Magnesium in PDB 8cip: Crystal Structure of Transketolase From Geobacillus Stearothermophilus
Enzymatic activity of Crystal Structure of Transketolase From Geobacillus Stearothermophilus
All present enzymatic activity of Crystal Structure of Transketolase From Geobacillus Stearothermophilus:
2.2.1.1;
Protein crystallography data
The structure of Crystal Structure of Transketolase From Geobacillus Stearothermophilus, PDB code: 8cip
was solved by
C.Leogrande,
F.Rabe Von Pappenheim,
K.Tittmann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.29 /
2.10
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.44,
82.71,
106.14,
80.89,
68.34,
69.99
|
|
R / Rfree (%)
|
16.8 /
22.8
|
Other elements in 8cip:
The structure of Crystal Structure of Transketolase From Geobacillus Stearothermophilus also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Transketolase From Geobacillus Stearothermophilus
(pdb code 8cip). 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 Transketolase From Geobacillus Stearothermophilus, PDB code: 8cip:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8cip
Go back to
Magnesium Binding Sites List in 8cip
Magnesium binding site 1 out
of 4 in the Crystal Structure of Transketolase From Geobacillus Stearothermophilus
 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 Transketolase From Geobacillus Stearothermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg810
b:27.4
occ:1.00
|
OD2
|
A:ASP157
|
2.0
|
26.6
|
1.0
|
|
O
|
A:ILE189
|
2.1
|
31.7
|
1.0
|
|
O3B
|
A:TPP809
|
2.1
|
30.7
|
1.0
|
|
O2A
|
A:TPP809
|
2.2
|
29.3
|
1.0
|
|
OD1
|
A:ASN187
|
2.2
|
27.0
|
1.0
|
|
O
|
A:HOH926
|
2.3
|
26.6
|
1.0
|
|
HD21
|
A:ASN187
|
3.0
|
32.7
|
1.0
|
|
CG
|
A:ASP157
|
3.1
|
25.6
|
1.0
|
|
CG
|
A:ASN187
|
3.2
|
32.8
|
1.0
|
|
H
|
A:ILE189
|
3.2
|
32.8
|
1.0
|
|
HB2
|
A:ASP157
|
3.3
|
26.9
|
1.0
|
|
C
|
A:ILE189
|
3.3
|
33.5
|
1.0
|
|
H
|
A:ASP157
|
3.3
|
30.9
|
1.0
|
|
PB
|
A:TPP809
|
3.3
|
30.0
|
1.0
|
|
PA
|
A:TPP809
|
3.4
|
34.4
|
1.0
|
|
ND2
|
A:ASN187
|
3.4
|
27.3
|
1.0
|
|
O3A
|
A:TPP809
|
3.5
|
34.7
|
1.0
|
|
CB
|
A:ASP157
|
3.7
|
22.4
|
1.0
|
|
HA
|
A:SER190
|
3.8
|
36.2
|
1.0
|
|
H
|
A:ASN187
|
3.9
|
34.1
|
1.0
|
|
N
|
A:ILE189
|
3.9
|
27.4
|
1.0
|
|
HB
|
A:ILE189
|
3.9
|
32.9
|
1.0
|
|
O7
|
A:TPP809
|
4.0
|
28.3
|
1.0
|
|
O
|
A:HOH998
|
4.0
|
36.1
|
1.0
|
|
CA
|
A:ILE189
|
4.1
|
27.7
|
1.0
|
|
N
|
A:ASP157
|
4.1
|
25.8
|
1.0
|
|
OD1
|
A:ASP157
|
4.2
|
24.4
|
1.0
|
|
HG22
|
A:ILE189
|
4.2
|
33.4
|
1.0
|
|
O1B
|
A:TPP809
|
4.2
|
34.0
|
1.0
|
|
N
|
A:SER190
|
4.3
|
