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Magnesium in PDB 6k28: Crystal Structure of the 5-(Hydroxyethyl)-Methylthiazole Kinase Thim From Klebsiella Pneumonia in Complex with Tze

Enzymatic activity of Crystal Structure of the 5-(Hydroxyethyl)-Methylthiazole Kinase Thim From Klebsiella Pneumonia in Complex with Tze

All present enzymatic activity of Crystal Structure of the 5-(Hydroxyethyl)-Methylthiazole Kinase Thim From Klebsiella Pneumonia in Complex with Tze:
2.7.1.50;

Protein crystallography data

The structure of Crystal Structure of the 5-(Hydroxyethyl)-Methylthiazole Kinase Thim From Klebsiella Pneumonia in Complex with Tze, PDB code: 6k28 was solved by Y.Chen, L.Wang, F.Shang, J.Lan, W.Liu, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.18 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.894, 109.330, 124.631, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 22.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the 5-(Hydroxyethyl)-Methylthiazole Kinase Thim From Klebsiella Pneumonia in Complex with Tze (pdb code 6k28). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the 5-(Hydroxyethyl)-Methylthiazole Kinase Thim From Klebsiella Pneumonia in Complex with Tze, PDB code: 6k28:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6k28

Go back to Magnesium Binding Sites List in 6k28
Magnesium binding site 1 out of 3 in the Crystal Structure of the 5-(Hydroxyethyl)-Methylthiazole Kinase Thim From Klebsiella Pneumonia in Complex with Tze


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 the 5-(Hydroxyethyl)-Methylthiazole Kinase Thim From Klebsiella Pneumonia in Complex with Tze within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:32.2
occ:1.00
OE1 A:GLU129 2.6 18.2 1.0
HH12 A:ARG124 2.7 26.3 1.0
OD1 A:ASP98 2.7 19.2 1.0
O A:HOH539 3.0 38.4 1.0
HG22 A:VAL100 3.0 18.2 1.0
HA2 A:GLY125 3.0 19.5 1.0
NH1 A:ARG124 3.1 21.9 1.0
HA A:VAL100 3.1 12.7 1.0
O A:HOH558 3.2 38.9 1.0
HH11 A:ARG124 3.4 26.3 1.0
CD A:GLU129 3.4 18.5 1.0
OE2 A:GLU129 3.5 16.6 1.0
HH22 A:ARG124 3.5 28.8 1.0
H A:ASN126 3.5 16.0 1.0
CZ A:ARG124 3.7 21.9 1.0
CG A:ASP98 3.7 20.8 1.0
O A:HOH455 3.7 34.1 1.0
HD2 A:PRO99 3.8 14.5 1.0
CG2 A:VAL100 3.8 15.2 1.0
NH2 A:ARG124 3.9 24.0 1.0
CA A:GLY125 3.9 16.2 1.0
HG23 A:VAL100 3.9 18.2 1.0
CA A:VAL100 3.9 10.6 1.0
OD2 A:ASP98 4.0 17.8 1.0
N A:VAL100 4.1 11.8 1.0
N A:ASN126 4.2 13.4 1.0
HA3 A:GLY125 4.2 19.5 1.0
O A:ARG124 4.2 16.2 1.0
HG13 A:VAL100 4.4 19.9 1.0
H A:VAL100 4.4 14.2 1.0
CB A:VAL100 4.4 12.8 1.0
C A:GLY125 4.5 16.4 1.0
C A:PRO99 4.5 13.3 1.0
HG2 A:PRO99 4.5 15.7 1.0
HH21 A:ARG124 4.5 28.8 1.0
HG21 A:VAL100 4.6 18.2 1.0
CD A:PRO99 4.6 12.1 1.0
HB3 A:ASN126 4.6 28.1 1.0
H A:ALA101 4.7 18.1 1.0
O A:PRO99 4.7 15.3 1.0
NE A:ARG124 4.7 22.0 1.0
N A:PRO99 4.7 12.0 1.0
CG A:GLU129 4.9 15.4 1.0
HE A:ARG124 4.9 26.4 1.0
N A:GLY125 4.9 11.5 1.0
HA A:ASP98 4.9 15.5 1.0
C A:ARG124 5.0 15.7 1.0
CG1 A:VAL100 5.0 16.6 1.0
C A:ASP98 5.0 9.8 1.0
HB2 A:GLU129 5.0 18.1 1.0

Magnesium binding site 2 out of 3 in 6k28

Go back to Magnesium Binding Sites List in 6k28
Magnesium binding site 2 out of 3 in the Crystal Structure of the 5-(Hydroxyethyl)-Methylthiazole Kinase Thim From Klebsiella Pneumonia in Complex with Tze


