Magnesium in PDB 8jk3: Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form
Enzymatic activity of Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form
All present enzymatic activity of Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form:
3.5.2.6;
Protein crystallography data
The structure of Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form, PDB code: 8jk3
was solved by
K.Dhankhar,
S.Hazra,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.13 /
1.50
|
Space group
|
P 65
|
Cell size a, b, c (Å), α, β, γ (°)
|
121.192,
121.192,
72.128,
90,
90,
120
|
R / Rfree (%)
|
15 /
20.9
|
Other elements in 8jk3:
The structure of Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form
(pdb code 8jk3). 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 Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form, PDB code: 8jk3:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8jk3
Go back to
Magnesium Binding Sites List in 8jk3
Magnesium binding site 1 out
of 4 in the Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form
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 Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg301
b:47.2
occ:1.00
|
HD2
|
B:ARG216
|
2.3
|
26.9
|
1.0
|
O
|
B:HOH655
|
2.5
|
35.5
|
1.0
|
HH11
|
B:ARG216
|
2.6
|
28.4
|
1.0
|
HH12
|
B:ARG216
|
2.6
|
28.5
|
1.0
|
NH1
|
B:ARG216
|
2.7
|
27.7
|
1.0
|
HG2
|
B:ARG216
|
2.8
|
23.3
|
1.0
|
O
|
B:HOH567
|
2.8
|
30.2
|
1.0
|
HB2
|
B:ALA247
|
2.8
|
22.4
|
1.0
|
HG21
|
B:THR193
|
2.9
|
17.0
|
1.0
|
HA
|
B:ALA247
|
3.0
|
20.8
|
1.0
|
CD
|
B:ARG216
|
3.0
|
27.1
|
1.0
|
HG3
|
B:ARG216
|
3.0
|
23.4
|
1.0
|
HG23
|
B:THR193
|
3.1
|
17.0
|
1.0
|
CG
|
B:ARG216
|
3.1
|
23.0
|
1.0
|
CG2
|
B:THR193
|
3.3
|
17.7
|
1.0
|
HG22
|
B:THR193
|
3.4
|
17.1
|
1.0
|
CB
|
B:ALA247
|
3.4
|
22.9
|
1.0
|
HB1
|
B:ALA247
|
3.4
|
22.3
|
1.0
|
CA
|
B:ALA247
|
3.5
|
20.5
|
1.0
|
CZ
|
B:ARG216
|
3.6
|
34.4
|
1.0
|
NE
|
B:ARG216
|
3.7
|
30.1
|
1.0
|
HD3
|
B:ARG216
|
3.8
|
26.6
|
1.0
|
HD12
|
B:ILE250
|
3.8
|
18.4
|
1.0
|
N
|
B:ALA247
|
3.9
|
19.4
|
1.0
|
O
|
B:HOH636
|
3.9
|
25.3
|
1.0
|
H
|
B:ALA247
|
4.1
|
20.1
|
1.0
|
O
|
B:HOH514
|
4.1
|
25.1
|
1.0
|
O
|
B:HOH627
|
4.3
|
36.0
|
1.0
|
HB3
|
B:ALA247
|
4.3
|
22.2
|
1.0
|
HD13
|
B:ILE250
|
4.5
|
18.5
|
1.0
|
C
|
B:ARG246
|
4.5
|
22.3
|
1.0
|
HB2
|
B:ARG246
|
4.5
|
25.2
|
1.0
|
HE
|
B:ARG216
|
4.5
|
29.8
|
1.0
|
CD1
|
B:ILE250
|
4.6
|
18.9
|
1.0
|
CB
|
B:ARG216
|
4.6
|
21.8
|
1.0
|
O
|
B:ARG246
|
4.7
|
19.9
|
1.0
|
CB
|
B:THR193
|
4.8
|
15.0