30.2
|
1.0
|
|
HD22
|
A:ASN187
|
4.3
|
32.7
|
1.0
|
|
HD12
|
A:ILE249
|
4.4
|
44.9
|
1.0
|
|
O
|
A:ASP185
|
4.4
|
29.2
|
1.0
|
|
CB
|
A:ILE189
|
4.4
|
27.4
|
1.0
|
|
CA
|
A:SER190
|
4.4
|
30.1
|
1.0
|
|
HB3
|
A:ASP157
|
4.5
|
26.9
|
1.0
|
|
O2B
|
A:TPP809
|
4.5
|
32.4
|
1.0
|
|
CB
|
A:ASN187
|
4.6
|
29.6
|
1.0
|
|
O1A
|
A:TPP809
|
4.6
|
35.8
|
1.0
|
|
CA
|
A:ASP157
|
4.6
|
23.4
|
1.0
|
|
H
|
A:ASP188
|
4.6
|
36.4
|
1.0
|
|
N
|
A:ASN187
|
4.6
|
28.4
|
1.0
|
|
HD13
|
A:LEU195
|
4.7
|
43.7
|
1.0
|
|
N
|
A:ASP188
|
4.8
|
30.4
|
1.0
|
|
HB3
|
A:SER190
|
4.8
|
35.8
|
1.0
|
|
HA3
|
A:GLY156
|
4.8
|
31.0
|
1.0
|
|
H
|
A:GLY158
|
4.8
|
34.4
|
1.0
|
|
CG2
|
A:ILE189
|
4.9
|
27.8
|
1.0
|
|
C
|
A:ASN187
|
4.9
|
28.3
|
1.0
|
|
CA
|
A:ASN187
|
4.9
|
28.4
|
1.0
|
|
HA
|
A:ILE189
|
4.9
|
33.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8cip
Go back to
Magnesium Binding Sites List in 8cip
Magnesium binding site 2 out
of 4 in the Crystal Structure of Transketolase From Geobacillus Stearothermophilus
 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 Transketolase From Geobacillus Stearothermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg805
b:27.2
occ:1.00
|
O2A
|
B:TPP804
|
2.0
|
28.5
|
1.0
|
|
O
|
B:ILE189
|
2.1
|
28.8
|
1.0
|
|
O3B
|
B:TPP804
|
2.1
|
31.6
|
1.0
|
|
OD1
|
B:ASN187
|
2.2
|
29.1
|
1.0
|
|
OD2
|
B:ASP157
|
2.2
|
34.3
|
1.0
|
|
O
|
B:HOH919
|
2.2
|
24.7
|
1.0
|
|
HD21
|
B:ASN187
|
2.9
|
37.1
|
1.0
|
|
CG
|
B:ASN187
|
3.1
|
32.4
|
1.0
|
|
HB2
|
B:ASP157
|
3.1
|
44.0
|
1.0
|
|
H
|
B:ASP157
|
3.2
|
40.1
|
1.0
|
|
H
|
B:ILE189
|
3.2
|
32.5
|
1.0
|
|
PA
|
B:TPP804
|
3.2
|
32.5
|
1.0
|
|
CG
|
B:ASP157
|
3.2
|
35.9
|
1.0
|
|
PB
|
B:TPP804
|
3.3
|
32.3
|
1.0
|
|
C
|
B:ILE189
|
3.3
|
33.4
|
1.0
|
|
O3A
|
B:TPP804
|
3.3
|
33.7
|
1.0
|
|
ND2
|
B:ASN187
|
3.3
|
30.9
|
1.0
|
|
CB
|
B:ASP157
|
3.7
|
36.6
|
1.0
|
|
HA
|
B:SER190
|
3.8
|
43.9
|
1.0
|
|
H
|
B:ASN187
|
3.9
|
40.7
|
1.0
|
|
O
|
B:HOH986
|
3.9
|
41.4
|
1.0
|
|
HB
|
B:ILE189
|
3.9
|
38.2
|
1.0
|
|
N
|
B:ILE189
|
4.0
|
27.1
|
1.0
|
|
O7
|
B:TPP804
|
4.0
|
31.4
|
1.0
|
|
N
|
B:ASP157
|
4.0
|
33.4
|
1.0
|
|
O2B
|
B:TPP804
|
4.1
|
38.1
|
1.0
|
|
CA
|
B:ILE189
|
4.1
|
31.4
|
1.0
|
|
HD22
|
B:ASN187
|
4.2
|
37.1
|
1.0
|
|
OD1
|
B:ASP157
|
4.3
|
35.3
|
1.0
|
|
N
|
B:SER190
|
4.3
|
33.2
|
1.0
|
|
O1A
|
B:TPP804
|
4.4
|
33.9
|
1.0
|
|
HG22
|
B:ILE189
|
4.4
|
37.1
|
1.0
|
|
O1B
|
B:TPP804
|
4.4
|
36.1
|
1.0
|
|
HB3
|
B:ASP157
|
4.5
|
44.0
|
1.0
|
|
O
|
B:ASP185
|
4.5
|
32.4
|
1.0
|
|
CA
|
B:ASP157
|
4.5
|
31.0
|
1.0
|
|
CB
|
B:ILE189
|