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 the 5-(Hydroxyethyl)-Methylthiazole Kinase Thim From Klebsiella Pneumonia in Complex with Tze within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:37.7
occ:1.00
HH22 B:ARG124 2.5 27.1 1.0
OD1 B:ASP98 2.6 16.2 1.0
OE1 B:GLU129 2.6 27.1 1.0
HG22 B:VAL100 2.9 25.4 1.0
NH2 B:ARG124 2.9 22.6 1.0
O B:HOH410 3.0 36.4 1.0
HA B:VAL100 3.1 22.1 1.0
HA2 B:GLY125 3.1 23.7 1.0
HH21 B:ARG124 3.3 27.1 1.0
O B:HOH474 3.4 42.3 1.0
HH12 B:ARG124 3.4 25.3 1.0
CD B:GLU129 3.4 30.1 1.0
OE2 B:GLU129 3.5 25.9 1.0
CZ B:ARG124 3.6 23.2 1.0
CG B:ASP98 3.6 18.9 1.0
NH1 B:ARG124 3.7 21.1 1.0
CG2 B:VAL100 3.7 21.2 1.0
H B:ASN126 3.8 27.4 1.0
CA B:VAL100 3.9 18.4 1.0
OD2 B:ASP98 3.9 20.9 1.0
HG23 B:VAL100 3.9 25.4 1.0
O B:HOH548 4.0 37.1 1.0
CA B:GLY125 4.0 19.7 1.0
HG13 B:VAL100 4.0 24.1 1.0
N B:VAL100 4.1 17.7 1.0
O B:ARG124 4.2 15.7 1.0
HD2 B:PRO99 4.2 20.4 1.0
CB B:VAL100 4.3 14.1 1.0
HA3 B:GLY125 4.3 23.7 1.0
H B:VAL100 4.3 21.2 1.0
N B:ASN126 4.4 22.8 1.0
HH11 B:ARG124 4.4 25.3 1.0
C B:PRO99 4.4 18.7 1.0
HG21 B:VAL100 4.5 25.4 1.0
NE B:ARG124 4.5 17.5 1.0
C B:GLY125 4.6 20.6 1.0
HD22 B:ASN126 4.7 42.4 1.0
CG1 B:VAL100 4.7 20.1 1.0
HE B:ARG124 4.7 21.1 1.0
O B:PRO99 4.7 21.6 1.0
H B:ALA101 4.7 18.5 1.0
HG2 B:PRO99 4.7 23.5 1.0
N B:PRO99 4.7 16.1 1.0
C B:ASP98 4.8 17.9 1.0
ND2 B:ASN126 4.9 35.3 1.0
CG B:GLU129 4.9 21.4 1.0
HA B:ASP98 4.9 18.3 1.0
CD B:PRO99 4.9 17.0 1.0
N B:GLY125 5.0 15.8 1.0
C B:ARG124 5.0 19.9 1.0
CB B:ASP98 5.0 13.1 1.0
HXT A:TZE301 5.0 60.3 1.0

Magnesium binding site 3 out of 3 in 6k28

Go back to Magnesium Binding Sites List in 6k28
Magnesium binding site 3 out of 3 in the Crystal Structure of the 5-(Hydroxyethyl)-Methylthiazole Kinase Thim From Klebsiella Pneumonia in Complex with Tze


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 the 5-(Hydroxyethyl)-Methylthiazole Kinase Thim From Klebsiella Pneumonia in Complex with Tze within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:43.6
occ:1.00
HH22 C:ARG124 2.5 49.1 1.0
OD1 C:ASP98 2.6 25.9 1.0
OE1 C:GLU129 2.7 38.5 1.0
NH2 C:ARG124 2.8 41.0 1.0
HG22 C:VAL100 2.9 25.4 1.0
O C:HOH462 2.9 34.4 1.0
HH21 C:ARG124 3.1 49.1 1.0
HA C:VAL100 3.1 32.8 1.0
HA2 C:GLY125 3.2 43.1 1.0
CZ C:ARG124 3.4 43.6 1.0
CD C:GLU129 3.5 47.2 1.0
HH12 C:ARG124 3.5 43.5 1.0
OE2 C:GLU129 3.5 40.1 1.0
CG C:ASP98 3.6 28.6 1.0
CG2 C:VAL100 3.7 21.2 1.0
NH1 C:ARG124 3.7 36.2 1.0
HG23 C:VAL100 3.8 25.4 1.0
OD2 C:ASP98 3.9 27.6 1.0
H C:ASN126 3.9 35.3 1.0
CA C:VAL100 3.9 27.3 1.0
HD2 C:PRO99 4.0 32.2 1.0
CA C:GLY125 4.1 35.9 1.0
N C:VAL100 4.2 24.9 1.0
O C:ARG124 4.2 23.1 1.0
HG13 C:VAL100 4.3 32.1 1.0
NE C:ARG124 4.3 35.8 1.0
CB C:VAL100 4.4 28.1 1.0
HH11 C:ARG124 4.4 43.5 1.0
HG21 C:VAL100 4.4 25.4 1.0
H C:VAL100 4.4 29.9 1.0
HA3 C:GLY125 4.4 43.1 1.0
HE C:ARG124 4.4 43.0 1.0
N C:ASN126 4.5 29.4 1.0
C C:PRO99 4.6 31.9 1.0
H C:ALA101 4.7 32.2 1.0
C C:GLY125 4.8 34.6 1.0
CD C:PRO99 4.8 26.9 1.0
N C:PRO99 4.8 25.9 1.0
O C:PRO99 4.8 27.2 1.0
CG1 C:VAL100 4.9 26.8 1.0
HA C:ASP98 4.9 27.0 1.0
C C:ASP98 4.9 26.9 1.0
CB C:ASP98 4.9 24.1 1.0
CG C:GLU129 4.9 39.4 1.0
HG2 C:PRO99 5.0 26.9 1.0

Reference:

Y.Chen, L.Wang, F.Shang, J.Lan, W.Liu, Y.Xu. Crystal Structure of the 5-(Hydroxyethyl)-Methylthiazole Kinase Thim From Klebsiella Pneumonia To Be Published.
Page generated: Tue Oct 1 06:24:04 2024

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