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Magnesium in PDB 3is5: Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720

Enzymatic activity of Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720

All present enzymatic activity of Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720:
2.7.11.17;

Protein crystallography data

The structure of Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720, PDB code: 3is5 was solved by A.K.Wernimont, J.D.Artz, G.Senisterra, F.Mackenzie, A.Hutchinson, I.Kozieradzki, D.Cossar, A.Bochkarev, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, R.Hui, Y.H.Lin, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.55
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 113.973, 113.973, 153.471, 90.00, 90.00, 120.00
R / Rfree (%) 21.8 / 25.9

Other elements in 3is5:

The structure of Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720 also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720 (pdb code 3is5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720, PDB code: 3is5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3is5

Go back to Magnesium Binding Sites List in 3is5
Magnesium binding site 1 out of 6 in the Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg399

b:49.3
occ:1.00
 OD1 A:ASN265 2.5 20.3 1.0
O2B A:ANP1 2.6 50.6 0.5
O2A A:ANP1 2.8 49.0 0.5
OD2 A:ASP281 2.9 24.3 1.0
CG A:ASP281 3.1 23.5 1.0
CG A:ASN265 3.5 20.5 1.0
OD1 A:ASP281 3.5 26.1 1.0
CB A:ASP281 3.6 21.9 1.0
O3G A:ANP1 3.9 50.9 0.5
ND2 A:ASN265 3.9 20.2 1.0
PB A:ANP1 4.1 51.2 0.5
O A:HOH482 4.2 24.7 1.0
PA A:ANP1 4.2 49.5 0.5
N3B A:ANP1 4.7 50.9 0.5
PG A:ANP1 4.7 51.0 0.5
O3A A:ANP1 4.7 50.4 0.5
O1G A:ANP1 4.7 51.0 0.5
CB A:ASN265 4.8 20.7 1.0
O A:GLU264 4.9 21.1 1.0

Magnesium binding site 2 out of 6 in 3is5

Go back to Magnesium Binding Sites List in 3is5
Magnesium binding site 2 out of 6 in the Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg397

b:55.0
occ:1.00
 O2B B:ANP1 2.0 72.9 1.0
OD1 B:ASN265 2.5 23.6 1.0
CG B:ASP281 3.1 26.8 1.0
OD2 B:ASP281 3.2 30.0 1.0
OD1 B:ASP281 3.3 28.7 1.0
PB B:ANP1 3.4 73.7 1.0
CG B:ASN265 3.5 23.1 1.0
O2A B:ANP1 3.6 68.7 1.0
CB B:ASP281 3.7 24.9 1.0
ND2 B:ASN265 3.8 22.3 1.0
O1B B:ANP1 4.1 73.0 1.0
O2G B:ANP1 4.2 74.5 1.0
O1G B:ANP1 4.3 74.8 1.0
PA B:ANP1 4.3 68.3 1.0
O3A B:ANP1 4.4 70.7 1.0
N3B B:ANP1 4.4 74.0 1.0
O1A B:ANP1 4.6 68.3 1.0
PG B:ANP1 4.6 74.8 1.0
CB B:ASN265 4.9 23.4 1.0
OD2 B:ASP260 5.0 23.3 1.0

Magnesium binding site 3 out of 6 in 3is5

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Magnesium binding site 3 out of 6 in the Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg398

b:61.7
occ:1.00
 O2B C:ANP1 2.7 73.3 1.0
OD1 C:ASN265 2.8 25.7 1.0
O1A C:ANP1 3.1 69.4 1.0
CG C:ASP281 3.2 28.4 1.0
O2G C:ANP1 3.2 74.7 1.0
OD1 C:ASP281 3.3 27.9 1.0
OD2 C:ASP281 3.3 30.4 1.0
O2A C:ANP1 3.6 69.8 1.0
PA C:ANP1 3.7 70.0 1.0
CB C:ASP281 3.8 27.3 1.0
CG C:ASN265 3.9 24.2 1.0
PB C:ANP1 4.0 73.5 1.0
O C:HOH488 4.0 25.6 1.0
ND2 C:ASN265 4.3 23.6 1.0
PG C:ANP1 4.4 74.4 1.0
O3A C:ANP1 4.4 71.4 1.0
O1G C:ANP1 4.6 73.8 1.0
N3B C:ANP1 4.7 74.0 1.0
O C:GLU264 4.8 24.5 1.0

