Zinc in PDB 5jf3: Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018
Enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018
All present enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018:
3.5.1.88;
Protein crystallography data
The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018, PDB code: 5jf3
was solved by
S.Fieulaine,
C.Giglione,
T.Meinnel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.41 /
1.60
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
41.070,
65.490,
88.790,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.6 /
21.4
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018
(pdb code 5jf3). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the
Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018, PDB code: 5jf3:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Zinc binding site 1 out
of 9 in 5jf3
Go back to
Zinc Binding Sites List in 5jf3
Zinc binding site 1 out
of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn304
b:14.4
occ:1.00
|
OD3
|
A:OCS131
|
1.7
|
17.1
|
1.0
|
NE2
|
A:HIS174
|
2.1
|
5.2
|
1.0
|
NE2
|
A:HIS178
|
2.1
|
9.7
|
1.0
|
O2
|
A:SF5301
|
2.2
|
18.6
|
1.0
|
O4
|
A:SF5301
|
2.3
|
25.0
|
1.0
|
N1
|
A:SF5301
|
2.8
|
23.7
|
1.0
|
C3
|
A:SF5301
|
2.8
|
25.4
|
1.0
|
CD2
|
A:HIS174
|
2.9
|
5.8
|
1.0
|
SG
|
A:OCS131
|
2.9
|
12.7
|
1.0
|
CD2
|
A:HIS178
|
3.0
|
6.0
|
1.0
|
CE1
|
A:HIS178
|
3.1
|
6.6
|
1.0
|
CE1
|
A:HIS174
|
3.1
|
6.8
|
1.0
|
OD2
|
A:OCS131
|
3.2
|
18.1
|
1.0
|
NE2
|
A:GLN77
|
3.5
|
10.8
|
1.0
|
OD1
|
A:OCS131
|
3.9
|
20.2
|
1.0
|
O
|
A:HOH473
|
3.9
|
16.7
|
1.0
|
CD
|
A:GLN77
|
4.0
|
7.8
|
1.0
|
CB
|
A:OCS131
|
4.1
|
13.8
|
1.0
|
CG
|
A:HIS174
|
4.1
|
3.4
|
1.0
|
OE1
|
A:GLN77
|
4.2
|
8.5
|
1.0
|
ND1
|
A:HIS174
|
4.2
|
4.9
|
1.0
|
ND1
|
A:HIS178
|
4.2
|
5.1
|
1.0
|
CG
|
A:HIS178
|
4.2
|
4.2
|
1.0
|
C5
|
A:SF5301
|
4.2
|
27.3
|
1.0
|
CA
|
A:OCS131
|
4.3
|
13.1
|
1.0
|
OE1
|
A:GLU175
|
4.4
|
11.7
|
1.0
|
OE2
|
A:GLU175
|
4.5
|
10.7
|
1.0
|
O
|
A:HOH504
|
4.6
|
13.7
|
1.0
|
C6
|
A:SF5301
|
4.6
|
29.5
|
1.0
|
N
|
A:LEU132
|
4.7
|
13.2
|
1.0
|
O
|
A:GLY130
|
4.7
|
13.4
|
1.0
|
CD
|
A:GLU175
|
4.8
|
6.7
|
1.0
|
C7
|
A:SF5301
|
4.8
|
28.0
|
1.0
|
|
Zinc binding site 2 out
of 9 in 5jf3
Go back to
Zinc Binding Sites List in 5jf3
Zinc binding site 2 out
of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn305
b:19.4
occ:1.00
|
NE2
|
A:HIS55
|
2.1
|
18.5
|
1.0
|
O
|
A:HOH565
|
2.1
|
21.3
|
1.0
|
CD2
|
A:HIS55
|
3.1
|
17.6
|
1.0
|
CE1
|
A:HIS55
|
3.1
|
17.5
|
1.0
|
NE2
|
A:GLN51
|
4.2
|
22.4
|
1.0
|
CG
|
A:HIS55
|
4.2
|
16.1
|
1.0
|
ND1
|
A:HIS55
|
4.2
|
16.8
|
1.0
|
O
|
A:HOH614
|
4.5
|
39.7
|
1.0
|
CG
|
A:GLN51
|
4.7
|
15.8
|
1.0
|
CG
|
A:MET61
|
4.7
|
27.4
|
1.0
|
CD
|
A:GLN51
|
4.9
|
18.6
|
1.0
|
CE
|
A:MET61
|
4.9
|
30.1
|
1.0
|