4.5
|
31.8
|
1.0
|
|
CB
|
B:ASN187
|
4.5
|
30.7
|
1.0
|
|
CA
|
B:SER190
|
4.5
|
36.6
|
1.0
|
|
H
|
B:ASP188
|
4.6
|
39.0
|
1.0
|
|
HD12
|
B:ILE249
|
4.6
|
37.4
|
1.0
|
|
N
|
B:ASN187
|
4.6
|
33.9
|
1.0
|
|
N
|
B:ASP188
|
4.7
|
32.5
|
1.0
|
|
HA3
|
B:GLY156
|
4.8
|
32.5
|
1.0
|
|
H
|
B:GLY158
|
4.8
|
34.2
|
1.0
|
|
C
|
B:ASN187
|
4.8
|
31.3
|
1.0
|
|
CA
|
B:ASN187
|
4.9
|
27.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8cip
Go back to
Magnesium Binding Sites List in 8cip
Magnesium binding site 3 out
of 4 in the Crystal Structure of Transketolase From Geobacillus Stearothermophilus
 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 Transketolase From Geobacillus Stearothermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg810
b:32.4
occ:1.00
|
OD2
|
C:ASP157
|
1.9
|
28.9
|
1.0
|
|
O
|
C:HOH931
|
2.0
|
22.1
|
1.0
|
|
O
|
C:ILE189
|
2.0
|
31.9
|
1.0
|
|
O1A
|
C:TPP809
|
2.1
|
29.1
|
1.0
|
|
O3B
|
C:TPP809
|
2.1
|
28.9
|
1.0
|
|
OD1
|
C:ASN187
|
2.2
|
27.7
|
1.0
|
|
HD21
|
C:ASN187
|
2.9
|
38.6
|
1.0
|
|
H
|
C:ASP157
|
3.1
|
35.4
|
1.0
|
|
CG
|
C:ASP157
|
3.1
|
33.1
|
1.0
|
|
CG
|
C:ASN187
|
3.1
|
32.4
|
1.0
|
|
H
|
C:ILE189
|
3.2
|
40.3
|
1.0
|
|
PA
|
C:TPP809
|
3.2
|
32.4
|
1.0
|
|
C
|
C:ILE189
|
3.2
|
32.7
|
1.0
|
|
PB
|
C:TPP809
|
3.3
|
29.7
|
1.0
|
|
O3A
|
C:TPP809
|
3.3
|
34.1
|
1.0
|
|
ND2
|
C:ASN187
|
3.3
|
32.2
|
1.0
|
|
HB2
|
C:ASP157
|
3.3
|
33.1
|
1.0
|
|
CB
|
C:ASP157
|
3.7
|
27.6
|
1.0
|
|
HA
|
C:SER190
|
3.8
|
43.0
|
1.0
|
|
HB
|
C:ILE189
|
3.9
|
36.5
|
1.0
|
|
N
|
C:ILE189
|
3.9
|
33.5
|
1.0
|
|
N
|
C:ASP157
|
3.9
|
29.5
|
1.0
|
|
H
|
C:ASN187
|
3.9
|
38.6
|
1.0
|
|
CA
|
C:ILE189
|
4.0
|
33.2
|
1.0
|
|
OD1
|
C:ASP157
|
4.1
|
28.0
|
1.0
|
|
O2B
|
C:TPP809
|
4.2
|
34.8
|
1.0
|
|
HD22
|
C:ASN187
|
4.2
|
38.6
|
1.0
|
|
O7
|
C:TPP809
|
4.2
|
33.1
|
1.0
|
|
N
|
C:SER190
|
4.3
|
38.7
|
1.0
|
|
O2A
|
C:TPP809
|
4.3
|
37.8
|
1.0
|
|
O1B
|
C:TPP809
|
4.4
|
37.5
|
1.0
|
|
CB
|
C:ILE189
|
4.4
|
30.4
|
1.0
|
|
O
|
C:ASP185
|
4.4
|
30.8
|
1.0
|
|
HG22
|
C:ILE189
|
4.5
|
38.3
|
1.0
|
|
CA
|
C:ASP157
|
4.5
|
29.9
|
1.0
|
|
CA
|
C:SER190
|
4.5
|
35.8
|
1.0
|
|
HD12
|
C:ILE249
|
4.5
|
31.6
|
1.0
|
|
CB
|
C:ASN187
|
4.5
|
29.9
|
1.0
|
|
HB3
|
C:ASP157
|
4.6
|
33.1
|
1.0
|
|
HA3
|
C:GLY156
|
4.6
|
29.3
|
1.0
|
|
H
|
C:ASP188
|
4.6
|
38.9
|
1.0
|
|
N
|
C:ASN187
|
4.7
|
32.2
|
1.0
|
|
H
|
C:GLY158
|
4.7
|
33.5
|
1.0
|
|
N
|
C:ASP188
|
4.8
|
32.4
|
1.0
|
|
C
|
C:ASN187
|
4.9
|
32.4
|
1.0
|
|
HA
|
C:ILE189
|
4.9
|
39.8
|
1.0
|
|
C
|
C:GLY156
|
4.9
|
27.2
|
1.0
|
|
CA
|
C:ASN187
|
4.9
|
