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Calcium in PDB 3pm8: Cad Domain of PFF0520W, Calcium Dependent Protein Kinase

Enzymatic activity of Cad Domain of PFF0520W, Calcium Dependent Protein Kinase

All present enzymatic activity of Cad Domain of PFF0520W, Calcium Dependent Protein Kinase:
2.7.11.1;

Protein crystallography data

The structure of Cad Domain of PFF0520W, Calcium Dependent Protein Kinase, PDB code: 3pm8 was solved by A.K.Wernimont, A.Hutchinson, J.Lew, K.Chamberlain, F.Mackenzie, P.Loppnau, D.Cossar, L.Crombet, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, 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) 26.61 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 47.019, 51.378, 51.639, 68.53, 65.75, 64.49
R / Rfree (%) 19.9 / 22.5

Other elements in 3pm8:

The structure of Cad Domain of PFF0520W, Calcium Dependent Protein Kinase also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cad Domain of PFF0520W, Calcium Dependent Protein Kinase (pdb code 3pm8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Cad Domain of PFF0520W, Calcium Dependent Protein Kinase, PDB code: 3pm8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3pm8

Go back to Calcium Binding Sites List in 3pm8
Calcium binding site 1 out of 6 in the Cad Domain of PFF0520W, Calcium Dependent Protein Kinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cad Domain of PFF0520W, Calcium Dependent Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:33.2
occ:1.00
 OD1 A:ASP455 2.2 33.0 1.0
O A:LYS461 2.3 37.2 1.0
O A:HOH2 2.3 46.7 1.0
OD1 A:ASN459 2.3 43.9 1.0
OD1 A:ASP457 2.4 41.2 1.0
OE1 A:GLU466 2.4 39.2 1.0
OE2 A:GLU466 2.6 37.1 1.0
CD A:GLU466 2.8 40.7 1.0
CG A:ASP455 3.3 32.8 1.0
CG A:ASN459 3.4 50.2 1.0
CG A:ASP457 3.4 44.8 1.0
C A:LYS461 3.5 37.8 1.0
OD2 A:ASP457 4.0 49.8 1.0
OD2 A:ASP455 4.1 29.6 1.0
ND2 A:ASN459 4.2 43.1 1.0
CA A:ASP455 4.2 26.6 1.0
N A:ASN459 4.2 36.4 1.0
N A:LYS461 4.2 33.3 1.0
CB A:ASP455 4.2 27.4 1.0
N A:ASP457 4.3 35.7 1.0
CG A:GLU466 4.3 38.6 1.0
C A:ASP455 4.4 31.8 1.0
CA A:LYS461 4.4 33.1 1.0
N A:ILE462 4.4 33.0 1.0
CB A:ASN459 4.4 33.4 1.0
CA A:ILE462 4.5 32.1 1.0
N A:GLY458 4.6 36.3 1.0
CB A:ASP457 4.6 38.4 1.0
N A:SER463 4.6 31.6 1.0
N A:ILE456 4.6 31.8 1.0
CA A:ASP457 4.7 36.2 1.0
CA A:ASN459 4.7 36.5 1.0
C A:ASP457 4.8 40.6 1.0
O A:ASP455 4.8 30.6 1.0
OG A:SER463 4.9 37.9 1.0
N A:GLY460 4.9 36.0 1.0
CB A:LYS461 4.9 35.5 1.0
C A:ILE462 5.0 36.5 1.0

Calcium binding site 2 out of 6 in 3pm8

Go back to Calcium Binding Sites List in 3pm8
Calcium binding site 2 out of 6 in the Cad Domain of PFF0520W, Calcium Dependent Protein Kinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cad Domain of PFF0520W, Calcium Dependent Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca514

b:32.6
occ:1.00
 O A:HOH3 2.2 35.6 1.0
OD1 A:ASP493 2.2 36.1 1.0
OD1 A:ASN495 2.3 33.4 1.0
OE1 A:GLU504 2.4 29.5 1.0
O A:GLU499 2.4 37.2 1.0
OE2 A:GLU504 2.4 31.3 1.0
OD1 A:ASP497 2.5 44.5 1.0
CD A:GLU504 2.7 40.2 1.0
CG A:ASP497 3.3 45.7 1.0
CG A:ASN495 3.3 45.2 1.0
CG A:ASP493 3.4 38.4 1.0
C A:GLU499 3.6 36.6 1.0
OD2 A:ASP497 3.7 49.0 1.0
ND2 A:ASN495 3.9 41.8 1.0
CB A:ASP493 4.2 33.3 1.0
CA A:ASP493 4.2 32.3 1.0
OD2 A:ASP493 4.2 37.6 1.0
N A:ASP497 4.2 43.3 1.0
N A:GLU499 4.2 39.3 1.0
CG A:GLU504 4.2 29.2 1.0
N A:ASN495 4.3 37.2 1.0
CB A:ASP497 4.4 43.4 1.0
N A:ILE500 4.5 30.9 1.0
CA A:GLU499 4.5 36.7 1.0
OD2 A:ASP501 4.5 41.1 1.0
N A:ASP501 4.5 27.5 1.0
CB A:ASN495 4.5 33.5 1.0
CA A:ILE500 4.5 28.6 1.0
C A:ASP493 4.5 39.4 1.0
N A:GLY496 4.6 42.7 1.0
N A:LEU494 4.7 38.4 1.0
CA A:ASN495 4.7 37.6 1.0
CG A:ASP501 4.7 37.3 1.0
CA A:ASP497 4.7 42.6 1.0
C A:ASN495 4.9 44.9 1.0
N A:GLY498 4.9 43.6 1.0
OD1 A:ASP501 4.9 38.2 1.0
C A:ILE500 5.0 31.0 1.0
O A:ASP493 5.0 39.2 1.0

