Calcium in PDB 6nvy: Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans
Protein crystallography data
The structure of Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans, PDB code: 6nvy
was solved by
W.Blankenfeldt,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.25 /
2.27
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
172.996,
172.996,
209.566,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.2 /
20
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans
(pdb code 6nvy). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the
Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans, PDB code: 6nvy:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 6nvy
Go back to
Calcium Binding Sites List in 6nvy
Calcium binding site 1 out
of 12 in the Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans
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 Penicillin G Acylase From Bacillus Thermotolerans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:76.0
occ:1.00
|
O
|
A:HOH404
|
2.3
|
64.5
|
1.0
|
OE2
|
A:GLU53
|
2.4
|
73.0
|
1.0
|
OD1
|
A:ASP136
|
2.4
|
68.2
|
1.0
|
O
|
A:HOH428
|
2.4
|
79.0
|
1.0
|
O
|
A:HOH417
|
2.4
|
56.9
|
1.0
|
O
|
A:HOH456
|
2.5
|
58.3
|
1.0
|
CG
|
A:ASP136
|
3.3
|
69.3
|
1.0
|
OD2
|
A:ASP136
|
3.5
|
70.9
|
1.0
|
CD
|
A:GLU53
|
3.5
|
70.4
|
1.0
|
HD2
|
A:ARG49
|
3.5
|
72.3
|
1.0
|
HH11
|
A:ARG49
|
4.0
|
79.7
|
1.0
|
OE1
|
A:GLU53
|
4.0
|
77.3
|
1.0
|
HE
|
A:ARG139
|
4.2
|
69.5
|
1.0
|
HD2
|
A:ARG139
|
4.4
|
65.1
|
1.0
|
OD2
|
A:ASP78
|
4.4
|
77.7
|
1.0
|
CD
|
A:ARG49
|
4.5
|
60.2
|
1.0
|
NH1
|
A:ARG49
|
4.5
|
66.4
|
1.0
|
OD1
|
A:ASP78
|
4.6
|
74.3
|
1.0
|
CB
|
A:ASP136
|
4.7
|
64.6
|
1.0
|
OD2
|
A:ASP133
|
4.7
|
69.6
|
1.0
|
CG
|
A:GLU53
|
4.7
|
66.7
|
1.0
|
HA
|
A:ASP136
|
4.8
|
76.3
|
1.0
|
HG2
|
A:GLU53
|
4.8
|
80.0
|
1.0
|
HH12
|
A:ARG49
|
4.9
|
79.7
|
1.0
|
OD1
|
A:ASP133
|
4.9
|
65.5
|
1.0
|
OG1
|
A:THR135
|
4.9
|
62.0
|
1.0
|
NE
|
A:ARG139
|
4.9
|
57.9
|
1.0
|
HD3
|
A:ARG49
|
4.9
|
72.3
|
1.0
|
HB3
|
A:ASP136
|
4.9
|
77.5
|
1.0
|
CG
|
A:ASP78
|
4.9
|
77.5
|
1.0
|
HG3
|
A:GLU53
|
5.0
|
80.0
|
1.0
|
HG3
|
A:ARG49
|
5.0
|
69.2
|
1.0
|
HG1
|
A:THR135
|
5.0
|
74.4
|
1.0
|
|
