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
|