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Magnesium in PDB 3c5i: Crystal Structure of Plasmodium Knowlesi Choline Kinase, PKH_134520

Protein crystallography data

The structure of Crystal Structure of Plasmodium Knowlesi Choline Kinase, PKH_134520, PDB code: 3c5i was solved by A.K.Wernimont, T.Hills, J.Lew, G.Wasney, G.Senesterra, I.Kozieradzki, D.Cossar, M.Vedadi, M.Schapira, A.Bochkarev, C.H.Arrowsmith, C.Bountra, J.Weigelt, A.M.Edwards, R.Hui, J.D.Artz, T.Xiao, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.79 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 112.985, 71.993, 116.393, 90.00, 97.72, 90.00
R / Rfree (%) 21.2 / 26

Other elements in 3c5i:

The structure of Crystal Structure of Plasmodium Knowlesi Choline Kinase, PKH_134520 also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Uranium (U) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Plasmodium Knowlesi Choline Kinase, PKH_134520 (pdb code 3c5i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Plasmodium Knowlesi Choline Kinase, PKH_134520, PDB code: 3c5i:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3c5i

Go back to Magnesium Binding Sites List in 3c5i
Magnesium binding site 1 out of 4 in the Crystal Structure of Plasmodium Knowlesi Choline Kinase, PKH_134520


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 Plasmodium Knowlesi Choline Kinase, PKH_134520 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg370

b:29.4
occ:1.00
OD2 A:ASP235 1.9 33.5 1.0
O A:HOH1040 1.9 32.5 1.0
O A:HOH1038 2.1 25.8 1.0
OD1 A:ASN223 2.1 37.8 1.0
O A:HOH1037 2.1 21.8 1.0
O A:HOH1039 2.1 27.6 1.0
CG A:ASP235 3.0 35.0 1.0
CG A:ASN223 3.2 37.6 1.0
CB A:ASP235 3.5 35.6 1.0
ND2 A:ASN223 3.7 38.4 1.0
OD1 A:ASN222 4.0 46.2 1.0
OD1 A:ASP235 4.1 33.0 1.0
O A:ASN222 4.2 37.9 1.0
O A:HOH1090 4.3 37.3 1.0
CB A:ASN223 4.5 38.1 1.0
O A:HOH1013 4.5 28.3 1.0
O A:HOH1035 4.6 31.9 1.0
CA A:ASN223 4.7 38.4 1.0
CG A:ASN222 4.7 42.0 1.0
C A:ASN222 4.7 38.6 1.0
N A:ASN223 4.9 38.5 1.0
CD1 A:ILE234 4.9 36.6 1.0

Magnesium binding site 2 out of 4 in 3c5i

Go back to Magnesium Binding Sites List in 3c5i
Magnesium binding site 2 out of 4 in the Crystal Structure of Plasmodium Knowlesi Choline Kinase, PKH_134520


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 Plasmodium Knowlesi Choline Kinase, PKH_134520 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg370

b:34.8
occ:1.00
O B:HOH1067 1.9 30.3 1.0
O B:HOH1036 2.0 32.9 1.0
O B:HOH1070 2.0 32.5 1.0
O B:HOH1046 2.0 33.3 1.0
OD2 B:ASP235 2.0 32.6 1.0
OD1 B:ASN223 2.1 37.5 1.0
CG B:ASP235 3.1 35.0 1.0
CG B:ASN223 3.1 37.2 1.0
CB B:ASP235 3.5 35.5 1.0
ND2 B:ASN223 3.6 38.7 1.0
OD1 B:ASN222 4.0 47.1 1.0
OD1 B:ASP235 4.2 35.3 1.0
O B:ASN222 4.3 38.4 1.0
O B:HOH1072 4.4 39.7 1.0
O B:HOH1019 4.4 36.1 1.0
CB B:ASN223 4.4 37.4 1.0
CA B:ASN223 4.6 38.0 1.0
CD1 B:ILE234 4.6 36.7 1.0
C B:ASN222 4.7 38.0 1.0
CG B:ASN222 4.8 42.6 1.0
N B:ASN223 4.8 37.6 1.0

Magnesium binding site 3 out of 4 in 3c5i

Go back to Magnesium Binding Sites List in 3c5i
Magnesium binding site 3 out of 4 in the Crystal Structure of Plasmodium Knowlesi Choline Kinase, PKH_134520


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 Plasmodium Knowlesi Choline Kinase, PKH_134520 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg370

b:34.4
occ:1.00
OD2 C:ASP235 2.0 40.9 1.0
O C:HOH453 2.0 26.9 1.0
OD1 C:ASN223 2.1 37.2 1.0
O C:HOH402 2.1 30.8 1.0
O C:HOH476 2.2 34.3 1.0
O C:HOH472 2.2 27.3 1.0
CG C:ASP235 3.1 39.1 1.0
CG C:ASN223 3.2 37.1 1.0
CB C:ASP235 3.5 37.7 1.0
ND2 C:ASN223 3.6 35.1 1.0
OD1 C:ASP235 4.2 39.7 1.0
ND2 C:ASN222 4.2 47.6 1.0
O C:ASN222 4.3 40.6 1.0
O C:HOH395 4.4 32.5 1.0
CB C:ASN223 4.5 37.4 1.0
CA C:ASN223 4.7 38.2 1.0
C C:ASN222 4.7 40.4 1.0
CG C:ASN222 4.8 45.7 1.0
N C:ASN223 4.9 38.9 1.0

Magnesium binding site 4 out of 4 in 3c5i

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Magnesium binding site 4 out of 4 in the Crystal Structure of Plasmodium Knowlesi Choline Kinase, PKH_134520


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 Plasmodium Knowlesi Choline Kinase, PKH_134520 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg370

b:31.9
occ:1.00
O D:HOH417 2.0 39.5 1.0
OD2 D:ASP235 2.0 38.1 1.0
O D:HOH380 2.1 26.7 1.0
OD1 D:ASN223 2.1 39.4 1.0
O D:HOH414 2.1 32.3 1.0
O D:HOH409 2.2 28.9 1.0
CG D:ASP235 3.2 37.3 1.0
CG D:ASN223 3.3 41.7 1.0
CB D:ASP235 3.8 38.4 1.0
ND2 D:ASN223 3.9 41.7 1.0
OD1 D:ASP235 4.2 34.2 1.0
O D:ASN222 4.3 41.0 1.0
CB D:ASN222 4.3 43.6 1.0
CB D:ASN223 4.5 38.8 1.0
C D:ASN222 4.6 41.6 1.0
CA D:ASN223 4.6 39.6 1.0
O D:HOH420 4.7 32.4 1.0
CG D:ASN222 4.7 46.7 1.0
N D:ASN223 4.7 39.2 1.0
ND2 D:ASN222 4.7 50.0 1.0
CD1 D:ILE234 4.8 37.9 1.0
CG1 D:ILE234 4.9 37.9 1.0

Reference:

A.K.Wernimont, T.Hills, J.Lew, G.Wasney, G.Senisterra, I.Kozieradzki, D.Cossar, M.Vedadi, M.Schapira, A.Bochkarev, C.H.Arrowsmith, C.Bountra, J.Weigelt, A.M.Edwards, R.Hui, J.D.Artz, T.Xiao. Crystal Structure of Plasmodium Knowlesi Choline Kinase, PKH_134520. To Be Published.
Page generated: Mon Dec 14 07:56:57 2020

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