Calcium binding site 2 out
of 12 in 6nvy
Go back to
Calcium Binding Sites List in 6nvy
Calcium binding site 2 out
of 12 in the Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans
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 Penicillin G Acylase From Bacillus Thermotolerans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca601
b:36.6
occ:1.00
|
OE1
|
A:GLU154
|
2.3
|
44.4
|
1.0
|
OD1
|
B:ASN73
|
2.3
|
35.7
|
1.0
|
O
|
B:THR75
|
2.3
|
42.0
|
1.0
|
OD1
|
B:ASP76
|
2.4
|
43.9
|
1.0
|
O
|
B:HOH751
|
2.4
|
33.0
|
1.0
|
OE2
|
B:GLU256
|
2.5
|
44.0
|
1.0
|
OE1
|
B:GLU256
|
2.5
|
41.5
|
1.0
|
CD
|
B:GLU256
|
2.8
|
42.2
|
1.0
|
HA
|
B:ASP76
|
3.0
|
48.7
|
1.0
|
HD21
|
B:ASN73
|
3.0
|
49.3
|
1.0
|
CG
|
B:ASN73
|
3.2
|
36.8
|
1.0
|
C
|
B:THR75
|
3.4
|
45.0
|
1.0
|
ND2
|
B:ASN73
|
3.4
|
41.1
|
1.0
|
CD
|
A:GLU154
|
3.5
|
48.5
|
1.0
|
CG
|
B:ASP76
|
3.5
|
38.9
|
1.0
|
HH21
|
B:ARG203
|
3.7
|
48.1
|
1.0
|
CA
|
B:ASP76
|
3.8
|
40.6
|
1.0
|
HG3
|
A:GLU154
|
3.9
|
48.5
|
1.0
|
N
|
B:ASP76
|
4.0
|
42.6
|
1.0
|
H
|
B:THR75
|
4.0
|
52.8
|
1.0
|
NH2
|
B:ARG203
|
4.2
|
40.1
|
1.0
|
CB
|
B:ASP76
|
4.2
|
43.5
|
1.0
|
CG
|
A:GLU154
|
4.2
|
40.4
|
1.0
|
H
|
B:GLU256
|
4.3
|
37.9
|
1.0
|
O
|
B:GLU209
|
4.3
|
46.5
|
1.0
|
HD22
|
B:ASN73
|
4.3
|
49.3
|
1.0
|
CG
|
B:GLU256
|
4.3
|
34.6
|
1.0
|
OE2
|
A:GLU154
|
4.4
|
45.6
|
1.0
|
HE
|
B:ARG203
|
4.4
|
44.5
|
1.0
|
OD2
|
B:ASP76
|
4.4
|
45.8
|
1.0
|
HH22
|
B:ARG203
|
4.5
|
48.1
|
1.0
|
HG2
|
A:GLU154
|
4.5
|
48.5
|
1.0
|
HA
|
B:ASN73
|
4.6
|
52.2
|
1.0
|
CB
|
B:ASN73
|
4.6
|
42.0
|
1.0
|
O
|
B:HOH940
|
4.6
|
34.1
|
1.0
|
HG3
|
B:GLU256
|
4.6
|
41.6
|
1.0
|
N
|
B:THR75
|
4.6
|
44.0
|
1.0
|
CA
|
B:THR75
|
4.6
|
44.7
|
1.0
|
O
|
A:HOH413
|
4.6
|
34.4
|
1.0
|
HB3
|
B:ASP76
|
4.7
|
52.2
|
1.0
|
HB3
|
B:GLU256
|
4.7
|
38.5
|
1.0
|
O
|
B:HOH704
|
4.7
|
60.1
|
1.0
|
H
|
B:ILE77
|
4.7
|
48.2
|
1.0
|
HD21
|
A:ASN151
|
4.7
|
62.3
|
1.0
|
HA3
|
B:GLY255
|
4.8
|
45.9
|
1.0
|
H
|
B:ASP76
|
4.8
|
51.2
|
1.0
|
HG2
|
B:GLU256
|
4.8
|
41.6
|
1.0
|
CZ
|
B:ARG203
|
4.9
|
39.8
|
1.0
|
HB
|
B:THR75
|
4.9
|
54.0
|
1.0
|
NE
|
B:ARG203
|
4.9
|
37.0
|
1.0
|
HB2
|
B:ASN73
|
4.9
|
50.5
|
1.0
|
CA
|
B:ASN73
|
4.9
|
43.5
|
1.0
|
HB3
|
B:GLU209