|
Zinc binding site 3 out
of 9 in 5jf3
Go back to
Zinc Binding Sites List in 5jf3
Zinc binding site 3 out
of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn306
b:23.6
occ:1.00
|
NE2
|
A:HIS118
|
2.0
|
12.0
|
1.0
|
O
|
A:HOH580
|
2.2
|
19.8
|
1.0
|
O
|
A:HOH604
|
2.4
|
25.6
|
1.0
|
O
|
A:HOH606
|
2.5
|
25.5
|
1.0
|
CD2
|
A:HIS118
|
3.0
|
10.5
|
1.0
|
CE1
|
A:HIS118
|
3.1
|
12.6
|
1.0
|
CG
|
A:HIS118
|
4.2
|
8.9
|
1.0
|
ND1
|
A:HIS118
|
4.2
|
11.8
|
1.0
|
O
|
A:HOH589
|
4.2
|
21.9
|
1.0
|
O
|
A:HOH578
|
4.5
|
23.2
|
1.0
|
O
|
A:HOH645
|
4.7
|
29.0
|
1.0
|
CE1
|
A:HIS145
|
4.9
|
9.6
|
1.0
|
|
Zinc binding site 4 out
of 9 in 5jf3
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Zinc Binding Sites List in 5jf3
Zinc binding site 4 out
of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn307
b:16.4
occ:1.00
|
OE2
|
A:GLU190
|
2.0
|
25.9
|
1.0
|
O
|
A:HOH440
|
2.1
|
14.2
|
1.0
|
O
|
A:HOH517
|
2.2
|
14.1
|
1.0
|
OE1
|
A:GLU190
|
2.6
|
23.5
|
1.0
|
CD
|
A:GLU190
|
2.7
|
25.8
|
1.0
|
O
|
A:HOH420
|
3.8
|
38.0
|
1.0
|
CG
|
A:GLU190
|
4.1
|
24.9
|
1.0
|
O
|
A:TYR185
|
4.2
|
10.5
|
1.0
|
O
|
A:ILE188
|
4.5
|
13.6
|
1.0
|
CA
|
A:GLU190
|
4.6
|
24.6
|
1.0
|
CB
|
A:GLU190
|
4.7
|
24.9
|
1.0
|
|
Zinc binding site 5 out
of 9 in 5jf3
Go back to
Zinc Binding Sites List in 5jf3
Zinc binding site 5 out
of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn308
b:15.6
occ:1.00
|
O
|
A:ACT302
|
2.0
|
15.4
|
1.0
|
NE2
|
A:HIS145
|
2.1
|
7.3
|
1.0
|
O
|
A:HOH589
|
2.2
|
21.9
|
1.0
|
OXT
|
A:ACT302
|
2.8
|
16.0
|
1.0
|
C
|
A:ACT302
|
2.8
|
15.1
|
1.0
|
CD2
|
A:HIS145
|
3.0
|
6.0
|
1.0
|
CE1
|
A:HIS145
|
3.1
|
9.6
|
1.0
|
O
|
A:HOH577
|
3.9
|
34.8
|
1.0
|
O
|
A:HOH580
|
4.1
|
19.8
|
1.0
|
O
|
A:HOH425
|
4.1
|
23.6
|
1.0
|
CG
|
A:HIS145
|
4.2
|
6.8
|
1.0
|
ND1
|
A:HIS145
|
4.2
|
7.4
|
1.0
|
CH3
|
A:ACT302
|
4.2
|
15.0
|
1.0
|
CD2
|
A:HIS118
|
4.7
|
10.5
|
1.0
|
O
|
A:HOH620
|
4.7
|
30.9
|
1.0
|
CG1
|
A:VAL115
|
4.9
|
4.7
|
1.0
|
NE2
|
A:HIS118
|
4.9
|
12.0
|
1.0
|
|
Zinc binding site 6 out
of 9 in 5jf3
Go back to
Zinc Binding Sites List in 5jf3
Zinc binding site 6 out
of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn309
b:34.4
occ:1.00
|
O
|
A:HOH416
|
2.1
|
21.2
|
1.0
|
NE2
|
A:HIS12
|
2.1
|
27.2
|
1.0
|
O
|
A:HOH453
|
2.2
|
22.8
|
1.0
|
OD1
|
A:ASP18
|
2.2
|
19.5
|
1.0
|
OD2
|
A:ASP18
|
2.3
|
20.7
|
1.0
|
O
|
A:HOH570
|
2.5
|
42.3
|
1.0
|
CG
|
A:ASP18
|
2.6
|
18.6
|
1.0
|
O
|
A:HOH417
|
2.7
|
37.0
|
1.0
|
CE1
|
A:HIS12
|
2.9
|
25.6
|
1.0
|
O
|
A:HOH644
|
3.2
|
18.2
|
1.0
|
CD2
|
A:HIS12
|
3.3
|
27.1
|
1.0
|
O
|
A:LEU13
|
3.9
|
18.0
|
1.0
|
OD1
|
A:ASP15
|
3.9
|
21.6
|
1.0
|
ND1
|
A:HIS12
|
4.1
|
26.0
|
1.0
|
CB
|
A:ASP18
|
4.1
|
15.9
|
1.0
|
CG
|
A:ASP15
|
4.3
|
21.8
|
1.0
|
CG
|
A:HIS12
|
4.3
|
25.2
|
1.0
|
OD2
