 4.4 50.2 1.0 OD2 A:ASP501 4.4 75.7 1.0 CA A:ASP499 4.4 56.7 1.0 CA A:VAL500 4.4 48.2 1.0 C A:ASP493 4.4 62.7 1.0 CB A:ASP497 4.6 66.6 1.0 N A:ASP501 4.6 52.0 1.0 N A:ASN495 4.6 63.2 1.0 N A:ASN496 4.7 66.1 1.0 N A:SER494 4.7 59.5 1.0 CB A:ASN495 4.8 64.8 1.0 CG A:ASP501 4.8 66.8 1.0 CA A:ASP497 4.8 64.7 1.0 CB A:ASP499 4.9 60.7 1.0 N A:GLY498 5.0 58.6 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Calcium Binding Domain of CPCDPK3, CGD5_820


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 Calcium Binding Domain of CPCDPK3, CGD5_820 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca8 b:45.9 occ:1.00 OD1 A:ASP379 2.1 45.1 1.0 O A:HOH87 2.2 49.4 1.0 OD2 A:ASP383 2.2 71.2 1.0 OD1 A:ASN381 2.3 64.0 1.0 OE2 A:GLU390 2.3 41.3 1.0 O A:GLN385 2.4 47.4 1.0 OE1 A:GLU390 2.7 56.8 1.0 CD A:GLU390 2.9 54.5 1.0 CG A:ASP383 3.3 67.3 1.0 CG A:ASN381 3.3 74.1 1.0 CG A:ASP379 3.3 44.4 1.0 C A:GLN385 3.6 47.6 1.0 ND2 A:ASN381 3.6 66.0 1.0 OD1 A:ASP383 3.8 69.6 1.0 OD2 A:ASP379 4.1 44.3 1.0 N A:ASP383 4.2 54.7 1.0 N A:GLN385 4.2 47.8 1.0 CA A:ASP379 4.2 45.2 1.0 CB A:ASP379 4.3 44.9 1.0 CG A:GLU390 4.4 47.5 1.0 CB A:ASP383 4.4 57.7 1.0 CA A:GLN385 4.4 47.6 1.0 N A:LEU386 4.5 40.3 1.0 CA A:LEU386 4.6 39.1 1.0 N A:ASN381 4.6 57.3 1.0 CG A:GLN385 4.6 70.6 1.0 CB A:ASN381 4.6 57.9 1.0 C A:ASP379 4.6 52.9 1.0 CA A:ASP383 4.7 54.7 1.0 N A:GLY382 4.7 55.0 1.0 OD2 A:ASP387 4.7 74.8 1.0 N A:ASP387 4.7 44.4 1.0 N A:LYS380 4.8 51.5 1.0 N A:GLY384 4.9 51.1 1.0 CA A:ASN381 4.9 57.5 1.0 C A:ASP383 5.0 57.8 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Calcium Binding Domain of CPCDPK3, CGD5_820