|
5.0
|
60.8
|
1.0
|
HB2
|
B:ASP76
|
5.0
|
52.2
|
1.0
|
|
Calcium binding site 3 out
of 12 in 6nvy
Go back to
Calcium Binding Sites List in 6nvy
Calcium binding site 3 out
of 12 in the Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans
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 Penicillin G Acylase From Bacillus Thermotolerans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca602
b:47.1
occ:1.00
|
O
|
B:LEU342
|
2.2
|
51.6
|
1.0
|
OD1
|
B:ASP336
|
2.3
|
46.7
|
1.0
|
O
|
B:HOH875
|
2.3
|
40.2
|
1.0
|
OD1
|
B:ASN338
|
2.4
|
64.6
|
1.0
|
OD1
|
B:ASP340
|
2.4
|
46.8
|
1.0
|
OD1
|
B:ASP344
|
2.4
|
42.9
|
1.0
|
CG
|
B:ASP340
|
3.1
|
52.8
|
1.0
|
HA
|
B:ASP336
|
3.2
|
53.2
|
1.0
|
H
|
B:LEU342
|
3.2
|
64.8
|
1.0
|
C
|
B:LEU342
|
3.3
|
46.0
|
1.0
|
CG
|
B:ASP336
|
3.4
|
52.0
|
1.0
|
H
|
B:ASP340
|
3.4
|
65.6
|
1.0
|
OD2
|
B:ASP340
|
3.4
|
50.0
|
1.0
|
HB2
|
B:LEU342
|
3.4
|
61.1
|
1.0
|
CG
|
B:ASN338
|
3.4
|
59.4
|
1.0
|
HD21
|
B:ASN338
|
3.4
|
70.4
|
1.0
|
HA
|
B:ASP344
|
3.6
|
56.2
|
1.0
|
CG
|
B:ASP344
|
3.6
|
42.3
|
1.0
|
ND2
|
B:ASN338
|
3.8
|
58.7
|
1.0
|
H
|
B:ASN338
|
3.8
|
59.7
|
1.0
|
N
|
B:LEU342
|
3.9
|
54.0
|
1.0
|
CA
|
B:ASP336
|
3.9
|
44.4
|
1.0
|
CA
|
B:LEU342
|
4.0
|
46.1
|
1.0
|
CB
|
B:LEU342
|
4.1
|
50.9
|
1.0
|
CB
|
B:ASP336
|
4.1
|
46.1
|
1.0
|
N
|
B:ASP344
|
4.1
|
43.6
|
1.0
|
CA
|
B:ASP344
|
4.2
|
46.8
|
1.0
|
H
|
B:LYS339
|
4.2
|
69.5
|
1.0
|
N
|
B:ASP340
|
4.2
|
54.7
|
1.0
|
OD2
|
B:ASP336
|
4.2
|
51.9
|
1.0
|
C
|
B:TYR343
|
4.3
|
49.1
|
1.0
|
HB2
|
B:ASP336
|
4.3
|
55.4
|
1.0
|
HB3
|
B:LEU342
|
4.3
|
61.1
|
1.0
|
H
|
B:ASP344
|
4.4
|
52.3
|
1.0
|
CB
|
B:ASP340
|
4.4
|
52.5
|
1.0
|
N
|
B:TYR343
|
4.4
|
47.2
|
1.0
|
HA
|
B:TYR343
|
4.4
|
53.6
|
1.0
|
C
|
B:ASP336
|
4.5
|
49.7
|
1.0
|
OD2
|
B:ASP344
|
4.5
|
42.9
|
1.0
|
CB
|
B:ASP344
|
4.5
|
45.9
|
1.0
|
H
|
B:LYS337
|
4.5
|
59.1
|
1.0
|
HB3
|
B:ASP340
|
4.6
|
63.0
|
1.0
|
N
|
B:LYS339
|
4.6
|
57.9
|
1.0
|
N
|
B:ASN338
|
4.6
|
49.8
|
1.0
|
H
|
B:GLY341
|
4.6
|
60.7
|
1.0
|
O
|
B:HOH863
|
4.6
|
49.2
|
1.0
|
CA
|
B:TYR343
|
4.6
|
44.6
|
1.0
|
O
|
B:TYR343
|
4.6
|
44.2
|
1.0
|
O
|
B:GLU335
|
4.7
|
45.5
|
1.0
|
HD22
|
B:ASN338
|
4.7
|
70.4
|
1.0
|
N
|
