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Calcium in PDB 3mwu: Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Rm-1-95

Enzymatic activity of Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Rm-1-95

All present enzymatic activity of Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Rm-1-95:
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 Rm-1-95, PDB code: 3mwu was solved by E.T.Larson, E.A.Merritt, Medical Structural Genomics Of Pathogenicprotozoa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.04 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.020, 55.970, 82.210, 90.00, 104.79, 90.00
R / Rfree (%) 19.4 / 22.9

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 Rm-1-95 (pdb code 3mwu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Rm-1-95, PDB code: 3mwu:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3mwu

Go back to Calcium Binding Sites List in 3mwu
Calcium binding site 1 out of 4 in the Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Rm-1-95


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 Rm-1-95 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca551

b:43.1
occ:1.00
 O A:MET399 2.2 43.2 1.0
O A:HOH609 2.2 47.2 1.0
OD1 A:ASP393 2.3 45.1 1.0
OE1 A:GLU404 2.4 42.6 1.0
OD1 A:ASN395 2.4 48.9 1.0
OD1 A:ASP397 2.5 43.9 1.0
OE2 A:GLU404 2.5 46.2 1.0
CD A:GLU404 2.8 40.5 1.0
CG A:ASP397 3.4 44.7 1.0
C A:MET399 3.4 42.0 1.0
CG A:ASP393 3.4 45.8 1.0
CG A:ASN395 3.5 48.1 1.0
OD2 A:ASP397 3.7 46.6 1.0
ND2 A:ASN395 4.1 51.0 1.0
N A:MET399 4.1 43.4 1.0
CA A:ASP393 4.2 44.5 1.0
OD2 A:ASP393 4.2 44.5 1.0
N A:LEU400 4.2 44.2 1.0
CA A:LEU400 4.3 43.3 1.0
CB A:ASP393 4.3 42.5 1.0
N A:ASP397 4.3 41.3 1.0
CG A:GLU404 4.3 42.2 1.0
CA A:MET399 4.3 43.0 1.0
N A:ASN395 4.4 49.1 1.0
C A:ASP393 4.5 48.1 1.0
N A:ASP401 4.5 44.6 1.0
CB A:ASP397 4.6 40.3 1.0
CB A:ASN395 4.7 49.9 1.0
CG A:MET399 4.7 52.4 1.0
OD2 A:ASP401 4.7 55.2 1.0
N A:THR394 4.7 50.6 1.0
N A:ASN396 4.8 46.5 1.0
N A:GLY398 4.8 42.3 1.0
CA A:ASP397 4.8 40.6 1.0
C A:LEU400 4.8 44.8 1.0
CA A:ASN395 4.8 49.6 1.0
C A:ASN395 4.9 48.7 1.0
O A:ASP393 4.9 44.6 1.0
CD2 A:LEU400 5.0 44.5 1.0

Calcium binding site 2 out of 4 in 3mwu

Go back to Calcium Binding Sites List in 3mwu
Calcium binding site 2 out of 4 in the Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Rm-1-95


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 Rm-1-95 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca552

b:49.2
occ:1.00
 OD1 A:ASP443 2.3 51.3 1.0
OG A:SER447 2.3 48.6 1.0
OE1 A:GLU451 2.4 48.7 1.0
O A:SER449 2.4 45.5 1.0
OD1 A:ASP445 2.4 55.5 1.0
OE1 A:GLU454 2.5 51.6 1.0
OE2 A:GLU454 2.7 60.5 1.0
CD A:GLU454 2.9 55.9 1.0
CD A:GLU451 3.2 48.9 1.0
CB A:SER447 3.4 52.6 1.0
CG A:ASP443 3.4 56.9 1.0
OE2 A:GLU451 3.4 56.2 1.0
CG A:ASP445 3.5 52.9 1.0
C A:SER449 3.6 48.8 1.0
OD2 A:ASP445 3.8 66.1 1.0
N A:SER447 3.9 58.6 1.0
CA A:ASP443 4.1 56.1 1.0
CB A:ASP443 4.2 55.1 1.0
CA A:SER447 4.2 55.8 1.0
N A:GLU451 4.2 45.8 1.0
OD2 A:ASP443 4.2 60.7 1.0
N A:SER449 4.4 48.8 1.0
C A:ASP443 4.4 56.2 1.0
CA A:ILE450 4.4 45.6 1.0
CG A:GLU454 4.4 54.3 1.0
N A:ILE450 4.5 45.5 1.0
N A:ASP445 4.5 60.5 1.0
N A:MET444 4.6 61.1 1.0
CA A:SER449 4.6 50.2 1.0
CG A:GLU451 4.6 47.8 1.0
N A:GLY446 4.7 62.6 1.0
O A:HOH670 4.8 65.8 1.0
CB A:ASP445 4.8 57.0 1.0
C A:ILE450 4.9 45.1 1.0
N A:GLY448 4.9 55.0 1.0
C A:SER447 4.9 56.1 1.0
CB A:GLU451 4.9 49.2 1.0
CA A:ASP445 5.0 59.6 1.0