|
1.0
|
HB3
|
B:ARG246
|
4.8
|
25.1
|
1.0
|
O
|
B:HOH575
|
4.8
|
46.5
|
1.0
|
O
|
B:GLY243
|
4.8
|
32.5
|
1.0
|
NH2
|
B:ARG216
|
4.9
|
32.3
|
1.0
|
HG21
|
B:THR208
|
5.0
|
16.6
|
1.0
|
C
|
B:ALA247
|
5.0
|
20.4
|
1.0
|
HB2
|
B:ARG216
|
5.0
|
21.1
|
1.0
|
HB
|
B:THR193
|
5.0
|
15.3
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8jk3
Go back to
Magnesium Binding Sites List in 8jk3
Magnesium binding site 2 out
of 4 in the Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form
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 Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg302
b:44.9
occ:1.00
|
CL
|
B:CL305
|
2.1
|
48.7
|
1.0
|
HG1
|
B:THR93
|
2.5
|
30.0
|
0.0
|
HB3
|
B:PRO63
|
2.9
|
24.7
|
1.0
|
HD12
|
B:ILE96
|
3.2
|
18.0
|
1.0
|
OG1
|
B:THR93
|
3.4
|
25.4
|
1.0
|
HG22
|
B:THR93
|
3.5
|
25.2
|
1.0
|
HD23
|
B:LEU53
|
3.5
|
18.3
|
1.0
|
HA
|
B:THR93
|
3.5
|
17.4
|
1.0
|
HB2
|
B:PRO63
|
3.6
|
24.8
|
1.0
|
CB
|
B:PRO63
|
3.7
|
25.4
|
1.0
|
HD11
|
B:ILE56
|
3.8
|
21.7
|
1.0
|
HD21
|
B:LEU53
|
3.8
|
18.3
|
1.0
|
OE1
|
B:GLN179
|
3.9
|
28.4
|
1.0
|
HD12
|
B:ILE56
|
3.9
|
21.7
|
1.0
|
CD1
|
B:ILE96
|
4.0
|
19.1
|
1.0
|
HD11
|
B:ILE96
|
4.1
|
18.1
|
1.0
|
CD2
|
B:LEU53
|
4.1
|
18.8
|
1.0
|
HA
|
B:PRO63
|
4.1
|
23.3
|
1.0
|
CB
|
B:THR93
|
4.1
|
23.1
|
1.0
|
CD1
|
B:ILE56
|
4.2
|
21.6
|
1.0
|
CG2
|
B:THR93
|
4.2
|
25.7
|
1.0
|
HD13
|
B:ILE56
|
4.2
|
21.5
|
1.0
|
HD13
|
B:ILE96
|
4.2
|
17.9
|
1.0
|
CA
|
B:THR93
|
4.2
|
17.0
|
1.0
|
HG12
|
B:VAL92
|
4.3
|
18.1
|
1.0
|
O
|
B:HOH589
|
4.3
|
38.2
|
1.0
|
O
|
B:HOH532
|
4.4
|
30.4
|
1.0
|
CA
|
B:PRO63
|
4.5
|
23.6
|
1.0
|
HG21
|
B:THR93
|
4.5
|
25.1
|
1.0
|
HD22
|
B:LEU53
|
4.5
|
18.5
|
1.0
|
O
|
B:HOH695
|
4.6
|
39.2
|
1.0
|
HB
|
B:ILE96
|
4.7
|
14.5
|
1.0
|
CD
|
B:GLN179
|
4.8
|
23.3
|
1.0
|
N
|
B:THR93
|
4.8
|
17.7
|
1.0
|
HG3
|
B:PRO63
|
4.8
|
23.4
|
1.0
|
HG23
|
B:ILE96
|
4.8
|
15.1
|
1.0
|
CG
|
B:PRO63
|
4.9
|
23.5
|
1.0
|
HE22
|
B:GLN179
|
4.9
|
26.9
|
1.0
|
HB3
|
B:GLN179
|
4.9
|
18.0
|
1.0
|
HG23
|
B:THR93
|
5.0
|
24.9
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8jk3
Go back to
Magnesium Binding Sites List in 8jk3
Magnesium binding site 3 out
of 4 in the Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form
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 Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg303
b:55.1
occ:1.00
|
O
|
B:HOH667
|
2.0
|
49.9
|
1.0
|
CL
|
B:CL306
|
2.0
|
57.3
|
1.0
|
O
|
B:HOH688
|
3.0
|
35.0
|
1.0
|
OH
|
B:TYR77
|
4.1
|
15.9
|
1.0
|