B:LYS337
|
4.7
|
49.3
|
1.0
|
CA
|
B:ASP340
|
4.7
|
53.9
|
1.0
|
CB
|
B:ASN338
|
4.8
|
55.4
|
1.0
|
N
|
B:GLY341
|
4.8
|
50.6
|
1.0
|
HB3
|
B:ASP344
|
4.9
|
55.1
|
1.0
|
HA
|
B:LEU342
|
4.9
|
55.3
|
1.0
|
C
|
B:ASP340
|
4.9
|
53.2
|
1.0
|
C
|
B:ASN338
|
5.0
|
54.0
|
1.0
|
HB3
|
B:ASP336
|
5.0
|
55.4
|
1.0
|
|
Calcium binding site 4 out
of 12 in 6nvy
Go back to
Calcium Binding Sites List in 6nvy
Calcium binding site 4 out
of 12 in the Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans
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 Penicillin G Acylase From Bacillus Thermotolerans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca603
b:61.7
occ:1.00
|
OE1
|
B:GLU8
|
2.4
|
72.7
|
1.0
|
O
|
B:HOH925
|
2.4
|
63.2
|
1.0
|
O
|
B:ARG189
|
2.5
|
61.5
|
1.0
|
OE2
|
B:GLU8
|
2.9
|
71.2
|
1.0
|
CD
|
B:GLU8
|
3.0
|
70.6
|
1.0
|
CA
|
B:CA605
|
3.7
|
0.1
|
1.0
|
C
|
B:ARG189
|
3.7
|
59.8
|
1.0
|
HA3
|
B:GLY190
|
3.9
|
60.9
|
1.0
|
HA
|
B:ARG189
|
4.2
|
64.8
|
1.0
|
HB3
|
B:ARG189
|
4.3
|
67.7
|
1.0
|
O
|
B:HOH912
|
4.3
|
52.6
|
1.0
|
CG
|
B:GLU8
|
4.4
|
63.6
|
1.0
|
CA
|
B:ARG189
|
4.5
|
54.0
|
1.0
|
N
|
B:GLY190
|
4.6
|
52.8
|
1.0
|
HB3
|
B:GLU8
|
4.7
|
65.1
|
1.0
|
CA
|
B:GLY190
|
4.7
|
50.8
|
1.0
|
HG2
|
B:GLU8
|
4.8
|
76.3
|
1.0
|
HB2
|
B:GLU8
|
4.9
|
65.1
|
1.0
|
CB
|
B:ARG189
|
4.9
|
56.5
|
1.0
|
HG3
|
B:GLU8
|
5.0
|
76.3
|
1.0
|
CB
|
B:GLU8
|
5.0
|
54.3
|
1.0
|
|
Calcium binding site 5 out
of 12 in 6nvy
Go back to
Calcium Binding Sites List in 6nvy
Calcium binding site 5 out
of 12 in the Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans
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 Penicillin G Acylase From Bacillus Thermotolerans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca604
b:70.2
occ:1.00
|
OD1
|
B:ASP284
|
2.3
|
42.3
|
1.0
|
O
|
B:HOH865
|
2.5
|
54.0
|
1.0
|
O
|
B:HOH784
|
2.5
|
50.0
|
1.0
|
O
|
B:HOH732
|
2.5
|
73.8
|
1.0
|
CG
|
B:ASP284
|
3.3
|
41.0
|
1.0
|
HZ1
|
B:LYS12
|
3.3
|
79.5
|
1.0
|
HZ2
|
B:LYS12
|
3.4
|
79.5
|
1.0
|
OD2
|
B:ASP284
|
3.6
|
45.4
|
1.0
|
NZ
|
B:LYS12
|
3.6
|
66.2
|
1.0
|
HZ3
|
B:LYS12
|
3.6
|
79.5
|
1.0
|
OE1
|
B:GLU287
|
3.7
|
51.0
|
1.0
|
HE
|
B:ARG277
|
3.7
|
47.2
|
1.0
