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Calcium in PDB 3ncg: Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Nm-PP1

Enzymatic activity of Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Nm-PP1

All present enzymatic activity of Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Nm-PP1:
2.7.11.17;

Protein crystallography data

The structure of Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Nm-PP1, PDB code: 3ncg was solved by E.T.Larson, E.A.Merritt, Medical Structural Genomics Of Pathogenicprotozoa (Msgpp), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.58 / 2.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.991, 55.968, 81.972, 90.00, 104.78, 90.00
R / Rfree (%) 25 / 30.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Nm-PP1 (pdb code 3ncg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Nm-PP1, PDB code: 3ncg:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3ncg

Go back to Calcium Binding Sites List in 3ncg
Calcium binding site 1 out of 3 in the Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Nm-PP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Nm-PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca551

b:45.4
occ:1.00
 O A:MET399 2.2 51.6 1.0
OD1 A:ASN395 2.3 46.1 1.0
OD1 A:ASP393 2.4 50.6 1.0
OE1 A:GLU404 2.5 43.6 1.0
OE2 A:GLU404 2.6 37.2 1.0
OD1 A:ASP397 2.7 46.9 1.0
CD A:GLU404 2.9 42.7 1.0
C A:MET399 3.4 51.2 1.0
CG A:ASN395 3.5 41.0 1.0
CG A:ASP397 3.5 46.0 1.0
CG A:ASP393 3.6 50.0 1.0
OD2 A:ASP397 3.8 51.3 1.0
ND2 A:ASN395 4.1 37.8 1.0
CA A:LEU400 4.1 48.0 1.0
N A:ASP401 4.2 48.7 1.0
N A:LEU400 4.2 50.1 1.0
N A:MET399 4.2 51.2 1.0
CA A:ASP393 4.3 51.5 1.0
OD2 A:ASP393 4.4 44.9 1.0
CA A:MET399 4.4 51.7 1.0
CG A:GLU404 4.4 42.9 1.0
CB A:ASP393 4.4 51.1 1.0
N A:ASP397 4.5 42.3 1.0
N A:ASN395 4.6 42.9 1.0
C A:ASP393 4.6 50.9 1.0
CB A:ASN395 4.6 42.7 1.0
CD2 A:LEU400 4.7 39.4 1.0
C A:LEU400 4.7 48.6 1.0
CG A:MET399 4.7 52.9 1.0
N A:ASN396 4.7 44.0 1.0
OD2 A:ASP401 4.8 58.4 1.0
CB A:ASP397 4.8 42.9 1.0
CG A:ASP401 4.9 55.6 1.0
CA A:ASN395 4.9 42.7 1.0
N A:GLY398 5.0 48.0 1.0
N A:THR394 5.0 50.4 1.0
C A:ASN395 5.0 43.9 1.0

Calcium binding site 2 out of 3 in 3ncg

Go back to Calcium Binding Sites List in 3ncg
Calcium binding site 2 out of 3 in the Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Nm-PP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Nm-PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca552

b:48.6
occ:1.00
 O A:SER449 2.3 49.0 1.0
OE1 A:GLU454 2.3 57.8 1.0
OD1 A:ASP445 2.3 51.6 1.0
OE2 A:GLU451 2.4 54.2 1.0
OG A:SER447 2.4 51.5 1.0
OE2 A:GLU454 2.5 54.4 1.0
OD1 A:ASP443 2.5 52.0 1.0
CD A:GLU454 2.7 54.5 1.0
CD A:GLU451 3.3 55.1 1.0
CG A:ASP445 3.3 59.6 1.0
CB A:SER447 3.4 57.6 1.0
C A:SER449 3.5 50.3 1.0
OE1 A:GLU451 3.5 56.8 1.0
CG A:ASP443 3.6 62.3 1.0
OD2 A:ASP445 3.7 61.8 1.0
CA A:ASP443 4.0 62.1 1.0
N A:SER447 4.0 62.3 1.0
N A:GLU451 4.1 54.3 1.0
CB A:ASP443 4.2 61.5 1.0
CG A:GLU454 4.2 57.5 1.0
CA A:SER447 4.3 58.7 1.0
N A:MET444 4.3 66.3 1.0
N A:ILE450 4.3 49.2 1.0
N A:ASP445 4.3 65.5 1.0
CA A:ILE450 4.3 49.0 1.0
N A:SER449 4.4 51.6 1.0
C A:ASP443 4.4 64.9 1.0
OD2 A:ASP443 4.5 66.4 1.0
CA A:SER449 4.5 50.7 1.0
CG A:GLU451 4.6 54.7 1.0
CB A:ASP445 4.6 63.2 1.0
N A:GLY446 4.7 64.3 1.0
C A:ILE450 4.7 51.0 1.0
CB A:GLU451 4.8 55.4 1.0
CA A:ASP445 4.8 65.2 1.0
N A:GLY448 5.0 54.9 1.0
C A:SER447 5.0 56.5 1.0

Calcium binding site 3 out of 3 in 3ncg

Go back to Calcium Binding Sites List in 3ncg
Calcium binding site 3 out of 3 in the Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Nm-PP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Nm-PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca553

b:54.2
occ:0.50
 OD1 A:ASP479 2.4 0.1 1.0
OD1 A:ASP481 2.4 0.8 1.0
O A:LYS485 2.4 0.1 1.0
OE2 A:GLU490 2.6 0.3 1.0
OG A:SER483 2.6 0.3 1.0
OE1 A:GLU490 2.6 0.8 1.0
CD A:GLU490 3.0 0.6 1.0
CG A:ASP481 3.5 0.1 1.0
C A:LYS485 3.6 0.9 1.0
CG A:ASP479 3.6 0.2 1.0
CA A:ILE486 3.7 0.3 1.0
CB A:SER483 3.8 0.2 1.0
N A:SER487 3.8 0.7 1.0
OD2 A:ASP481 3.8 0.3 1.0
N A:ILE486 4.1 0.1 1.0
C A:ILE486 4.1 0.5 1.0
CA A:ASP479 4.3 0.8 1.0
OD2 A:ASP479 4.5 0.4 1.0
CB A:ASP479 4.5 0.2 1.0
CG A:GLU490 4.5 0.3 1.0
N A:SER483 4.6 0.9 1.0
CB A:SER487 4.6 0.4 1.0
N A:LYS480 4.8 0.3 1.0
CB A:ASP481 4.8 0.8 1.0
C A:ASP479 4.8 0.5 1.0
CA A:SER483 4.8 0.1 1.0
CA A:LYS485 4.8 0.1 1.0
N A:ASP481 4.8 0.4 1.0
CA A:SER487 4.9 1.0 1.0
N A:LYS485 4.9 0.4 1.0
CB A:ILE486 4.9 0.9 1.0

Reference:

R.C.Murphy, K.K.Ojo, E.T.Larson, A.Castellanos-Gonzalez, B.G.Perera, K.R.Keyloun, J.E.Kim, J.G.Bhandari, N.R.Muller, C.L.Verlinde, A.C.White, E.A.Merritt, W.C.Van Voorhis, D.J.Maly. Discovery of Potent and Selective Inhibitors of Calcium-Dependent Protein Kinase 1 (CDPK1) From C. Parvum and T. Gondii. Acs Med Chem Lett V. 1 331 2010.
ISSN: ISSN 1948-5875
PubMed: 21116453
DOI: 10.1021/ML100096T
Page generated: Sat Jul 13 14:55:59 2024

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