Calcium in PDB 3lez: Crystal Structure of A Halotolerant Bacterial Beta-Lactamase
Enzymatic activity of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase
All present enzymatic activity of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase:
3.5.2.6;
Protein crystallography data
The structure of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase, PDB code: 3lez
was solved by
C.A.Smith,
S.B.Vakulenko,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.85 /
1.25
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.980,
55.980,
165.890,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
15.4 /
17.4
|
Other elements in 3lez:
The structure of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of A Halotolerant Bacterial Beta-Lactamase
(pdb code 3lez). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Crystal Structure of A Halotolerant Bacterial Beta-Lactamase, PDB code: 3lez:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 3lez
Go back to
Calcium Binding Sites List in 3lez
Calcium binding site 1 out
of 8 in the Crystal Structure of A Halotolerant Bacterial Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1
b:18.9
occ:1.00
|
O
|
A:MET175
|
2.4
|
16.3
|
1.0
|
OE2
|
A:GLU174
|
2.4
|
12.3
|
0.4
|
OE1
|
A:GLU162
|
2.4
|
14.9
|
1.0
|
OD2
|
A:ASP159
|
2.4
|
20.8
|
1.0
|
OD1
|
A:ASP176
|
2.5
|
18.6
|
1.0
|
CG
|
A:ASP176
|
3.2
|
17.9
|
1.0
|
OD2
|
A:ASP176
|
3.5
|
19.4
|
1.0
|
CD
|
A:GLU162
|
3.5
|
15.1
|
1.0
|
C
|
A:MET175
|
3.5
|
14.7
|
1.0
|
CD
|
A:GLU174
|
3.5
|
13.2
|
0.4
|
CG
|
A:ASP159
|
3.6
|
19.4
|
1.0
|
CA
|
A:CA2
|
3.7
|
19.0
|
1.0
|
OE2
|
A:GLU162
|
3.8
|
17.8
|
1.0
|
N
|
A:MET175
|
3.9
|
13.6
|
1.0
|
OE1
|
A:GLU174
|
4.2
|
14.4
|
0.4
|
O
|
A:HOH773
|
4.2
|
36.6
|
1.0
|
OD1
|
A:ASP159
|
4.3
|
18.7
|
1.0
|
CA
|
A:MET175
|
4.3
|
13.7
|
1.0
|
N
|
A:ASP176
|
4.3
|
15.2
|
1.0
|
CA
|
A:ASP176
|
4.3
|
15.3
|
1.0
|
CB
|
A:ASP176
|
4.3
|
16.8
|
1.0
|
CG
|
A:GLU174
|
4.4
|
13.2
|
0.4
|
CA
|
A:ASP159
|
4.5
|
16.9
|
1.0
|
CB
|
A:ASP159
|
4.5
|
17.7
|
1.0
|
OE1
|
A:GLU174
|
4.5
|
21.4
|
0.6
|
O
|
A:HOH518
|
4.7
|
20.5
|
1.0
|
C
|
A:GLU174
|
4.7
|
13.9
|
1.0
|
CG
|
A:GLU162
|
4.7
|
14.9
|
1.0
|
O
|
A:HOH755
|
4.8
|
40.8
|
1.0
|
CB
|
A:GLU162
|
4.9
|
13.9
|
1.0
|
O
|
A:HOH517
|
4.9
|
20.7
|
1.0
|
|
Calcium binding site 2 out
