Magnesium in PDB 6kd2: Room Temperature Structure of Glucose Isomerase Delivered in Gelatin By Serial Millisecond Crystallography
Enzymatic activity of Room Temperature Structure of Glucose Isomerase Delivered in Gelatin By Serial Millisecond Crystallography
All present enzymatic activity of Room Temperature Structure of Glucose Isomerase Delivered in Gelatin By Serial Millisecond Crystallography:
5.3.1.5;
Protein crystallography data
The structure of Room Temperature Structure of Glucose Isomerase Delivered in Gelatin By Serial Millisecond Crystallography, PDB code: 6kd2
was solved by
K.H.Nam,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
72.00 /
1.70
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.520,
100.170,
103.570,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.3 /
22.4
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Room Temperature Structure of Glucose Isomerase Delivered in Gelatin By Serial Millisecond Crystallography
(pdb code 6kd2). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the
Room Temperature Structure of Glucose Isomerase Delivered in Gelatin By Serial Millisecond Crystallography, PDB code: 6kd2:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 6kd2
Go back to
Magnesium Binding Sites List in 6kd2
Magnesium binding site 1 out
of 2 in the Room Temperature Structure of Glucose Isomerase Delivered in Gelatin By Serial Millisecond Crystallography
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Room Temperature Structure of Glucose Isomerase Delivered in Gelatin By Serial Millisecond Crystallography within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:16.7
occ:1.00
|
OE1
|
A:GLU217
|
2.0
|
26.8
|
1.0
|
OD2
|
A:ASP255
|
2.2
|
31.6
|
1.0
|
O
|
A:HOH535
|
2.2
|
32.5
|
1.0
|
OD1
|
A:ASP255
|
2.3
|
30.0
|
1.0
|
OD1
|
A:ASP257
|
2.3
|
32.0
|
1.0
|
NE2
|
A:HIS220
|
2.6
|
27.2
|
1.0
|
CG
|
A:ASP255
|
2.6
|
32.6
|
1.0
|
CD
|
A:GLU217
|
3.1
|
21.2
|
1.0
|
HD2
|
A:HIS220
|
3.1
|
28.6
|
1.0
|
CD2
|
A:HIS220
|
3.2
|
23.8
|
1.0
|
CG
|
A:ASP257
|
3.2
|
30.0
|
1.0
|
OD2
|
A:ASP257
|
3.3
|
31.9
|
1.0
|
HD21
|
A:ASN247
|
3.4
|
30.0
|
1.0
|
OE2
|
A:GLU217
|
3.5
|
27.3
|
1.0
|
O
|
A:HOH656
|
3.7
|
35.9
|
1.0
|
CE1
|
A:HIS220
|
3.7
|
22.7
|
1.0
|
HE1
|
A:HIS220
|
4.0
|
27.3
|
1.0
|
HD22
|
A:ASN247
|
4.0
|
30.0
|
1.0
|
ND2
|
A:ASN247
|
4.0
|
25.0
|
1.0
|
HE3
|
A:LYS183
|
4.1
|
29.9
|
1.0
|
O
|
A:HOH562
|
4.1
|
25.6
|
1.0
|
CB
|
A:ASP255
|
4.1
|
19.7
|
1.0
|
HZ2
|
A:LYS183
|
4.2
|
37.8
|
1.0
|
CG
|
A:HIS220
|
4.4
|
19.3
|
1.0
|
HG2