|
OE2
|
B:GLU287
|
3.9
|
59.7
|
1.0
|
HA
|
B:ASP284
|
4.2
|
50.1
|
1.0
|
CD
|
B:GLU287
|
4.2
|
55.4
|
1.0
|
HG2
|
B:GLU283
|
4.2
|
74.7
|
1.0
|
OE2
|
B:GLU283
|
4.3
|
75.9
|
1.0
|
NE
|
B:ARG277
|
4.5
|
39.4
|
1.0
|
CB
|
B:ASP284
|
4.6
|
40.9
|
1.0
|
HD3
|
B:ARG277
|
4.7
|
45.0
|
1.0
|
HH21
|
B:ARG277
|
4.7
|
52.0
|
1.0
|
CA
|
B:ASP284
|
4.8
|
41.8
|
1.0
|
OD1
|
B:ASP281
|
4.8
|
43.1
|
1.0
|
N
|
B:ASP284
|
5.0
|
40.7
|
1.0
|
H
|
B:ASP284
|
5.0
|
48.8
|
1.0
|
|
Calcium binding site 6 out
of 12 in 6nvy
Go back to
Calcium Binding Sites List in 6nvy
Calcium binding site 6 out
of 12 in the Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans
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 Penicillin G Acylase From Bacillus Thermotolerans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca605
b:0.1
occ:1.00
|
O
|
B:GLY14
|
2.4
|
52.7
|
1.0
|
O
|
B:HOH912
|
2.5
|
52.6
|
1.0
|
O
|
B:HOH950
|
2.5
|
55.2
|
1.0
|
OE1
|
B:GLU8
|
2.5
|
72.7
|
1.0
|
O
|
B:HOH761
|
2.7
|
51.0
|
1.0
|
HB2
|
B:GLU8
|
3.1
|
65.1
|
1.0
|
C
|
B:GLY14
|
3.4
|
47.0
|
1.0
|
HB3
|
B:GLU8
|
3.5
|
65.1
|
1.0
|
CA
|
B:CA603
|
3.7
|
61.7
|
1.0
|
CD
|
B:GLU8
|
3.7
|
70.6
|
1.0
|
CB
|
B:GLU8
|
3.7
|
54.3
|
1.0
|
HA3
|
B:GLY14
|
3.8
|
51.4
|
1.0
|
HA
|
B:ASN15
|
3.9
|
57.1
|
1.0
|
CA
|
B:GLY14
|
4.1
|
42.8
|
1.0
|
HA3
|
B:GLY190
|
4.3
|
60.9
|
1.0
|
HA2
|
B:GLY14
|
4.3
|
51.4
|
1.0
|
CG
|
B:GLU8
|
4.3
|
63.6
|
1.0
|
O
|
B:ARG189
|
4.3
|
61.5
|
1.0
|
OD1
|
B:ASN15
|
4.4
|
51.7
|
1.0
|
N
|
B:ASN15
|
4.4
|
43.3
|
1.0
|
CA
|
B:ASN15
|
4.7
|
47.6
|
1.0
|
OE2
|
B:GLU8
|
4.7
|
71.2
|
1.0
|
HG3
|
B:GLU8
|
4.8
|
76.3
|
1.0
|
HA2
|
B:GLY190
|
4.9
|
60.9
|
1.0
|
C
|
B:ARG189
|
4.9
|
59.8
|
1.0
|
CA
|
B:GLY190
|
4.9
|
50.8
|
1.0
|
HA
|
B:GLU8
|
4.9
|
67.3
|
1.0
|
|
Calcium binding site 7 out
of 12 in 6nvy
Go back to
Calcium Binding Sites List in 6nvy
Calcium binding site 7 out
of 12 in the Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans
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 Penicillin G Acylase From Bacillus Thermotolerans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca301
b:70.9
occ:1.00
|
OE2
|
C:GLU53
|
2.3
|
74.9
|
1.0
|
O
|
C:HOH419
|
2.4
|
63.0
|
1.0