|
A:ASP15
|
4.3
|
24.8
|
1.0
|
O
|
A:HOH640
|
4.4
|
35.2
|
1.0
|
N
|
A:ASP15
|
4.5
|
15.3
|
1.0
|
O
|
A:HOH428
|
4.6
|
33.0
|
1.0
|
N
|
A:ASP18
|
4.7
|
17.1
|
1.0
|
CA
|
A:ILE14
|
4.8
|
15.6
|
1.0
|
CA
|
A:ASP18
|
4.8
|
16.6
|
1.0
|
C
|
A:LEU13
|
4.8
|
18.2
|
1.0
|
O
|
A:HOH612
|
4.9
|
16.6
|
1.0
|
O
|
A:HOH526
|
5.0
|
33.8
|
1.0
|
|
Zinc binding site 7 out
of 9 in 5jf3
Go back to
Zinc Binding Sites List in 5jf3
Zinc binding site 7 out
of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn310
b:43.0
occ:1.00
|
OE2
|
A:GLU47
|
2.1
|
26.4
|
1.0
|
O
|
A:HOH550
|
2.1
|
36.0
|
1.0
|
OE1
|
A:GLU43
|
2.4
|
34.7
|
1.0
|
CD
|
A:GLU47
|
2.9
|
24.5
|
1.0
|
OE1
|
A:GLU47
|
3.0
|
26.3
|
1.0
|
CD
|
A:GLU43
|
3.2
|
32.2
|
1.0
|
CG
|
A:GLU43
|
3.7
|
23.4
|
1.0
|
NZ
|
A:LYS155
|
3.9
|
29.1
|
1.0
|
OE2
|
A:GLU43
|
4.1
|
35.0
|
1.0
|
O
|
A:HOH424
|
4.3
|
40.9
|
1.0
|
CG
|
A:GLU47
|
4.4
|
17.1
|
1.0
|
CE
|
A:LYS155
|
4.4
|
27.6
|
1.0
|
|
Zinc binding site 8 out
of 9 in 5jf3
Go back to
Zinc Binding Sites List in 5jf3
Zinc binding site 8 out
of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn311
b:24.4
occ:1.00
|
OE2
|
A:GLU151
|
2.0
|
17.8
|
1.0
|
O
|
A:HOH595
|
2.1
|
23.8
|
1.0
|
O
|
A:HOH597
|
2.7
|
26.7
|
1.0
|
CD
|
A:GLU151
|
2.7
|
15.0
|
1.0
|
OE1
|
A:GLU151
|
2.8
|
15.8
|
1.0
|
O
|
A:HOH571
|
3.0
|
25.2
|
1.0
|
NZ
|
A:LYS159
|
3.8
|
26.7
|
1.0
|
NH1
|
A:ARG161
|
4.0
|
22.4
|
1.0
|
NE
|
A:ARG161
|
4.0
|
17.1
|
1.0
|
CG
|
A:GLU151
|
4.2
|
12.9
|
1.0
|
CZ
|
A:ARG161
|
4.3
|
21.1
|
1.0
|
CE
|
A:LYS159
|
4.6
|
23.1
|
1.0
|
CG1
|
A:VAL116
|
4.7
|
12.0
|
1.0
|
O
|
A:HOH588
|
4.9
|
32.9
|
1.0
|
CD
|
A:ARG161
|
5.0
|
15.6
|
1.0
|
|
Zinc binding site 9 out
of 9 in 5jf3
Go back to
Zinc Binding Sites List in 5jf3
Zinc binding site 9 out
of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT018 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn312
b:53.2
occ:1.00
|
OE2
|
A:GLU32
|
2.0
|
33.5
|
1.0
|
O
|
A:HOH408
|
2.1
|
25.9
|
1.0
|
N3
|
A:IMD303
|
2.5
|
33.5
|
1.0
|
O
|
A:HOH634
|
2.5
|
42.2
|
1.0
|
C2
|
A:IMD303
|
2.9
|
33.7
|
1.0
|
O
|
A:HOH623
|
3.0
|
46.4
|
1.0
|
CD
|
A:GLU32
|
3.1
|
26.1
|
1.0
|
O
|
A:HOH437
|
3.3
|
20.2
|
1.0
|
C4
|
A:IMD303
|
3.8
|
33.4
|
1.0
|
OE1
|
A:GLU32
|
3.9
|
31.6
|
1.0
|
CG
|
A:GLU32
|
4.0
|
22.5
|
1.0
|
N1
|
A:IMD303
|
4.2
|
33.3
|
1.0
|
C5
|
A:IMD303
|
4.6
|
33.2
|
1.0
|
|
Reference:
S.Fieulaine,
R.Alves De Sousa,
L.Maigre,
K.Hamiche,
M.Alimi,
J.M.Bolla,
A.Taleb,
A.Denis,
J.M.Pages,
I.Artaud,
T.Meinnel,
C.Giglione.
A Unique Peptide Deformylase Platform to Rationally Design and Challenge Novel Active Compounds. Sci Rep V. 6 35429 2016.
ISSN: ESSN 2045-2322
PubMed: 27762275
DOI: 10.1038/SREP35429
Page generated: Sun Oct 27 18:48:28 2024
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