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 Calcium Binding Domain of CPCDPK3, CGD5_820 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4 b:38.3 occ:1.00 OD1 B:ASP423 2.2 38.7 1.0 OD1 B:ASP425 2.3 49.1 1.0 O B:TYR429 2.3 38.3 1.0 OD1 B:ASN427 2.4 32.6 1.0 OE2 B:GLU434 2.5 34.6 1.0 OE1 B:GLU434 2.6 30.9 1.0 CD B:GLU434 2.9 40.1 1.0 CG B:ASP423 3.3 42.4 1.0 CG B:ASP425 3.3 49.6 1.0 CG B:ASN427 3.4 49.3 1.0 C B:TYR429 3.5 41.2 1.0 OD2 B:ASP425 3.8 47.3 1.0 ND2 B:ASN427 3.9 40.2 1.0 OD2 B:ASP423 4.1 45.3 1.0 N B:TYR429 4.2 39.8 1.0 CB B:ASP423 4.2 47.6 1.0 CA B:ASP423 4.3 45.8 1.0 N B:ASN427 4.3 49.9 1.0 CA B:TYR429 4.4 38.9 1.0 CG B:GLU434 4.4 23.9 1.0 N B:ILE430 4.4 36.3 1.0 N B:ASP425 4.4 47.3 1.0 N B:ASP431 4.5 29.6 1.0 CA B:ILE430 4.5 32.5 1.0 CB B:ASN427 4.6 43.9 1.0 C B:ASP423 4.6 53.2 1.0 CB B:ASP425 4.6 48.4 1.0 N B:PHE424 4.6 47.5 1.0 CB B:TYR429 4.7 40.2 1.0 OD2 B:ASP431 4.7 51.5 1.0 N B:ARG426 4.7 50.6 1.0 CA B:ASN427 4.9 49.6 1.0 CA B:ASP425 4.9 47.6 1.0 O B:HOH13 4.9 41.0 1.0 C B:ASP425 4.9 53.4 1.0 N B:GLY428 5.0 47.9 1.0 CG B:ASP431 5.0 42.4 1.0 C B:ILE430 5.0 33.6 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Calcium Binding Domain of CPCDPK3, CGD5_820


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 Calcium Binding Domain of CPCDPK3, CGD5_820 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5 b:41.4 occ:1.00 O B:HOH59 2.2 45.0 1.0 OE2 B:GLU390 2.2 38.1 1.0 OD1 B:ASP379 2.3 40.6 1.0 OD2 B:ASP383 2.3 65.2 1.0 O B:GLN385 2.3 37.2 1.0 OD1 B:ASN381 2.4 44.3 1.0 OE1 B:GLU390 2.7 61.4 1.0 CD B:GLU390 2.8 46.4 1.0 CG B:ASP383 3.3 57.9 1.0 CG B:ASN381 3.3 56.6 1.0 CG B:ASP379 3.5 42.0 1.0 C B:GLN385 3.5 37.8 1.0 ND2 B:ASN381 3.6 41.9 1.0 OD1 B:ASP383 3.8 58.4 1.0 CA B:ASP379 4.2 37.0 1.0 N B:GLN385 4.2 37.9 1.0 CG B:GLU390 4.3 45.1 1.0 CB B:ASP379 4.3 37.2 1.0 N B:ASP383 4.3 47.4 1.0 OD2 B:ASP379 4.3 43.6 1.0 N B:LEU386 4.4 33.9 1.0 CB B:ASP383 4.4 47.7 1.0 CA B:GLN385 4.4 36.3 1.0 CA B:LEU386 4.5 34.7 1.0 C B:ASP379 4.6 44.7 1.0 CG B:GLN385 4.6 50.7 1.0 OD2 B:ASP387 4.6 69.6 1.0 N B:ASP387 4.6 39.5 1.0 N B:ASN381 4.7 50.2 1.0 CB B:ASN381 4.7 49.8 1.0 CA B:ASP383 4.7 45.4 1.0 N B:GLY382 4.8 50.2 1.0 N B:LYS380 4.8 44.0 1.0 N B:GLY384 4.9 41.3 1.0 CG B:ASP387 5.0 59.6 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Calcium Binding Domain of CPCDPK3, CGD5_820