|
OD1
|
C:ASP136
|
2.4
|
58.0
|
1.0
|
O
|
C:HOH412
|
2.5
|
65.6
|
1.0
|
O
|
C:HOH401
|
2.5
|
82.8
|
1.0
|
O
|
C:HOH415
|
2.5
|
60.9
|
1.0
|
O
|
C:HOH454
|
2.5
|
60.9
|
1.0
|
CG
|
C:ASP136
|
3.4
|
55.1
|
1.0
|
CD
|
C:GLU53
|
3.5
|
71.2
|
1.0
|
OD2
|
C:ASP136
|
3.6
|
63.6
|
1.0
|
HD2
|
C:ARG49
|
3.7
|
77.9
|
1.0
|
OE1
|
C:GLU53
|
4.0
|
75.6
|
1.0
|
HE
|
C:ARG139
|
4.1
|
74.5
|
1.0
|
OD2
|
C:ASP78
|
4.2
|
79.4
|
1.0
|
HH11
|
C:ARG49
|
4.3
|
82.8
|
1.0
|
HD2
|
C:ARG139
|
4.3
|
63.3
|
1.0
|
OD2
|
C:ASP133
|
4.4
|
80.9
|
1.0
|
OD1
|
C:ASP78
|
4.5
|
72.2
|
1.0
|
HG2
|
C:GLU53
|
4.6
|
80.6
|
1.0
|
CG
|
C:GLU53
|
4.6
|
67.2
|
1.0
|
OG1
|
C:THR135
|
4.6
|
62.7
|
1.0
|
CD
|
C:ARG49
|
4.7
|
64.9
|
1.0
|
HA
|
C:ASP136
|
4.7
|
70.8
|
1.0
|
CB
|
C:ASP136
|
4.7
|
53.4
|
1.0
|
CG
|
C:ASP78
|
4.8
|
75.5
|
1.0
|
NE
|
C:ARG139
|
4.8
|
62.0
|
1.0
|
HG1
|
C:THR135
|
4.8
|
75.2
|
1.0
|
NH1
|
C:ARG49
|
4.9
|
69.0
|
1.0
|
HG3
|
C:GLU53
|
4.9
|
80.6
|
1.0
|
HD3
|
C:ARG49
|
5.0
|
77.9
|
1.0
|
OD1
|
C:ASP133
|
5.0
|
76.3
|
1.0
|
|
Calcium binding site 8 out
of 12 in 6nvy
Go back to
Calcium Binding Sites List in 6nvy
Calcium binding site 8 out
of 12 in the Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans
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 Penicillin G Acylase From Bacillus Thermotolerans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca601
b:37.8
occ:1.00
|
OE1
|
C:GLU154
|
2.3
|
50.9
|
1.0
|
O
|
D:THR75
|
2.3
|
41.3
|
1.0
|
OD1
|
D:ASN73
|
2.4
|
40.9
|
1.0
|
OD1
|
D:ASP76
|
2.4
|
45.9
|
1.0
|
OE2
|
D:GLU256
|
2.4
|
37.1
|
1.0
|
O
|
D:HOH739
|
2.4
|
39.4
|
1.0
|
OE1
|
D:GLU256
|
2.5
|
37.9
|
1.0
|
CD
|
D:GLU256
|
2.8
|
41.0
|
1.0
|
HA
|
D:ASP76
|
2.9
|
45.6
|
1.0
|
HD21
|
D:ASN73
|
3.1
|
49.1
|
1.0
|
CG
|
D:ASN73
|
3.3
|
36.7
|
1.0
|
C
|
D:THR75
|
3.4
|
43.2
|
1.0
|
CD
|
C:GLU154
|
3.5
|
53.8
|
1.0
|
CG
|
D:ASP76
|
3.5
|
46.6
|
1.0
|
ND2
|
D:ASN73
|
3.6
|
40.9
|
1.0
|
HH21
|
D:ARG203
|
3.6
|
50.5
|
1.0
|
CA
|
D:ASP76
|
3.7
|
38.0
|
1.0
|
HG3
|
C:GLU154
|
3.9
|
56.5
|
1.0
|
N
|
D:ASP76
|
3.9
|
39.2
|
1.0
|
H
|
D:THR75
|
4.1
|
55.5
|
1.0
|
NH2
|
D:ARG203
|
4.1
|
42.1
|
1.0
|
CB
|
D:ASP76
|
4.2
|
43.1
|
1.0
|
H
|
D:GLU256
|
4.2
|
43.2
