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Magnesium in PDB 3g15: Crystal Structure of Human Choline Kinase Alpha in Complex with Hemicholinium-3 and Adp

Enzymatic activity of Crystal Structure of Human Choline Kinase Alpha in Complex with Hemicholinium-3 and Adp

All present enzymatic activity of Crystal Structure of Human Choline Kinase Alpha in Complex with Hemicholinium-3 and Adp:
2.7.1.32;

Protein crystallography data

The structure of Crystal Structure of Human Choline Kinase Alpha in Complex with Hemicholinium-3 and Adp, PDB code: 3g15 was solved by B.S.Hong, W.Tempel, W.M.Rabeh, F.Mackenzie, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, A.Bochkarev, H.W.Park, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.802, 118.986, 131.039, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Choline Kinase Alpha in Complex with Hemicholinium-3 and Adp (pdb code 3g15). 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 Human Choline Kinase Alpha in Complex with Hemicholinium-3 and Adp, PDB code: 3g15:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3g15

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Choline Kinase Alpha in Complex with Hemicholinium-3 and Adp


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 Human Choline Kinase Alpha in Complex with Hemicholinium-3 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:27.8
occ:1.00
 O2B A:ADP601 2.0 32.5 1.0
O2A A:ADP601 2.1 34.5 1.0
OD1 A:ASN311 2.1 18.0 1.0
O2 A:SO4604 2.1 28.8 1.0
OD1 A:ASP330 2.1 28.3 1.0
O A:HOH49 2.1 29.2 1.0
PB A:ADP601 3.1 40.2 1.0
CG A:ASN311 3.1 20.1 1.0
CG A:ASP330 3.1 24.4 1.0
S A:SO4604 3.3 38.1 1.0
PA A:ADP601 3.3 33.9 1.0
O4 A:SO4604 3.4 33.7 1.0
O3A A:ADP601 3.5 34.3 1.0
ND2 A:ASN311 3.5 20.4 1.0
CB A:ASP330 3.6 21.0 1.0
O1B A:ADP601 3.6 37.3 1.0
MG A:MG605 3.6 33.9 1.0
O3 A:SO4604 4.0 35.0 1.0
OD2 A:ASP330 4.2 26.1 1.0
O5' A:ADP601 4.3 34.2 1.0
C5' A:ADP601 4.3 33.2 1.0
O A:GLY310 4.3 21.3 1.0
O1A A:ADP601 4.4 33.7 1.0
CB A:ASN311 4.4 18.4 1.0
O3B A:ADP601 4.4 38.7 1.0
O1 A:SO4604 4.5 29.0 1.0
O A:HOH39 4.5 27.7 1.0
C A:GLY310 4.7 19.5 1.0
CA A:ASN311 4.7 18.6 1.0
N A:ASN311 4.8 17.4 1.0
O3' A:ADP601 4.8 32.1 1.0

Magnesium binding site 2 out of 4 in 3g15

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Choline Kinase Alpha in Complex with Hemicholinium-3 and Adp


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 Human Choline Kinase Alpha in Complex with Hemicholinium-3 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:33.9
occ:1.00
 OE2 A:GLU332 1.7 42.1 1.0
O4 A:SO4604 1.8 33.7 1.0
O1B A:ADP601 2.1 37.3 1.0
OD1 A:ASP330 2.2 28.3 1.0
O A:HOH39 2.6 27.7 1.0
OD2 A:ASP330 2.7 26.1 1.0
CG A:ASP330 2.8 24.4 1.0
CD A:GLU332 2.8 38.6 1.0
S A:SO4604 3.1 38.1 1.0
PB A:ADP601 3.3 40.2 1.0
CG A:GLU332 3.4 32.9 1.0
O2B A:ADP601 3.4 32.5 1.0
O2 A:SO4604 3.6 28.8 1.0
O A:HOH50 3.6 31.4 1.0
MG A:MG602 3.6 27.8 1.0
OE1 A:GLU332 3.9 41.0 1.0
O1 A:SO4604 4.0 29.0 1.0
O3 A:SO4604 4.1 35.0 1.0
OD2 A:ASP306 4.2 17.9 1.0
CE2 A:TYR333 4.3 20.6 1.0
CB A:ASP330 4.3 21.0 1.0
O3A A:ADP601 4.3 34.3 1.0
O3B A:ADP601 4.4 38.7 1.0
CB A:GLU332 4.5 27.4 1.0
O2A A:ADP601 4.7 34.5 1.0
CD2 A:TYR333 4.8 17.6 1.0
ND2 A:ASN311 4.9 20.4 1.0
OD1 A:ASN311 5.0 18.0 1.0
O A:ASP330 5.0 21.7 1.0