Magnesium binding site 4 out of 6 in 3is5

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Magnesium binding site 4 out of 6 in the Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg399

b:40.4
occ:1.00
 OD2 D:ASP281 2.3 30.7 1.0
OD1 D:ASN265 2.6 31.9 1.0
CG D:ASP281 3.3 28.4 1.0
CG D:ASN265 3.5 31.0 1.0
O1A D:ANP1 3.7 56.5 0.5
ND2 D:ASN265 3.7 31.3 1.0
CB D:ASP281 3.8 26.8 1.0
O1G D:ANP1 3.9 56.2 0.5
N3B D:ANP1 4.0 57.0 0.5
O2A D:ANP1 4.3 56.5 0.5
PA D:ANP1 4.3 56.3 0.5
OD1 D:ASP281 4.4 30.7 1.0
O D:HOH564 4.5 33.9 1.0
O3A D:ANP1 4.6 56.7 0.5
PG D:ANP1 4.7 56.8 0.5
CE D:LYS262 4.8 29.8 1.0
CB D:ASN265 5.0 30.4 1.0

Magnesium binding site 5 out of 6 in 3is5

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Magnesium binding site 5 out of 6 in the Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg398

b:52.8
occ:1.00
 OD1 E:ASN265 2.4 26.4 1.0
O1B E:ANP1 2.7 45.3 0.5
OD1 E:ASP281 3.1 31.2 1.0
O3G E:ANP1 3.1 45.4 0.5
O2A E:ANP1 3.1 43.3 0.5
CG E:ASP281 3.3 30.4 1.0
CG E:ASN265 3.4 26.0 1.0
ND2 E:ASN265 3.7 26.0 1.0
CB E:ASP281 3.8 28.7 1.0
OD2 E:ASP281 3.9 32.5 1.0
PB E:ANP1 3.9 45.4 0.5
PA E:ANP1 4.1 43.2 0.5
O3A E:ANP1 4.2 44.6 0.5
PG E:ANP1 4.4 45.2 0.5
N3B E:ANP1 4.4 45.3 0.5
O1A E:ANP1 4.6 43.3 0.5
CB E:ASN265 4.8 25.8 1.0
O E:GLU264 4.8 26.3 1.0

Magnesium binding site 6 out of 6 in 3is5

Go back to Magnesium Binding Sites List in 3is5
Magnesium binding site 6 out of 6 in the Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg397

b:33.3
occ:1.00
 O F:HOH534 2.0 22.6 1.0
O F:HOH535 2.1 23.4 1.0
O F:HOH532 2.1 13.1 1.0
OD1 F:ASN265 2.2 17.5 1.0
OD2 F:ASP281 2.2 17.3 1.0
O F:HOH533 2.7 28.0 1.0
CG F:ASN265 3.4 17.0 1.0
CG F:ASP281 3.4 15.5 1.0
ND2 F:ASN265 4.0 16.0 1.0
CB F:ASP281 4.0 14.2 1.0
O F:GLU264 4.2 17.3 1.0
OD1 F:ASP281 4.4 17.6 1.0
O2A F:ANP398 4.5 66.4 1.0
C F:GLU264 4.6 17.4 1.0
CB F:ASN265 4.6 16.9 1.0
CA F:ASN265 4.7 17.0 1.0
N F:ASN265 4.8 17.2 1.0
CE F:LYS262 4.8 19.7 1.0
CD1 F:ILE280 4.9 8.7 1.0
O5' F:ANP398 5.0 61.4 1.0

Reference:

A.K.Wernimont, J.D.Artz, G.Senisterra, F.Mackenzie, A.Hutchinson, I.Kozieradzki, D.Cossar, A.Bochkarev, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, R.Hui, Y.H.Lin. Crystal Structure of Cdpk Kinase Domain From Toxoplasma Gondii, TGME49_018720 To Be Published.
Page generated: Wed Aug 14 16:15:35 2024

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