Calcium binding site 3 out of 4 in 3mwu

Go back to Calcium Binding Sites List in 3mwu
Calcium binding site 3 out of 4 in the Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Rm-1-95


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 Rm-1-95 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca553

b:91.0
occ:1.00
 OD2 A:ASP479 2.3 0.5 1.0
OD1 A:ASP481 2.4 0.8 1.0
O A:LYS485 2.4 0.3 1.0
OG A:SER483 2.5 0.7 1.0
CG A:ASP481 3.3 0.7 1.0
OE2 A:GLU490 3.4 0.4 1.0
CG A:ASP479 3.4 0.4 1.0
OD2 A:ASP481 3.5 0.5 1.0
C A:LYS485 3.5 0.5 1.0
CB A:SER483 3.6 0.3 1.0
OE1 A:GLU490 3.7 0.2 1.0
N A:SER483 3.7 0.9 1.0
CD A:GLU490 4.0 0.1 1.0
OD1 A:ASP479 4.1 0.3 1.0
N A:LYS485 4.1 0.9 1.0
CA A:SER483 4.1 0.7 1.0
CA A:LYS485 4.4 0.4 1.0
N A:GLY482 4.4 0.5 1.0
N A:ILE486 4.4 0.8 1.0
CB A:ASP479 4.5 0.1 1.0
N A:GLY484 4.5 0.1 1.0
CA A:ASP479 4.5 0.3 1.0
CA A:ILE486 4.5 0.3 1.0
C A:SER483 4.6 0.7 1.0
CB A:ASP481 4.7 0.1 1.0
N A:ASP481 4.7 0.2 1.0
C A:GLY482 4.8 0.0 1.0
C A:ASP481 4.9 0.2 1.0
OE2 A:GLU521 4.9 0.7 1.0
CA A:ASP481 5.0 0.7 1.0
C A:ASP479 5.0 1.0 1.0

Calcium binding site 4 out of 4 in 3mwu

Go back to Calcium Binding Sites List in 3mwu
Calcium binding site 4 out of 4 in the Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Rm-1-95


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Activated Calcium-Dependent Protein Kinase 1 From Cryptosporidium Parvum (CPCDPK1) in Complex with Bumped Kinase Inhibitor Rm-1-95 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca554

b:0.0
occ:1.00
 O A:GLU521 2.7 1.0 1.0
OD1 A:ASP515 2.8 1.0 1.0
OD1 A:ASP519 2.8 0.9 1.0
OE2 A:GLU526 2.9 0.9 1.0
OD1 A:ASN517 3.3 1.0 1.0
ND2 A:ASN517 3.3 0.2 1.0
CD A:GLU526 3.4 0.2 1.0
CG A:ASN517 3.5 0.7 1.0
OE1 A:GLU526 3.5 0.1 1.0
CG A:ASP519 3.8 0.7 1.0
C A:GLU521 3.8 0.5 1.0
CG A:ASP515 4.0 0.4 1.0
OD2 A:ASP519 4.3 0.0 1.0
N A:ASP523 4.4 0.8 1.0
OD2 A:ASP523 4.5 0.2 1.0
CA A:ASP515 4.6 0.4 1.0
N A:ASN517 4.6 0.1 1.0
N A:VAL522 4.6 0.4 1.0
CA A:VAL522 4.6 0.6 1.0
N A:ASP519 4.6 0.4 1.0
CG A:GLU526 4.6 0.2 1.0
N A:GLU521 4.7 0.3 1.0
CA A:GLU521 4.7 0.7 1.0
CB A:ASN517 4.7 0.4 1.0
CG A:ASP523 4.7 0.6 1.0
OD2 A:ASP515 4.7 0.4 1.0
N A:LYS518 4.7 0.0 1.0
N A:ASN516 4.8 0.6 1.0
CB A:ASP519 4.8 0.4 1.0
CB A:ASP515 4.8 0.5 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 13:46:06 2024

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