Calcium in PDB 3q5i: Crystal Structure of PBANKA_031420

The structure of Crystal Structure of PBANKA_031420, PDB code: 3q5i was solved by A.K.Wernimont, A.Hutchinson, H.Sullivan, E.Panico, L.Crombet, D.Cossar, A.Hassani, M.Vedadi, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, R.Hui, A.M.Neculai, 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)	50.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.467, 107.138, 54.303, 90.00, 108.21, 90.00
R / Rfree (%)	19.4 / 25

The structure of Crystal Structure of PBANKA_031420 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Crystal Structure of PBANKA_031420 (pdb code 3q5i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of PBANKA_031420, PDB code: 3q5i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of PBANKA_031420


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 PBANKA_031420 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:2.0 occ:1.00 O A:HOH530 2.2 2.8 1.0 OD1 A:ASP384 2.2 4.1 1.0 O A:GLN390 2.3 3.9 1.0 OD1 A:ASP388 2.3 2.1 1.0 OD1 A:ASN386 2.4 5.2 1.0 OE1 A:GLU395 2.5 5.8 1.0 OE2 A:GLU395 2.6 4.7 1.0 CD A:GLU395 2.9 9.3 1.0 CG A:ASP388 3.3 8.5 1.0 CG A:ASN386 3.4 7.0 1.0 CG A:ASP384 3.4 4.2 1.0 C A:GLN390 3.5 4.0 1.0 OD2 A:ASP388 3.7 12.8 1.0 ND2 A:ASN386 3.9 2.5 1.0 N A:GLN390 4.2 2.8 1.0 OD2 A:ASP384 4.2 4.4 1.0 N A:ASP388 4.2 4.8 1.0 CA A:GLN390 4.3 3.6 1.0 CG A:GLU395 4.4 5.0 1.0 CA A:ASP384 4.4 4.6 1.0 CB A:ASP384 4.4 4.8 1.0 N A:LEU391 4.5 3.4 1.0 CB A:ASP388 4.5 4.3 1.0 CA A:LEU391 4.5 3.7 1.0 N A:ASN386 4.5 5.7 1.0 N A:ASP392 4.6 2.7 1.0 O A:HOH563 4.6 15.9 1.0 CB A:ASN386 4.6 4.6 1.0 C A:ASP384 4.6 6.4 1.0 CB A:GLN390 4.7 5.2 1.0 O A:HOH605 4.7 13.7 1.0 N A:GLY387 4.7 5.4 1.0 CA A:ASP388 4.7 3.8 1.0 N A:LYS385 4.8 7.7 1.0 OD2 A:ASP392 4.8 12.7 1.0 N A:GLY389 4.9 2.9 1.0 CG A:ASP392 4.9 6.5 1.0 CA A:ASN386 4.9 5.5 1.0 C A:LEU391 4.9 3.7 1.0 C A:ASP388 5.0 3.2 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of PBANKA_031420


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 PBANKA_031420 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca527 b:29.9 occ:0.80 OE1 A:GLN36 2.2 14.2 1.0 O A:GLU31 2.3 14.3 1.0 O A:TYR34 2.3 8.9 1.0 O A:HOH12 2.7 22.3 1.0 O A:PHE35 2.9 8.7 1.0 CD A:GLN36 3.3 20.1 1.0 C A:GLU31 3.5 15.5 1.0 C A:TYR34 3.5 9.9 1.0 C A:PHE35 3.6 8.3 1.0 CG A:GLN36 4.0 13.6 1.0 N A:GLN36 4.2 7.6 1.0 CG A:GLU31 4.2 18.0 1.0 CB A:PHE35 4.3 8.6 1.0 CA A:PHE35 4.3 8.1 1.0 CA A:GLN36 4.3 8.8 1.0 NE2 A:GLN36 4.3 19.5 1.0 N A:PHE35 4.3 8.5 1.0 CA A:GLU31 4.4 14.9 1.0 N A:ASN32 4.4 15.0 1.0 CA A:ASN32 4.5 15.6 1.0 N A:TYR34 4.5 11.6 1.0 CA A:TYR34 4.6 9.9 1.0 O A:HOH593 4.7 9.4 1.0 CB A:GLN36 4.8 9.8 1.0 CB A:GLU31 4.8 15.3 1.0 C A:ASN32 4.9 15.9 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of PBANKA_031420