CZ
|
B:TYR77
|
4.1
|
16.8
|
1.0
|
HH
|
B:TYR77
|
4.2
|
30.0
|
0.0
|
HG21
|
B:THR189
|
4.3
|
14.6
|
1.0
|
CE1
|
B:TYR77
|
4.4
|
17.6
|
1.0
|
HE1
|
B:TYR77
|
4.5
|
17.3
|
1.0
|
CL
|
B:CL307
|
4.6
|
27.5
|
1.0
|
CE2
|
B:TYR77
|
4.6
|
15.1
|
1.0
|
O
|
B:HOH672
|
4.6
|
38.0
|
1.0
|
MG
|
B:MG304
|
4.7
|
38.0
|
1.0
|
HB3
|
B:SER103
|
4.7
|
14.9
|
1.0
|
HG23
|
B:THR189
|
4.8
|
14.7
|
1.0
|
O
|
B:HOH685
|
4.8
|
39.2
|
1.0
|
HE2
|
B:TYR77
|
4.8
|
15.4
|
1.0
|
O
|
B:HOH575
|
4.9
|
46.5
|
1.0
|
HB
|
B:THR189
|
4.9
|
14.8
|
1.0
|
CG2
|
B:THR189
|
5.0
|
14.5
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8jk3
Go back to
Magnesium Binding Sites List in 8jk3
Magnesium binding site 4 out
of 4 in the Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form
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 Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg304
b:38.0
occ:1.00
|
CL
|
B:CL307
|
1.7
|
27.5
|
1.0
|
HG
|
B:SER42
|
2.8
|
30.0
|
0.0
|
OG
|
B:SER103
|
2.8
|
17.3
|
1.0
|
HB2
|
B:SER42
|
3.0
|
18.0
|
1.0
|
O
|
B:HOH619
|
3.0
|
35.4
|
1.0
|
CL
|
B:CL306
|
3.0
|
57.3
|
1.0
|
O
|
B:HOH465
|
3.1
|
25.4
|
1.0
|
HG
|
B:SER103
|
3.1
|
30.0
|
0.0
|
OG
|
B:SER42
|
3.2
|
20.0
|
1.0
|
HB3
|
B:SER103
|
3.2
|
14.9
|
1.0
|
CB
|
B:SER103
|
3.4
|
14.8
|
1.0
|
CB
|
B:SER42
|
3.5
|
17.2
|
1.0
|
HA2
|
B:GLY209
|
3.5
|
15.6
|
1.0
|
HB2
|
B:SER103
|
3.6
|
14.9
|
1.0
|
HZ3
|
B:LYS207
|
3.6
|
14.6
|
1.0
|
H
|
B:SER210
|
3.7
|
19.3
|
1.0
|
HB3
|
B:SER42
|
3.8
|
17.7
|
1.0
|
HB3
|
B:SER210
|
3.8
|
25.6
|
1.0
|
O
|
B:HOH685
|
3.9
|
39.2
|
1.0
|
HB2
|
B:SER210
|
4.0
|
25.2
|
1.0
|
HZ2
|
B:LYS45
|
4.1
|
18.2
|
1.0
|
N
|
B:SER210
|
4.3
|
19.7
|
1.0
|
CB
|
B:SER210
|
4.3
|
24.9
|
1.0
|
NZ
|
B:LYS207
|
4.3
|
14.8
|
1.0
|
HZ2
|
B:LYS207
|
4.4
|
14.6
|
1.0
|
CA
|
B:GLY209
|
4.4
|
15.3
|
1.0
|
O
|
B:THR208
|
4.5
|
15.1
|
1.0
|
O
|
B:HOH576
|
4.5
|
28.9
|
1.0
|
HZ1
|
B:LYS207
|
4.5
|
14.7
|
1.0
|
H
|
B:SER42
|
4.6
|
18.5
|
1.0
|
MG
|
B:MG303
|
4.7
|
55.1
|
1.0
|
C
|
B:GLY209
|
4.7
|
17.1
|
1.0
|
O
|
B:HOH414
|
4.8
|
27.6
|
1.0
|
O
|
B:HOH636
|
4.8
|
25.3
|
1.0
|
CA
|
B:SER103
|
4.8
|
14.3
|
1.0
|
OG1
|
B:THR208
|
4.8
|
14.8
|
1.0
|
O
|
B:SER103
|
4.9
|
16.8
|
1.0
|
CA
|
B:SER42
|
4.9
|
17.5
|
1.0
|
NZ
|
B:LYS45
|
4.9
|
18.3
|
1.0
|
C
|
B:THR208
|
4.9
|
16.1
|
1.0
|
CA
|
B:SER210
|
5.0
|
22.5
|
1.0
|
N
|
B:GLY209
|
5.0
|
15.7
|
1.0
|
|
Reference:
K.Dhankhar,
S.Hazra.
Crystal Structure of Bel-1 Esbl in Hexagonal Form To Be Published.
Page generated: Fri Oct 4 13:11:06 2024
|