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Sodium 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
Calcium (Ca) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Cad Domain of PFF0520W, Calcium Dependent Protein Kinase, PDB code: 3pm8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3pm8

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na516

b:43.7
occ:1.00
N A:HIS503 3.2 28.8 1.0
CB A:HIS503 3.5 28.2 1.0
O A:HOH108 3.5 34.9 1.0
N A:PHE502 3.6 29.4 1.0
CG A:ASP501 3.8 37.3 1.0
CB A:ASP501 3.8 28.1 1.0
CA A:HIS503 3.9 28.1 1.0
OD1 A:ASP501 3.9 38.2 1.0
C A:PHE502 4.0 32.3 1.0
CA A:PHE502 4.1 28.0 1.0
CB A:PHE502 4.1 29.2 1.0
ND2 B:ASN386 4.1 32.8 1.0
CL B:CL518 4.1 55.9 1.0
OD2 A:ASP501 4.2 41.1 1.0
C A:ASP501 4.4 31.6 1.0
O A:HOH125 4.6 45.8 1.0
CA A:ASP501 4.7 28.0 1.0
O A:HOH207 4.8 38.6 1.0
CG A:HIS503 4.9 29.9 1.0

Sodium binding site 2 out of 3 in 3pm8

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cad Domain of PFF0520W, Calcium Dependent Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na516

b:37.8
occ:1.00
O B:HOH145 2.9 41.6 1.0
O B:HOH142 2.9 60.6 1.0
N B:GLU354 3.2 30.2 1.0
CG B:GLU354 3.6 41.0 1.0
CB B:ASN353 3.7 34.8 1.0
CB B:GLU354 3.7 32.0 1.0
CD1 B:LEU488 3.7 42.4 1.0
CA B:ASN353 3.9 32.0 1.0
C B:ASN353 4.0 34.4 1.0
CA B:GLU354 4.0 29.9 1.0
CB B:LEU488 4.4 37.8 1.0
O B:HOH90 4.6 43.9 1.0
CG B:LEU488 4.6 42.3 1.0
CG B:ASN353 4.7 46.6 1.0
CD B:GLU354 4.8 54.4 1.0
OD1 B:ASN353 4.9 36.7 1.0
CA B:LEU488 4.9 37.9 1.0
CD2 B:LEU488 4.9 43.5 1.0
OE2 B:GLU354 5.0 46.3 1.0
N B:LEU355 5.0 27.2 1.0

Sodium binding site 3 out of 3 in 3pm8

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cad Domain of PFF0520W, Calcium Dependent Protein Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na517

b:51.2
occ:1.00
N B:VAL370 3.4 35.2 1.0
CG2 B:VAL370 3.4 41.4 1.0
N B:ASP369 3.8 34.0 1.0
CB B:VAL370 3.9 41.4 1.0
CB B:CYS368 3.9 35.9 0.5
CB B:CYS368 4.0 40.2 0.5
SG B:CYS368 4.1 40.2 0.5
CB B:ASP369 4.1 36.3 1.0
CA B:ASP369 4.1 34.2 1.0
C B:ASP369 4.2 37.0 1.0
CA B:VAL370 4.2 35.9 1.0
C B:CYS368 4.4 37.7 0.5
C B:CYS368 4.5 36.1 0.5
CA B:CYS368 4.8 34.8 0.5
CA B:CYS368 4.8 38.0 0.5
O A:LYS512 4.8 53.9 1.0
C A:LYS512 4.9 88.5 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: Tue Dec 15 06:21:47 2020

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