Calcium binding site 3 out of 6 in 3pm8

Go back to Calcium Binding Sites List in 3pm8
Calcium binding site 3 out of 6 in the Cad Domain of PFF0520W, Calcium Dependent Protein Kinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cad Domain of PFF0520W, Calcium Dependent Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca515

b:76.3
occ:1.00
 OD2 A:ASP385 2.3 97.5 1.0
OE1 A:GLU394 2.4 53.0 1.0
O A:THR389 2.5 64.7 1.0
OE2 A:GLU394 2.6 54.7 1.0
CD A:GLU394 2.8 66.5 1.0
OD1 A:ASP383 2.9 63.4 1.0
OG A:SER387 3.0 77.3 1.0
CG A:ASP385 3.2 88.7 1.0
OD1 A:ASP385 3.5 89.7 1.0
C A:THR389 3.5 66.0 1.0
NE2 A:GLN425 3.6 84.1 1.0
OG1 A:THR389 4.0 83.5 1.0
CG A:ASP383 4.1 63.8 1.0
CA A:LEU390 4.1 59.5 1.0
N A:LEU390 4.2 60.3 1.0
N A:SER391 4.2 62.2 1.0
CG A:GLU394 4.2 62.7 1.0
CB A:SER387 4.4 73.3 1.0
CA A:ASP383 4.4 53.4 1.0
CB A:ASP385 4.5 74.5 1.0
C A:LEU390 4.5 64.8 1.0
CA A:THR389 4.6 66.7 1.0
CB A:ASP383 4.6 55.0 1.0
N A:ASP385 4.7 70.8 1.0
N A:THR389 4.7 68.0 1.0
OG A:SER391 4.8 72.6 1.0
CD A:GLN425 4.8 97.4 1.0
CB A:THR389 4.8 81.0 1.0
CB A:SER391 4.9 65.6 1.0
N A:SER387 4.9 71.5 1.0
C A:ASP383 4.9 62.0 1.0
N A:VAL384 5.0 61.5 1.0
CA A:ASP385 5.0 72.1 1.0

Calcium binding site 4 out of 6 in 3pm8

Go back to Calcium Binding Sites List in 3pm8
Calcium binding site 4 out of 6 in the Cad Domain of PFF0520W, Calcium Dependent Protein Kinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cad Domain of PFF0520W, Calcium Dependent Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1

b:33.7
occ:1.00
 OD2 B:ASP385 2.3 47.3 1.0
OD1 B:ASP383 2.3 29.4 1.0
O B:THR389 2.4 30.6 1.0
OE1 B:GLU394 2.4 32.6 1.0
O B:HOH519 2.4 36.4 1.0
OG B:SER387 2.5 34.3 1.0
OE2 B:GLU394 2.5 34.1 1.0
CD B:GLU394 2.8 49.4 1.0
CG B:ASP385 3.5 42.1 1.0
CG B:ASP383 3.5 31.9 1.0
C B:THR389 3.6 32.7 1.0
CB B:SER387 3.6 32.8 1.0
N B:SER387 4.0 30.1 1.0
OD1 B:ASP385 4.0 42.9 1.0
CA B:ASP383 4.1 28.9 1.0
OG1 B:THR389 4.2 34.8 1.0
CB B:ASP383 4.3 30.2 1.0
CG B:GLU394 4.3 38.7 1.0
CA B:SER387 4.3 29.9 1.0
CA B:LEU390 4.4 30.2 1.0
OD2 B:ASP383 4.4 30.8 1.0
N B:LEU390 4.4 28.5 1.0
N B:THR389 4.4 30.1 1.0
N B:ASP385 4.4 33.0 1.0
OE1 B:GLN425 4.5 47.9 1.0
C B:ASP383 4.5 35.6 1.0
CA B:THR389 4.6 29.4 1.0
CB B:ASP385 4.6 34.6 1.0
O B:HOH189 4.6 44.8 1.0
N B:ASN386 4.7 30.7 1.0
N B:VAL384 4.7 33.8 1.0
CD2 B:LEU390 4.8 34.8 1.0
CA B:ASP385 4.8 32.7 1.0
N B:SER391 4.8 33.5 1.0
C B:ASP385 4.9 34.5 1.0
N B:GLY388 4.9 30.0 1.0
C B:SER387 4.9 33.1 1.0
O B:ASP383 5.0 34.4 1.0