31.1
|
1.0
|
|
HA2
|
C:GLY156
|
5.0
|
29.3
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8cip
Go back to
Magnesium Binding Sites List in 8cip
Magnesium binding site 4 out
of 4 in the Crystal Structure of Transketolase From Geobacillus Stearothermophilus
 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 Transketolase From Geobacillus Stearothermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg805
b:23.5
occ:1.00
|
OD2
|
D:ASP157
|
1.9
|
27.6
|
1.0
|
|
O1B
|
D:TPP804
|
2.0
|
29.0
|
1.0
|
|
O
|
D:ILE189
|
2.0
|
27.0
|
1.0
|
|
OD1
|
D:ASN187
|
2.0
|
26.0
|
1.0
|
|
O1A
|
D:TPP804
|
2.1
|
27.9
|
1.0
|
|
O
|
D:HOH938
|
2.2
|
27.2
|
1.0
|
|
HD21
|
D:ASN187
|
3.0
|
28.9
|
1.0
|
|
CG
|
D:ASN187
|
3.0
|
27.6
|
1.0
|
|
CG
|
D:ASP157
|
3.1
|
30.2
|
1.0
|
|
H
|
D:ILE189
|
3.1
|
33.4
|
1.0
|
|
PB
|
D:TPP804
|
3.2
|
32.6
|
1.0
|
|
C
|
D:ILE189
|
3.2
|
25.6
|
1.0
|
|
PA
|
D:TPP804
|
3.3
|
34.3
|
1.0
|
|
H
|
D:ASP157
|
3.3
|
35.7
|
1.0
|
|
HB2
|
D:ASP157
|
3.3
|
33.3
|
1.0
|
|
O3A
|
D:TPP804
|
3.4
|
32.5
|
1.0
|
|
ND2
|
D:ASN187
|
3.4
|
24.1
|
1.0
|
|
HA
|
D:SER190
|
3.7
|
39.1
|
1.0
|
|
CB
|
D:ASP157
|
3.8
|
27.8
|
1.0
|
|
H
|
D:ASN187
|
3.8
|
32.2
|
1.0
|
|
N
|
D:ILE189
|
3.9
|
27.9
|
1.0
|
|
HB
|
D:ILE189
|
3.9
|
32.7
|
1.0
|
|
O7
|
D:TPP804
|
4.0
|
30.0
|
1.0
|
|
O3B
|
D:TPP804
|
4.0
|
35.4
|
1.0
|
|
CA
|
D:ILE189
|
4.0
|
32.6
|
1.0
|
|
HG22
|
D:ILE189
|
4.1
|
41.8
|
1.0
|
|
N
|
D:ASP157
|
4.1
|
29.7
|
1.0
|
|
OD1
|
D:ASP157
|
4.1
|
34.9
|
1.0
|
|
N
|
D:SER190
|
4.2
|
33.1
|
1.0
|
|
HD22
|
D:ASN187
|
4.2
|
28.9
|
1.0
|
|
O2B
|
D:TPP804
|
4.3
|
31.6
|
1.0
|
|
HD12
|
D:ILE249
|
4.3
|
42.8
|
1.0
|
|
H
|
D:ASP188
|
4.4
|
35.8
|
1.0
|
|
CA
|
D:SER190
|
4.4
|
32.6
|
1.0
|
|
CB
|
D:ILE189
|
4.4
|
27.3
|
1.0
|
|
CB
|
D:ASN187
|
4.5
|
25.3
|
1.0
|
|
O
|
D:ASP185
|
4.5
|
28.5
|
1.0
|
|
O2A
|
D:TPP804
|
4.5
|
32.6
|
1.0
|
|
HB3
|
D:ASP157
|
4.5
|
33.3
|
1.0
|
|
CA
|
D:ASP157
|
4.6
|
25.0
|
1.0
|
|
N
|
D:ASN187
|
4.6
|
26.9
|
1.0
|
|
N
|
D:ASP188
|
4.6
|
29.8
|
1.0
|
|
C
|
D:ASN187
|
4.7
|
24.3
|
1.0
|
|
HB3
|
D:SER190
|
4.7
|
40.2
|
1.0
|
|
CG2
|
D:ILE189
|
4.8
|
34.9
|
1.0
|
|
CA
|
D:ASN187
|
4.8
|
24.3
|
1.0
|
|
HA3
|
D:GLY156
|
4.8
|
29.2
|
1.0
|
|
HA
|
D:ILE189
|
4.9
|
39.2
|
1.0
|
|
HB2
|
D:ASN187
|
5.0
|
30.3
|
1.0
|
|
H
|
D:GLY158
|
5.0
|
32.1
|
1.0
|
|
Reference:
C.Leogrande,
F.Rabe Von Pappenheim,
K.Tittman.
Crystal Structure of Transketolase From Geobacillus Stearothermophilus To Be Published.
Page generated: Thu Oct 3 21:37:31 2024
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