|
1.0
|
CG
|
D:GLU256
|
4.3
|
39.6
|
1.0
|
CG
|
C:GLU154
|
4.3
|
47.1
|
1.0
|
O
|
D:GLU209
|
4.3
|
40.7
|
1.0
|
HE
|
D:ARG203
|
4.3
|
51.5
|
1.0
|
OE2
|
C:GLU154
|
4.3
|
48.1
|
1.0
|
OD2
|
D:ASP76
|
4.4
|
47.1
|
1.0
|
HD22
|
D:ASN73
|
4.4
|
49.1
|
1.0
|
HH22
|
D:ARG203
|
4.5
|
50.5
|
1.0
|
HG3
|
D:GLU256
|
4.6
|
47.6
|
1.0
|
O
|
C:HOH434
|
4.6
|
35.3
|
1.0
|
HB3
|
D:GLU256
|
4.6
|
40.7
|
1.0
|
HA
|
D:ASN73
|
4.6
|
51.9
|
1.0
|
O
|
D:HOH924
|
4.6
|
42.4
|
1.0
|
HG2
|
C:GLU154
|
4.6
|
56.5
|
1.0
|
HB3
|
D:ASP76
|
4.6
|
51.7
|
1.0
|
H
|
D:ILE77
|
4.6
|
47.3
|
1.0
|
CA
|
D:THR75
|
4.6
|
45.3
|
1.0
|
N
|
D:THR75
|
4.6
|
46.2
|
1.0
|
CB
|
D:ASN73
|
4.7
|
38.6
|
1.0
|
H
|
D:ASP76
|
4.8
|
47.1
|
1.0
|
HG2
|
D:GLU256
|
4.8
|
47.6
|
1.0
|
HA3
|
D:GLY255
|
4.8
|
57.1
|
1.0
|
CZ
|
D:ARG203
|
4.8
|
44.9
|
1.0
|
NE
|
D:ARG203
|
4.8
|
42.9
|
1.0
|
HB
|
D:THR75
|
4.9
|
59.9
|
1.0
|
HB2
|
D:ASP76
|
4.9
|
51.7
|
1.0
|
C
|
D:ASP76
|
4.9
|
42.4
|
1.0
|
|
Calcium binding site 9 out
of 12 in 6nvy
Go back to
Calcium Binding Sites List in 6nvy
Calcium binding site 9 out
of 12 in the Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca602
b:47.6
occ:1.00
|
O
|
D:LEU342
|
2.3
|
44.1
|
1.0
|
OD1
|
D:ASP336
|
2.3
|
44.9
|
1.0
|
OD1
|
D:ASP344
|
2.3
|
44.1
|
1.0
|
OD1
|
D:ASP340
|
2.4
|
57.5
|
1.0
|
O
|
D:HOH748
|
2.4
|
39.0
|
1.0
|
OD1
|
D:ASN338
|
2.4
|
56.2
|
1.0
|
CG
|
D:ASP340
|
3.1
|
59.8
|
1.0
|
HA
|
D:ASP336
|
3.2
|
57.7
|
1.0
|
H
|
D:LEU342
|
3.3
|
56.9
|
1.0
|
OD2
|
D:ASP340
|
3.4
|
54.5
|
1.0
|
C
|
D:LEU342
|
3.4
|
45.9
|
1.0
|
CG
|
D:ASP336
|
3.4
|
51.7
|
1.0
|
H
|
D:ASP340
|
3.4
|
69.1
|
1.0
|
CG
|
D:ASN338
|
3.4
|
55.0
|
1.0
|
HB2
|
D:LEU342
|
3.5
|
61.8
|
1.0
|
HD21
|
D:ASN338
|
3.5
|
69.0
|
1.0
|
CG
|
D:ASP344
|
3.6
|
41.5
|
1.0
|
HA
|
D:ASP344
|
3.6
|
54.2
|
1.0
|
H
|
D:ASN338
|
3.8
|
58.2
|
1.0
|
ND2
|
D:ASN338
|
3.9
|
57.5
|
1.0
|
CA
|
D:ASP336
|
4.0
|
48.1
|
1.0
|
N
|
D:LEU342
|
4.0
|
47.4
|
1.0
|
CA
|
D:LEU342
|
4.1
|
43.3
|
1.0
|
N
|
D:ASP344
|
4.1
|
44.5
|
1.0
|
CB
|
D:ASP336
|
4.2
|
44.5
|
1.0
|
CA
|
D:ASP344
|
4.2
|
45.2
|
1.0
|
C
|
D:TYR343
|
4.2
|
43.0
|
1.0
|
CB
|
D:LEU342
|
4.2
|
51.5
|
1.0
|
N
|
D:ASP340
|
4.3
|
57.6
|
1.0
|
OD2
|
