Calcium in PDB 5mxx: Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1

The structure of Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1, PDB code: 5mxx was solved by C.Tallant, C.Redondo, J.Batson, H.D.Toop, R.Babaebi-Jadidib, P.Savitsky, J.M.Elkins, J.A.Newman, N.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, D.O.Bates, J.C.Morris, S.Knapp, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.29 / 1.75
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	82.572, 82.572, 133.837, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.5

The structure of Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1 also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1 (pdb code 5mxx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1, PDB code: 5mxx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1


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 Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca714 b:17.0 occ:0.50 OE2 A:GLU617 2.2 22.4 1.0 O A:GLU614 2.5 22.0 1.0 OE1 A:GLU617 2.5 24.1 1.0 CD A:GLU617 2.7 22.4 1.0 CA A:CA715 3.3 20.1 0.5 C A:GLU614 3.6 19.3 1.0 O A:HOH858 4.0 25.7 1.0 CG A:GLU617 4.2 23.3 1.0 CA A:GLU614 4.2 18.6 1.0 N A:LYS615 4.7 18.9 1.0 CA A:LYS615 4.9 18.8 1.0 CB A:GLU614 4.9 20.8 1.0 O A:VAL613 4.9 20.5 1.0 O A:LYS615 5.0 19.8 1.0 O A:HOH980 5.0 31.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1


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 Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca715 b:20.1 occ:0.50 OE2 A:GLU617 2.1 22.4 1.0 O A:HOH858 2.3 25.7 1.0 O A:HOH980 2.4 31.2 1.0 CA A:CA714 3.3 17.0 0.5 CD A:GLU617 3.4 22.4 1.0 CG A:GLU617 4.0 23.3 1.0 OE1 A:GLU617 4.3 24.1 1.0 O A:LYS615 4.4 19.8 1.0 O A:GLU614 4.5 22.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1


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 Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca716 b:17.6 occ:0.50 O A:HOH977 2.2 25.7 1.0 OE1 A:GLU614 2.3 23.3 1.0 OE2 A:GLU614 2.3 23.9 1.0 O A:HOH989 2.5 24.0 1.0 OE2 A:GLU610 2.6 19.7 1.0 CD A:GLU614 2.6 24.2 1.0 CD A:GLU610 3.7 21.0 1.0 CG A:GLU614 4.1 21.9 1.0 CG A:GLU610 4.2 19.7 1.0 O A:HOH1003 4.4 46.9 1.0 C2 A:EDO710 4.5 29.9 1.0 CA A:CA717 4.6 21.3 0.5 C1 A:EDO710 4.7 34.6 1.0 OE1 A:GLU610 4.8 21.6 1.0 O A:HOH831 4.8 31.1 1.0 CB A:GLU614 5.0 20.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1


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 Human Sr Protein Kinase 1 (SRPK1) in Complex with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca717 b:21.3 occ:0.50 O A:HOH992 2.2 26.1 1.0 OE1 A:GLU610 2.5 21.6 1.0 OE2 A:GLU610 2.8 19.7 1.0 CD A:GLU610 3.0 21.0 1.0 O A:HOH893 4.1 21.0 1.0 O A:HOH1011 4.2 43.2 1.0 O A:HOH902 4.5 20.1 1.0 CG A:GLU610 4.5 19.7 1.0 O A:HOH808 4.5 36.8 1.0 CA A:CA716 4.6 17.6 0.5 O A:HOH989 4.7 24.0 1.0

J.Batson, H.D.Toop, C.Redondo, R.Babaei-Jadidi, A.Chaikuad, S.F.Wearmouth, B.Gibbons, C.Allen, C.Tallant, J.Zhang, C.Du, J.C.Hancox, T.Hawtrey, J.Da Rocha, R.Griffith, S.Knapp, D.O.Bates, J.C.Morris. Development of Potent, Selective SRPK1 Inhibitors As Potential Topical Therapeutics For Neovascular Eye Disease. Acs Chem. Biol. V. 12 825 2017.
ISSN: ESSN 1554-8937
PubMed: 28135068
DOI: 10.1021/ACSCHEMBIO.6B01048