of 8 in 3lez
Go back to
Calcium Binding Sites List in 3lez
Calcium binding site 2 out
of 8 in the Crystal Structure of A Halotolerant Bacterial Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2
b:19.0
occ:1.00
|
O
|
A:HOH517
|
2.5
|
20.7
|
1.0
|
O
|
A:HOH516
|
2.5
|
20.8
|
1.0
|
OD1
|
A:ASP176
|
2.5
|
18.6
|
1.0
|
O
|
A:HOH518
|
2.5
|
20.5
|
1.0
|
OD1
|
A:ASP159
|
2.6
|
18.7
|
1.0
|
O
|
A:HOH519
|
2.6
|
23.3
|
1.0
|
OD2
|
A:ASP159
|
2.8
|
20.8
|
1.0
|
CG
|
A:ASP159
|
3.0
|
19.4
|
1.0
|
CG
|
A:ASP176
|
3.6
|
17.9
|
1.0
|
CA
|
A:CA1
|
3.7
|
18.9
|
1.0
|
CB
|
A:ASP176
|
4.0
|
16.8
|
1.0
|
O
|
A:HOH773
|
4.2
|
36.6
|
1.0
|
CA
|
A:ASP176
|
4.3
|
15.3
|
1.0
|
O
|
A:MET175
|
4.5
|
16.3
|
1.0
|
CB
|
A:ASP159
|
4.5
|
17.7
|
1.0
|
O
|
A:ASP176
|
4.6
|
17.6
|
1.0
|
OD2
|
A:ASP176
|
4.7
|
19.4
|
1.0
|
O
|
A:HOH648
|
4.8
|
43.8
|
1.0
|
O
|
A:HOH500
|
4.9
|
20.3
|
1.0
|
CL
|
A:CL20
|
5.0
|
22.2
|
1.0
|
C
|
A:ASP176
|
5.0
|
15.6
|
1.0
|
|
Calcium binding site 3 out
of 8 in 3lez
Go back to
Calcium Binding Sites List in 3lez
Calcium binding site 3 out
of 8 in the Crystal Structure of A Halotolerant Bacterial Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca3
b:21.5
occ:1.00
|
O
|
A:HOH521
|
2.4
|
24.1
|
1.0
|
O
|
A:HOH522
|
2.4
|
21.1
|
1.0
|
O
|
A:HOH520
|
2.4
|
21.9
|
1.0
|
OD2
|
A:ASP213
|
2.5
|
15.9
|
1.0
|
CG
|
A:ASP213
|
3.5
|
14.6
|
1.0
|
O
|
A:HOH23
|
3.9
|
30.0
|
1.0
|
CA
|
A:CA8
|
4.1
|
34.4
|
1.0
|
OD1
|
A:ASP213
|
4.2
|
17.6
|
1.0
|
O
|
A:HOH529
|
4.2
|
20.1
|
1.0
|
CB
|
A:ASP213
|
4.3
|
13.2
|
1.0
|
NE
|
A:ARG216
|
4.4
|
20.4
|
1.0
|
O
|
A:HOH596
|
4.5
|
25.1
|
1.0
|
CZ
|
A:ARG216
|
4.6
|
20.0
|
1.0
|
NH2
|
A:ARG216
|
4.6
|
21.8
|
1.0
|
O
|
A:HOH24
|
4.7
|
30.9
|
1.0
|
OD1
|
A:ASP101
|
4.7
|
28.1
|
1.0
|
O
|
A:HOH489
|
4.8
|
15.3
|
1.0
|
CD
|
A:ARG216
|
4.9
|
18.8
|
1.0
|
OD1
|
A:ASP215
|
5.0
|
17.1
|
1.0
|
|
Calcium binding site 4 out
of 8 in 3lez
Go back to
Calcium Binding Sites List in 3lez
Calcium binding site 4 out
of 8 in the Crystal Structure of A Halotolerant Bacterial Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4
b:19.2
occ:0.50
|
OD1
|
A:ASP70
|
2.4
|
25.2
|
1.0
|
O
|
A:THR67
|
2.4
|
19.6
|
1.0
|
O
|
A:HOH523
|
2.5
|
34.3
|
1.0
|
CG
|
A:ASP70
|
3.5
|
25.4
|
1.0
|
C
|
A:THR67
|
3.6
|
17.7
|
1.0
|
OD2
|
A:ASP70
|
3.9
|
27.4