D:ASP336
|
4.3
|
50.9
|
1.0
|
H
|
D:LYS339
|
4.3
|
67.1
|
1.0
|
H
|
D:LYS337
|
4.3
|
58.1
|
1.0
|
HB2
|
D:ASP336
|
4.4
|
53.4
|
1.0
|
CB
|
D:ASP340
|
4.4
|
54.7
|
1.0
|
HA
|
D:TYR343
|
4.4
|
46.7
|
1.0
|
H
|
D:ASP344
|
4.4
|
53.4
|
1.0
|
N
|
D:TYR343
|
4.4
|
44.5
|
1.0
|
OD2
|
D:ASP344
|
4.4
|
45.7
|
1.0
|
O
|
D:HOH857
|
4.5
|
51.1
|
1.0
|
CB
|
D:ASP344
|
4.5
|
39.1
|
1.0
|
C
|
D:ASP336
|
4.5
|
44.2
|
1.0
|
N
|
D:ASN338
|
4.5
|
48.5
|
1.0
|
H
|
D:GLY341
|
4.6
|
60.9
|
1.0
|
O
|
D:TYR343
|
4.6
|
44.1
|
1.0
|
HB3
|
D:ASP340
|
4.6
|
65.6
|
1.0
|
N
|
D:LYS337
|
4.6
|
48.4
|
1.0
|
CA
|
D:TYR343
|
4.6
|
38.9
|
1.0
|
O
|
D:GLU335
|
4.6
|
43.7
|
1.0
|
HB3
|
D:LEU342
|
4.6
|
61.8
|
1.0
|
N
|
D:LYS339
|
4.7
|
55.9
|
1.0
|
CA
|
D:ASP340
|
4.7
|
57.6
|
1.0
|
HD22
|
D:ASN338
|
4.7
|
69.0
|
1.0
|
CB
|
D:ASN338
|
4.8
|
54.9
|
1.0
|
N
|
D:GLY341
|
4.8
|
50.8
|
1.0
|
HB3
|
D:ASP344
|
4.9
|
47.0
|
1.0
|
C
|
D:ASP340
|
4.9
|
53.5
|
1.0
|
C
|
D:ASN338
|
5.0
|
52.0
|
1.0
|
CA
|
D:ASN338
|
5.0
|
51.4
|
1.0
|
|
Calcium binding site 10 out
of 12 in 6nvy
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Calcium Binding Sites List in 6nvy
Calcium binding site 10 out
of 12 in the Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of Penicillin G Acylase From Bacillus Thermotolerans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca603
b:54.4
occ:1.00
|
O
|
D:HOH827
|
2.2
|
47.3
|
1.0
|
OD1
|
D:ASP9
|
2.4
|
46.6
|
1.0
|
OD2
|
D:ASP9
|
2.5
|
42.6
|
1.0
|
CG
|
D:ASP9
|
2.8
|
37.7
|
1.0
|
O
|
D:HOH780
|
3.3
|
65.3
|
1.0
|
CB
|
D:ASP9
|
4.3
|
36.8
|
1.0
|
HG3
|
D:GLU8
|
4.4
|
59.8
|
1.0
|
HB3
|
D:ASP9
|
4.6
|
44.1
|
1.0
|
OE2
|
D:GLU8
|
4.7
|
63.7
|
1.0
|
HB2
|
D:ASP9
|
4.8
|
44.1
|
1.0
|
O
|
D:HOH706
|
4.8
|
47.1
|
1.0
|
HA
|
D:ASP9
|
4.8
|
40.8
|
1.0
|
|
Reference:
J.Mayer,
J.Pippel,
G.Gunther,
C.Muller,
A.Lauermann,
T.Knuuti,
W.Blankenfeldt,
D.Jahn,
R.Biedendieck.
Crystal Structures and Protein Engineering of Three Different Penicillin G Acylases From Gram-Positive Bacteria with Different Thermostability. Appl.Microbiol.Biotechnol. V. 103 7537 2019.
ISSN: ESSN 1432-0614
PubMed: 31227867
DOI: 10.1007/S00253-019-09977-8
Page generated: Tue Jul 16 11:46:13 2024
|