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 PBANKA_031420 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca524 b:23.5 occ:1.00 OD1 A:ASP428 2.2 10.0 1.0 OD1 A:ASP430 2.2 5.3 1.0 O A:TYR434 2.3 2.5 1.0 OE2 A:GLU436 2.3 5.3 1.0 OD1 A:ASN432 2.4 7.2 1.0 OE1 A:GLU439 2.5 3.9 1.0 OE2 A:GLU439 2.8 2.0 1.0 CD A:GLU439 3.0 4.5 1.0 CG A:ASN432 3.3 7.4 1.0 CG A:ASP428 3.3 8.4 1.0 CG A:ASP430 3.4 4.1 1.0 CD A:GLU436 3.4 13.0 1.0 C A:TYR434 3.5 2.0 1.0 ND2 A:ASN432 3.8 2.0 1.0 OE1 A:GLU436 3.9 18.3 1.0 OD2 A:ASP430 3.9 5.3 1.0 OD2 A:ASP428 4.0 12.1 1.0 N A:TYR434 4.2 3.9 1.0 N A:ASP430 4.2 3.0 1.0 N A:GLU436 4.2 2.0 1.0 CB A:ASP428 4.3 4.3 1.0 CA A:ASP428 4.3 3.5 1.0 CA A:TYR434 4.3 2.7 1.0 N A:ASN432 4.3 6.3 1.0 N A:ILE435 4.4 2.0 1.0 CA A:ILE435 4.4 2.0 1.0 CB A:ASN432 4.4 5.1 1.0 CG A:GLU439 4.4 2.0 1.0 CB A:ASP430 4.5 3.9 1.0 C A:ASP428 4.5 3.3 1.0 N A:PHE429 4.6 2.7 1.0 N A:LYS431 4.6 5.5 1.0 CG A:GLU436 4.7 8.0 1.0 CA A:ASP430 4.7 4.2 1.0 O A:HOH725 4.7 19.0 1.0 C A:ILE435 4.8 2.0 1.0 CA A:ASN432 4.8 6.1 1.0 CB A:TYR434 4.8 3.1 1.0 N A:GLY433 4.8 6.7 1.0 C A:ASP430 4.8 5.5 1.0 CB A:GLU436 4.9 2.0 1.0 O A:HOH663 5.0 2.4 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of PBANKA_031420


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 PBANKA_031420 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca525 b:29.6 occ:1.00 OD1 A:ASP464 2.2 3.7 1.0 OE2 A:GLU475 2.2 2.3 1.0 O A:LYS470 2.3 2.7 1.0 OD1 A:ASP466 2.3 15.7 1.0 O A:HOH2 2.4 4.6 1.0 OG A:SER468 2.4 13.6 1.0 OE1 A:GLU475 2.7 6.9 1.0 CD A:GLU475 2.8 4.1 1.0 CG A:ASP466 3.3 13.3 1.0 CG A:ASP464 3.4 5.9 1.0 C A:LYS470 3.5 3.3 1.0 CB A:SER468 3.6 10.8 1.0 OD2 A:ASP466 3.6 14.8 1.0 N A:SER468 4.1 9.8 1.0 CA A:ASP464 4.1 5.5 1.0 CB A:ASP464 4.2 5.2 1.0 OD2 A:ASP464 4.3 5.4 1.0 CG A:GLU475 4.3 3.5 1.0 CA A:SER468 4.3 9.7 1.0 N A:LYS470 4.3 4.2 1.0 N A:ILE471 4.4 2.6 1.0 O A:HOH566 4.4 17.1 1.0 C A:ASP464 4.4 7.0 1.0 CA A:ILE471 4.4 2.6 1.0 N A:ASP466 4.5 11.0 1.0 CA A:LYS470 4.5 3.9 1.0 CB A:ASP466 4.5 11.9 1.0 N A:THR465 4.7 7.9 1.0 N A:THR472 4.7 2.7 1.0 N A:GLY469 4.8 7.0 1.0 N A:LYS467 4.8 11.3 1.0 C A:SER468 4.8 8.6 1.0 CA A:ASP466 4.9 11.4 1.0 O A:ASP464 4.9 7.7 1.0 CG2 A:THR472 4.9 3.0 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of PBANKA_031420