Magnesium binding site 3 out of 4 in 3g15

Go back to Magnesium Binding Sites List in 3g15
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Choline Kinase Alpha in Complex with Hemicholinium-3 and Adp


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 Human Choline Kinase Alpha in Complex with Hemicholinium-3 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:25.6
occ:1.00
 O2A B:ADP601 2.1 29.3 1.0
O1B B:ADP601 2.1 24.1 1.0
OD2 B:ASP330 2.1 27.4 1.0
OD1 B:ASN311 2.2 16.7 1.0
O B:HOH2 2.2 25.5 1.0
O2 B:SO4604 2.2 24.7 1.0
PB B:ADP601 3.2 31.9 1.0
CG B:ASP330 3.2 20.9 1.0
CG B:ASN311 3.2 18.5 1.0
PA B:ADP601 3.3 28.6 1.0
S B:SO4604 3.5 32.9 1.0
O3A B:ADP601 3.5 30.7 1.0
ND2 B:ASN311 3.6 17.3 1.0
CB B:ASP330 3.6 20.4 1.0
O3B B:ADP601 3.7 31.2 1.0
O3 B:SO4604 3.7 29.1 1.0
MG B:MG605 3.8 24.8 1.0
C5' B:ADP601 4.2 28.0 1.0
O5' B:ADP601 4.3 28.7 1.0
OD1 B:ASP330 4.3 24.9 1.0
O1 B:SO4604 4.3 29.0 1.0
O1A B:ADP601 4.4 28.9 1.0
O B:GLY310 4.4 21.0 1.0
O4 B:SO4604 4.5 24.9 1.0
CB B:ASN311 4.5 17.7 1.0
O2B B:ADP601 4.5 34.2 1.0
O3' B:ADP601 4.5 32.3 1.0
O B:HOH1 4.6 25.8 1.0
C B:GLY310 4.7 19.2 1.0
CA B:ASN311 4.8 17.1 1.0
N B:ASN311 4.9 17.5 1.0
C3' B:ADP601 4.9 30.5 1.0
NE2 B:GLN308 4.9 35.7 1.0

Magnesium binding site 4 out of 4 in 3g15

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Choline Kinase Alpha in Complex with Hemicholinium-3 and Adp


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 Human Choline Kinase Alpha in Complex with Hemicholinium-3 and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg605

b:24.8
occ:1.00
 OE2 B:GLU332 1.8 25.9 1.0
O3B B:ADP601 2.1 31.2 1.0
OD2 B:ASP330 2.2 27.4 1.0
O B:HOH1 2.2 25.8 1.0
O3 B:SO4604 2.3 29.1 1.0
OD1 B:ASP330 2.5 24.9 1.0
CG B:ASP330 2.7 20.9 1.0
CD B:GLU332 2.9 28.8 1.0
CG B:GLU332 3.4 26.1 1.0
PB B:ADP601 3.4 31.9 1.0
S B:SO4604 3.6 32.9 1.0
O1B B:ADP601 3.7 24.1 1.0
MG B:MG602 3.8 25.6 1.0
O B:HOH549 3.8 31.2 1.0
O2 B:SO4604 3.8 24.7 1.0
OE1 B:GLU332 4.0 30.5 1.0
OD2 B:ASP306 4.1 18.7 1.0
CB B:ASP330 4.2 20.4 1.0
O3A B:ADP601 4.2 30.7 1.0
CE2 B:TYR333 4.2 21.5 1.0
O B:HOH550 4.3 36.4 1.0
O4 B:SO4604 4.4 24.9 1.0
CB B:GLU332 4.4 23.8 1.0
O1 B:SO4604 4.5 29.0 1.0
O2B B:ADP601 4.6 34.2 1.0
CD2 B:TYR333 4.7 20.3 1.0
O2A B:ADP601 4.9 29.3 1.0
ND2 B:ASN311 4.9 17.3 1.0
O B:ASP330 4.9 18.9 1.0

Reference:

B.S.Hong, A.Allali-Hassani, W.Tempel, P.J.Finerty, F.Mackenzie, S.Dimov, M.Vedadi, H.W.Park. Crystal Structures of Human Choline Kinase Isoforms in Complex with Hemicholinium-3: Single Amino Acid Near the Active Site Influences Inhibitor Sensitivity. J.Biol.Chem. V. 285 16330 2010.
ISSN: ISSN 0021-9258
PubMed: 20299452
DOI: 10.1074/JBC.M109.039024
Page generated: Mon Dec 14 08:09:43 2020

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