|
1.0
|
CA
|
A:THR67
|
4.2
|
16.1
|
1.0
|
O
|
A:HOH751
|
4.6
|
53.1
|
1.0
|
N
|
A:GLY68
|
4.6
|
18.1
|
1.0
|
OE1
|
A:GLU269
|
4.7
|
30.0
|
0.5
|
CB
|
A:THR67
|
4.7
|
16.5
|
1.0
|
CB
|
A:ASP70
|
4.7
|
22.9
|
1.0
|
O
|
A:HOH768
|
4.7
|
53.4
|
1.0
|
O
|
A:HOH32
|
4.7
|
54.9
|
0.5
|
CA
|
A:GLY68
|
4.8
|
19.2
|
1.0
|
CA
|
A:ASP70
|
4.9
|
20.2
|
1.0
|
O
|
A:GLY68
|
4.9
|
23.4
|
1.0
|
|
Calcium binding site 5 out
of 8 in 3lez
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Calcium Binding Sites List in 3lez
Calcium binding site 5 out
of 8 in the Crystal Structure of A Halotolerant Bacterial Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca5
b:41.5
occ:1.00
|
O
|
A:HOH12
|
2.3
|
43.8
|
1.0
|
O
|
A:HOH10
|
2.4
|
43.0
|
1.0
|
O
|
A:HOH13
|
2.5
|
34.5
|
1.0
|
O
|
A:HOH11
|
2.5
|
37.9
|
1.0
|
O
|
A:HOH9
|
2.7
|
42.4
|
1.0
|
O
|
A:HOH622
|
3.3
|
48.8
|
1.0
|
O
|
A:HOH360
|
4.2
|
56.4
|
1.0
|
O
|
A:HOH527
|
4.4
|
20.0
|
1.0
|
O
|
A:HOH548
|
4.5
|
27.9
|
1.0
|
O
|
A:HOH578
|
4.6
|
24.0
|
1.0
|
O
|
A:HOH510
|
4.7
|
49.9
|
1.0
|
O
|
A:HOH566
|
4.7
|
35.9
|
1.0
|
OE1
|
A:GLU123
|
4.8
|
18.4
|
1.0
|
CB
|
A:LEU115
|
4.8
|
19.7
|
1.0
|
OE2
|
A:GLU112
|
4.8
|
37.0
|
0.6
|
O
|
A:VAL116
|
4.9
|
16.2
|
1.0
|
O
|
A:LEU115
|
4.9
|
22.4
|
1.0
|
|
Calcium binding site 6 out
of 8 in 3lez
Go back to
Calcium Binding Sites List in 3lez
Calcium binding site 6 out
of 8 in the Crystal Structure of A Halotolerant Bacterial Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca6
b:29.4
occ:1.00
|
OG
|
A:SER74
|
2.4
|
25.6
|
1.0
|
O
|
A:HOH16
|
2.5
|
29.1
|
1.0
|
O
|
A:HOH15
|
2.6
|
30.5
|
1.0
|
O
|
A:HOH14
|
2.6
|
28.8
|
1.0
|
OE2
|
A:GLU77
|
2.9
|
26.8
|
1.0
|
CD
|
A:GLU77
|
3.2
|
21.6
|
1.0
|
OE1
|
A:GLU77
|
3.2
|
22.4
|
1.0
|
CB
|
A:SER74
|
3.4
|
23.1
|
1.0
|
O
|
A:HOH31
|
3.4
|
57.4
|
0.5
|
O
|
A:SER74
|
4.2
|
18.6
|
1.0
|
CA
|
A:SER74
|
4.3
|
18.1
|
1.0
|
C
|
A:SER74
|
4.3
|
16.2
|
1.0
|
CG
|
A:GLU77
|
4.3
|
16.8
|
1.0
|
O
|
A:HOH389
|
4.5
|
43.2
|
1.0
|
OE1
|
A:GLU72
|
4.6
|
20.8
|
1.0
|
N
|
A:SER74
|
4.7
|
16.1
|
1.0
|
OE2
|
A:GLU72
|
4.7
|
21.6
|
1.0
|
O
|
A:HOH41
|
4.8
|
19.3
|
1.0
|
N
|
A:TYR75
|
5.0
|
15.3
|
1.0
|
|
Calcium binding site 7 out
of 8 in 3lez
Go back to
Calcium Binding Sites List in 3lez
Calcium binding site 7 out