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 PBANKA_031420 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca526 b:31.5 occ:1.00 OD1 A:ASN500 2.3 41.5 1.0 OD1 A:ASP498 2.3 41.5 1.0 OD2 A:ASP502 2.3 41.9 1.0 OE2 A:GLU509 2.4 32.3 1.0 O A:HOH3 2.4 5.9 1.0 OE1 A:GLU509 2.5 27.8 1.0 O A:MET504 2.5 27.5 1.0 CD A:GLU509 2.8 30.6 1.0 CG A:ASP502 3.3 40.0 1.0 CG A:ASN500 3.3 43.0 1.0 CG A:ASP498 3.4 43.6 1.0 C A:MET504 3.6 27.6 1.0 OD1 A:ASP502 3.8 41.1 1.0 ND2 A:ASN500 3.9 40.1 1.0 OD2 A:ASP498 4.2 41.9 1.0 N A:ASP502 4.2 38.8 1.0 CA A:ASP498 4.3 45.9 1.0 N A:MET504 4.3 29.9 1.0 CG A:GLU509 4.3 27.7 1.0 CB A:ASP498 4.4 45.7 1.0 CA A:ILE505 4.4 24.7 1.0 N A:ILE505 4.4 26.4 1.0 N A:ASN500 4.4 44.9 1.0 CA A:MET504 4.5 28.7 1.0 CB A:ASN500 4.5 43.1 1.0 CB A:ASP502 4.5 37.3 1.0 N A:ASP506 4.6 25.4 1.0 OD2 A:ASP506 4.6 45.5 1.0 N A:LYS501 4.6 43.0 1.0 O A:HOH557 4.6 37.8 1.0 N A:GLN499 4.7 47.0 1.0 C A:ASP498 4.7 47.7 1.0 CA A:ASP502 4.7 36.6 1.0 CA A:ASN500 4.8 43.7 1.0 C A:ASN500 4.8 44.2 1.0 CB A:MET504 4.9 29.7 1.0 N A:ASN503 4.9 34.3 0.5 C A:ILE505 5.0 25.9 1.0 CD1 A:ILE505 5.0 21.3 1.0 N A:ASN503 5.0 34.4 0.5

Calcium binding site 6 out of 6 in the Crystal Structure of PBANKA_031420


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 PBANKA_031420 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca528 b:29.1 occ:1.00 O2G A:ANP1634 2.2 41.9 0.8 O A:HOH531 2.3 20.1 1.0 O3A A:ANP1634 2.4 45.3 0.6 O A:HOH532 2.4 15.5 1.0 OD1 A:ASN195 2.4 2.0 1.0 OD2 A:ASP211 2.4 14.5 1.0 O1B A:ANP1634 3.3 40.2 0.8 PB A:ANP1634 3.3 44.2 0.8 CG A:ASP211 3.4 8.2 1.0 CG A:ASN195 3.5 2.0 1.0 PG A:ANP1634 3.6 45.2 0.8 PA A:ANP1634 3.6 46.6 0.8 O1A A:ANP1634 3.7 48.5 0.8 CB A:ASP211 3.8 2.0 1.0 ND2 A:ASN195 3.9 2.0 1.0 N3B A:ANP1634 4.0 43.3 0.8 MG A:MG529 4.3 28.6 1.0 OD1 A:ASP211 4.4 13.5 1.0 O2A A:ANP1634 4.5 44.8 0.8 O1G A:ANP1634 4.5 46.4 0.8 O A:GLU194 4.5 2.0 1.0 O5' A:ANP1634 4.6 40.5 0.8 C5' A:ANP1634 4.6 33.6 0.8 O3G A:ANP1634 4.7 45.4 0.8 O2B A:ANP1634 4.7 43.8 0.6 CB A:ASN195 4.8 2.0 1.0 C A:GLU194 5.0 2.0 1.0 CA A:ASN195 5.0 2.0 1.0

A.K.Wernimont, A.Hutchinson, H.Sullivan, E.Panico, L.Crombet, D.Cossar, A.Hassani, M.Vedadi, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, R.Hui, A.M.Neculai, M.Amani. Crystal Structure of CDPK1 From Plasmodium Bergheii, PBANKA_031420 To Be Published.