Calcium binding site 5 out of 6 in 3pm8

Go back to Calcium Binding Sites List in 3pm8
Calcium binding site 5 out of 6 in the Cad Domain of PFF0520W, Calcium Dependent Protein Kinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cad Domain of PFF0520W, Calcium Dependent Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca514

b:50.3
occ:1.00
 OD1 B:ASP455 2.1 45.7 1.0
OD1 B:ASP457 2.2 67.2 1.0
O B:LYS461 2.3 50.4 1.0
OE1 B:GLU466 2.3 45.9 1.0
OD1 B:ASN459 2.4 67.5 1.0
OE2 B:GLU466 2.6 50.2 1.0
CD B:GLU466 2.8 57.8 1.0
CG B:ASP457 3.1 66.2 1.0
CG B:ASP455 3.4 49.2 1.0
OD2 B:ASP457 3.4 70.4 1.0
CG B:ASN459 3.5 70.9 1.0
C B:LYS461 3.5 49.0 1.0
CA B:ASP455 4.1 42.9 1.0
N B:ASN459 4.2 49.7 1.0
ND2 B:ASN459 4.2 59.9 1.0
CB B:ASP455 4.2 44.4 1.0
OD2 B:ASP455 4.3 49.8 1.0
N B:LYS461 4.3 47.5 1.0
CG B:GLU466 4.3 45.2 1.0
N B:ASP457 4.3 53.4 1.0
C B:ASP455 4.3 49.3 1.0
N B:GLY458 4.4 53.4 1.0
N B:ILE462 4.4 42.2 1.0
CA B:ILE462 4.4 40.7 1.0
CB B:ASP457 4.4 55.3 1.0
N B:SER463 4.4 44.3 1.0
CA B:LYS461 4.4 46.8 1.0
N B:ILE456 4.5 49.6 1.0
CB B:ASN459 4.5 46.2 1.0
CA B:ASN459 4.8 49.4 1.0
CA B:ASP457 4.8 53.4 1.0
OG B:SER463 4.9 53.0 1.0
O B:ASP455 4.9 47.6 1.0
C B:ASP457 4.9 58.1 1.0
C B:ILE462 5.0 46.5 1.0
N B:GLY460 5.0 49.5 1.0
CB B:LYS461 5.0 50.7 1.0

Calcium binding site 6 out of 6 in 3pm8

Go back to Calcium Binding Sites List in 3pm8
Calcium binding site 6 out of 6 in the Cad Domain of PFF0520W, Calcium Dependent Protein Kinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cad Domain of PFF0520W, Calcium Dependent Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca515

b:38.5
occ:1.00
 O B:HOH4 2.0 34.2 1.0
OD1 B:ASP493 2.1 41.3 1.0
OD1 B:ASN495 2.2 53.3 1.0
O B:GLU499 2.4 44.0 1.0
OD1 B:ASP497 2.5 48.0 1.0
OE1 B:GLU504 2.5 38.3 1.0
OE2 B:GLU504 2.6 41.4 1.0
CD B:GLU504 2.9 51.7 1.0
CG B:ASP493 3.3 44.7 1.0
CG B:ASN495 3.3 53.9 1.0
CG B:ASP497 3.3 51.5 1.0
C B:GLU499 3.5 46.4 1.0
OD2 B:ASP497 3.7 54.0 1.0
ND2 B:ASN495 3.9 44.3 1.0
CB B:ASP493 4.0 41.1 1.0
CA B:ASP493 4.1 39.0 1.0
N B:GLU499 4.2 49.0 1.0
N B:ASP497 4.2 48.8 1.0
OD2 B:ASP493 4.2 48.4 1.0
N B:ASN495 4.3 43.7 1.0
C B:ASP493 4.4 43.0 1.0
CB B:ASN495 4.4 38.5 1.0
CA B:GLU499 4.4 47.3 1.0
CG B:GLU504 4.4 41.0 1.0
N B:ILE500 4.4 40.3 1.0
CB B:ASP497 4.4 48.9 1.0
OD2 B:ASP501 4.5 53.3 1.0
CA B:ILE500 4.5 38.1 1.0
N B:ASP501 4.6 36.3 1.0
N B:GLY496 4.6 49.4 1.0
CA B:ASN495 4.6 44.2 1.0
N B:LEU494 4.7 39.0 1.0
CA B:ASP497 4.7 48.1 1.0
C B:ASN495 4.8 52.1 1.0
N B:GLY498 4.9 50.8 1.0
C B:ASP497 4.9 53.2 1.0
O B:ASP493 5.0 43.7 1.0
CB B:GLU499 5.0 48.9 1.0

Reference:

A.K.Wernimont, A.Hutchinson, J.Lew, K.Chamberlain, F.Mackenzie, P.Loppnau, D.Cossar, L.Crombet, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, R.Hui, M.Amani. Cad Domain of PFF0520W, Calcium Dependent Protein Kinase To Be Published.
Page generated: Sat Jul 13 16:51:24 2024

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