of 8 in the Crystal Structure of A Halotolerant Bacterial Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca7
b:32.1
occ:1.00
|
O
|
A:HOH22
|
2.3
|
35.2
|
1.0
|
O
|
A:GLY169
|
2.4
|
17.4
|
1.0
|
O
|
A:HOH17
|
2.4
|
35.6
|
1.0
|
O
|
A:HOH21
|
2.5
|
31.3
|
1.0
|
O
|
A:HOH19
|
2.5
|
32.6
|
1.0
|
O
|
A:HOH18
|
2.6
|
36.3
|
1.0
|
O
|
A:HOH524
|
2.7
|
34.8
|
1.0
|
C
|
A:GLY169
|
3.5
|
15.5
|
1.0
|
CA
|
A:GLY169
|
4.1
|
16.1
|
1.0
|
CG
|
A:GLU171
|
4.2
|
25.3
|
0.5
|
O
|
A:HOH413
|
4.2
|
40.0
|
1.0
|
OE2
|
A:GLU171
|
4.2
|
32.5
|
0.5
|
CD
|
A:GLU171
|
4.3
|
30.1
|
0.5
|
O
|
A:HOH569
|
4.4
|
41.7
|
1.0
|
N
|
A:GLU171
|
4.5
|
15.6
|
1.0
|
OE1
|
A:GLU171
|
4.5
|
31.4
|
0.5
|
N
|
A:ASP170
|
4.6
|
15.0
|
1.0
|
CB
|
A:GLU171
|
4.7
|
19.8
|
0.5
|
O
|
A:HOH692
|
4.7
|
36.0
|
1.0
|
CB
|
A:GLU171
|
4.7
|
20.2
|
0.5
|
CD
|
A:GLU171
|
4.8
|
30.0
|
0.5
|
CG
|
A:GLU171
|
4.8
|
24.6
|
0.5
|
O
|
A:HOH549
|
4.8
|
23.4
|
1.0
|
CA
|
A:ASP170
|
4.8
|
14.4
|
1.0
|
OE1
|
A:GLU171
|
5.0
|
31.4
|
0.5
|
|
Calcium binding site 8 out
of 8 in 3lez
Go back to
Calcium Binding Sites List in 3lez
Calcium binding site 8 out
of 8 in the Crystal Structure of A Halotolerant Bacterial Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of A Halotolerant Bacterial Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca8
b:34.4
occ:1.00
|
O
|
A:HOH26
|
2.2
|
34.8
|
1.0
|
O
|
A:HOH24
|
2.5
|
30.9
|
1.0
|
O
|
A:HOH23
|
2.5
|
30.0
|
1.0
|
OD2
|
A:ASP215
|
2.5
|
23.4
|
1.0
|
O
|
A:HOH520
|
2.6
|
21.9
|
1.0
|
O
|
A:HOH25
|
2.8
|
37.3
|
1.0
|
O
|
A:HOH521
|
3.3
|
24.1
|
1.0
|
CG
|
A:ASP215
|
3.6
|
17.7
|
1.0
|
OD1
|
A:ASP101
|
3.7
|
28.1
|
1.0
|
OD2
|
A:ASP101
|
3.7
|
28.7
|
1.0
|
OD1
|
A:ASP215
|
3.9
|
17.1
|
1.0
|
O
|
A:HOH757
|
4.1
|
42.6
|
1.0
|
CA
|
A:CA3
|
4.1
|
21.5
|
1.0
|
CG
|
A:ASP101
|
4.1
|
28.0
|
1.0
|
O
|
A:HOH353
|
4.3
|
50.7
|
1.0
|
O
|
A:HOH529
|
4.5
|
20.1
|
1.0
|
O
|
A:HOH372
|
4.7
|
56.6
|
1.0
|
O
|
A:HOH557
|
4.8
|
36.0
|
1.0
|
CB
|
A:ASP215
|
4.9
|
16.5
|
1.0
|
NE
|
A:ARG216
|
4.9
|
20.4
|
1.0
|
|
Reference:
M.Toth,
C.Smith,
H.Frase,
S.Mobashery,
S.Vakulenko.
An Antibiotic-Resistance Enzyme From A Deep-Sea Bacterium J.Am.Chem.Soc. V. 132 816 2010.
ISSN: ISSN 0002-7863
PubMed: 20000704
DOI: 10.1021/JA908850P
Page generated: Sat Jul 13 13:01:20 2024
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