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 Calcium Binding Domain of CPCDPK3, CGD5_820 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca6 b:46.1 occ:1.00 OE2 B:GLU470 2.3 42.3 1.0 OD2 B:ASP461 2.3 56.4 1.0 OE1 B:GLU470 2.3 52.3 1.0 OD1 B:ASN463 2.3 53.5 1.0 OD1 B:ASP459 2.4 46.1 1.0 O B:LYS465 2.4 48.1 1.0 O B:HOH64 2.5 40.8 1.0 CD B:GLU470 2.6 54.2 1.0 CG B:ASP461 3.2 60.1 1.0 CG B:ASN463 3.3 68.4 1.0 OD1 B:ASP461 3.6 64.6 1.0 CG B:ASP459 3.6 45.9 1.0 C B:LYS465 3.6 46.7 1.0 ND2 B:ASN463 3.8 58.4 1.0 CG B:GLU470 4.1 55.2 1.0 CA B:ASP459 4.2 38.8 1.0 N B:ASN463 4.3 43.8 1.0 N B:ASP461 4.3 48.4 1.0 CB B:ASP459 4.4 40.1 1.0 N B:LYS465 4.4 41.5 1.0 C B:ASP459 4.4 42.4 1.0 CB B:ASN463 4.4 44.4 1.0 CB B:ASP461 4.4 51.7 1.0 OD2 B:ASP459 4.5 52.4 1.0 OG B:SER467 4.5 51.8 1.0 CA B:ILE466 4.5 38.3 1.0 CA B:LYS465 4.5 42.2 1.0 N B:ILE466 4.5 40.7 1.0 N B:GLN460 4.6 41.0 1.0 N B:GLY462 4.6 45.3 1.0 N B:SER467 4.7 40.3 1.0 CA B:ASP461 4.8 49.1 1.0 CG B:LYS465 4.8 76.1 1.0 CA B:ASN463 4.8 44.2 1.0 C B:ASP461 4.9 51.8 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Calcium Binding Domain of CPCDPK3, CGD5_820


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 Calcium Binding Domain of CPCDPK3, CGD5_820 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca7 b:48.6 occ:1.00 O B:HOH58 2.0 35.2 1.0 OD1 B:ASP493 2.2 67.8 1.0 OD1 B:ASN495 2.3 51.3 1.0 O B:ASP499 2.4 52.1 1.0 OE2 B:GLU504 2.5 60.8 1.0 OE1 B:GLU504 2.6 45.1 1.0 OD1 B:ASP497 2.6 69.0 1.0 CD B:GLU504 2.9 63.5 1.0 CG B:ASP497 3.3 70.5 1.0 CG B:ASP493 3.4 68.0 1.0 CG B:ASN495 3.4 68.3 1.0 C B:ASP499 3.6 50.9 1.0 OD2 B:ASP497 3.7 76.4 1.0 ND2 B:ASN495 4.0 56.7 1.0 N B:ASP497 4.1 60.1 1.0 CA B:ASP493 4.2 62.3 1.0 CB B:ASP493 4.3 63.7 1.0 N B:ASP499 4.3 50.3 1.0 OD2 B:ASP493 4.3 73.3 1.0 N B:ASN495 4.4 65.5 1.0 OD2 B:ASP501 4.4 68.2 1.0 CG B:GLU504 4.4 49.0 1.0 CB B:ASP497 4.4 60.5 1.0 CA B:ASP499 4.4 48.0 1.0 C B:ASP493 4.5 67.8 1.0 N B:VAL500 4.5 45.0 1.0 N B:SER494 4.5 63.9 1.0 N B:ASN496 4.6 65.4 1.0 CA B:ASP497 4.6 58.6 1.0 CA B:VAL500 4.6 42.7 1.0 CB B:ASN495 4.7 63.5 1.0 C B:ASN495 4.7 70.0 1.0 N B:ASP501 4.7 39.0 1.0 N B:GLY498 4.8 53.3 1.0 CA B:ASN495 4.8 66.2 1.0 CB B:ASP499 4.9 50.4 1.0 CG B:ASP501 4.9 54.7 1.0 C B:ASP497 4.9 58.9 1.0

W.Qiu, A.Hutchinson, A.Wernimont, J.R.Walker, H.Sullivan, Y.-H.Lin, F.Mackenzie, I.Kozieradzki, D.Cossar, M.Schapira, G.Senisterra, M.Vedadi, C.H.Arrowsmith, C.Bountra, J.Weigelt, A.M.Edwards, A.Bochkarev, R.Hui, M.Amani. Crystal Structure of Calcium Binding Domain of CPCDPK3, CGD5_820 To Be Published.