|
A:GLU217
|
4.4
|
23.6
|
1.0
|
CG
|
A:GLU217
|
4.4
|
19.6
|
1.0
|
HB3
|
A:ASP255
|
4.5
|
23.6
|
1.0
|
HB2
|
A:ASP255
|
4.5
|
23.6
|
1.0
|
HZ1
|
A:LYS183
|
4.6
|
37.8
|
1.0
|
ND1
|
A:HIS220
|
4.6
|
23.1
|
1.0
|
H
|
A:ASP257
|
4.6
|
27.7
|
1.0
|
CB
|
A:ASP257
|
4.6
|
23.4
|
1.0
|
HA
|
A:ASP257
|
4.7
|
28.6
|
1.0
|
NZ
|
A:LYS183
|
4.7
|
31.5
|
1.0
|
O
|
A:HOH574
|
4.8
|
34.0
|
1.0
|
CE
|
A:LYS183
|
4.8
|
24.9
|
1.0
|
OD2
|
A:ASP287
|
4.9
|
31.9
|
1.0
|
HA
|
A:ASP255
|
5.0
|
20.7
|
1.0
|
HD2
|
A:LYS183
|
5.0
|
29.6
|
1.0
|
HA3
|
A:GLY219
|
5.0
|
27.4
|
1.0
|
HG3
|
A:GLU217
|
5.0
|
23.6
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 6kd2
Go back to
Magnesium Binding Sites List in 6kd2
Magnesium binding site 2 out
of 2 in the Room Temperature Structure of Glucose Isomerase Delivered in Gelatin By Serial Millisecond Crystallography
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Room Temperature Structure of Glucose Isomerase Delivered in Gelatin By Serial Millisecond Crystallography within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:23.1
occ:1.00
|
OE2
|
A:GLU181
|
2.2
|
44.8
|
1.0
|
OD2
|
A:ASP287
|
2.2
|
31.9
|
1.0
|
OE2
|
A:GLU217
|
2.3
|
27.3
|
1.0
|
OD2
|
A:ASP245
|
2.3
|
29.2
|
1.0
|
O
|
A:HOH574
|
2.6
|
34.0
|
1.0
|
CD
|
A:GLU181
|
2.9
|
32.8
|
1.0
|
O
|
A:HOH510
|
3.0
|
42.8
|
1.0
|
OE1
|
A:GLU181
|
3.1
|
32.9
|
1.0
|
CG
|
A:ASP287
|
3.3
|
30.8
|
1.0
|
CG
|
A:ASP245
|
3.5
|
24.8
|
1.0
|
CD
|
A:GLU217
|
3.5
|
21.2
|
1.0
|
HE1
|
A:HIS220
|
3.6
|
27.3
|
1.0
|
HB3
|
A:ASP287
|
3.6
|
28.6
|
1.0
|
HB2
|
A:GLU217
|
3.6
|
23.7
|
1.0
|
HB2
|
A:ASP287
|
3.7
|
28.6
|
1.0
|
CB
|
A:ASP287
|
3.8
|
23.8
|
1.0
|
HB3
|
A:ASP245
|
4.0
|
26.9
|
1.0
|
HB2
|
A:ASP245
|
4.1
|
26.9
|
1.0
|
O
|
A:HOH618
|
4.1
|
51.8
|
1.0
|
CB
|
A:ASP245
|
4.1
|
22.4
|
1.0
|
CE1
|
A:HIS220
|
4.2
|
22.7
|
1.0
|
O
|
A:HOH535
|
4.2
|
32.5
|
1.0
|
CG
|
A:GLU217
|
4.3
|
19.6
|
1.0
|
CG
|
A:GLU181
|
4.3
|
28.5
|
1.0
|
HD21
|
A:ASN215
|
4.3
|
30.8
|
1.0
|
OE1
|
A:GLU217
|
4.4
|
26.8
|
1.0
|
HG3
|
A:GLU217
|
4.4
|
23.6
|
1.0
|
CB
|
A:GLU217
|
4.4
|
19.8
|
1.0
|
OD1
|
A:ASP287
|
4.4
|
30.4
|
1.0
|
OD1
|
A:ASP245
|
4.4
|
25.2
|
1.0
|
HG3
|
A:GLU181
|
4.5
|
34.2
|
1.0
|
HG2
|
A:GLU181
|
4.7
|
34.2
|
1.0
|
HZ2
|
A:TRP16
|
4.7
|
32.5
|
1.0
|
HD22
|
A:ASN215
|
4.7
|
30.8
|
1.0
|
HB3
|
A:GLU217
|
4.7
|
23.7
|
1.0
|
NE2
|
A:HIS220
|
4.7
|
27.2
|
1.0
|
ND2
|
A:ASN215
|
4.8
|
25.7
|
1.0
|
ND1
|
A:HIS220
|
4.9
|
23.1
|
1.0
|
|
Reference:
K.H.Nam,
K.H.Nam.
N/A N/A.
Page generated: Mon Dec 14 23:05:26 2020
|