Zinc in PDB 5jf6: Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)
Enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)
All present enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47):
3.5.1.88;
Protein crystallography data
The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47), PDB code: 5jf6
was solved by
S.Fieulaine,
C.Giglione,
T.Meinnel,
K.Hamiche,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.15 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
40.920,
66.280,
88.290,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.4 /
17.5
|
Other elements in 5jf6:
The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47) also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)
(pdb code 5jf6). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47), PDB code: 5jf6:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 5jf6
Go back to
Zinc Binding Sites List in 5jf6
Zinc binding site 1 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)
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 6B (AB47) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn303
b:9.3
occ:1.00
|
OD3
|
A:OCS131
|
2.0
|
13.4
|
1.0
|
O14
|
A:BB4301
|
2.0
|
11.8
|
1.0
|
NE2
|
A:HIS174
|
2.1
|
9.0
|
1.0
|
NE2
|
A:HIS178
|
2.1
|
8.4
|
1.0
|
O2
|
A:BB4301
|
2.2
|
16.1
|
1.0
|
C13
|
A:BB4301
|
2.6
|
18.2
|
1.0
|
N1
|
A:BB4301
|
2.7
|
15.8
|
1.0
|
CD2
|
A:HIS174
|
3.0
|
8.0
|
1.0
|
CD2
|
A:HIS178
|
3.0
|
8.9
|
1.0
|
CE1
|
A:HIS178
|
3.1
|
8.8
|
1.0
|
CE1
|
A:HIS174
|
3.1
|
8.4
|
1.0
|
SG
|
A:OCS131
|
3.2
|
11.3
|
1.0
|
OD2
|
A:OCS131
|
3.4
|
11.4
|
1.0
|
NE2
|
A:GLN77
|
3.4
|
10.1
|
1.0
|
O
|
A:HOH564
|
3.9
|
10.5
|
1.0
|
CD
|
A:GLN77
|
4.0
|
10.0
|
1.0
|
C12
|
A:BB4301
|
4.1
|
15.4
|
1.0
|
OD1
|
A:OCS131
|
4.1
|
14.4
|
1.0
|
OE1
|
A:GLN77
|
4.1
|
10.1
|
1.0
|
CG
|
A:HIS174
|
4.2
|
7.0
|
1.0
|
CG
|
A:HIS178
|
4.2
|
7.8
|
1.0
|
ND1
|
A:HIS178
|
4.2
|
8.7
|
1.0
|
ND1
|
A:HIS174
|
4.2
|
8.1
|
1.0
|
CB
|
A:OCS131
|
4.2
|
11.8
|
1.0
|
OE1
|
A:GLU175
|
4.3
|
11.5
|
1.0
|
CA
|
A:OCS131
|
4.4
|
12.3
|
1.0
|
O
|
A:HOH594
|
4.5
|
9.6
|
1.0
|
OE2
|
A:GLU175
|
4.6
|
11.6
|
1.0
|
O
|
A:GLY130
|
4.6
|
14.2
|
1.0
|
C5
|
A:BB4301
|
4.7
|
18.1
|
1.0
|
CD
|
A:GLU175
|
4.7
|
9.5
|
1.0
|
N
|
A:LEU132
|
4.9
|
11.1
|
1.0
|
|
Zinc binding site 2 out
of 8 in 5jf6
Go back to
Zinc Binding Sites List in 5jf6
Zinc binding site 2 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)
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 6B (AB47) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn304
b:15.1
occ:1.00
|
NE2
|
A:HIS55
|
2.1
|
11.8
|
1.0
|
CD2
|
A:HIS55
|
3.0
|
11.5
|
1.0
|
CE1
|
A:HIS55
|
3.1
|
11.1
|
1.0
|
O
|
A:HOH730
|
3.1
|
26.6
|
1.0
|
NE2
|
A:GLN51
|
4.0
|
13.8
|
1.0
|
O
|
A:HOH643
|
4.1
|
30.9
|
1.0
|
ND1
|
A:HIS55
|
4.2
|
10.3
|
1.0
|
CG
|
A:HIS55
|
4.2
|
10.3
|
1.0
|
CG
|
A:GLN51
|
4.7
|
11.4
|
1.0
|
CG
|
A:MET61
|
4.7
|
18.8
|
1.0
|
CD
|
A:GLN51
|
4.8
|
12.6
|
1.0
|
CE
|
A:MET61
|
4.9
|
20.4
|
1.0
|
|
Zinc binding site 3 out
of 8 in 5jf6
Go back to
Zinc Binding Sites List in 5jf6
Zinc binding site 3 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)
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 6B (AB47) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn305
b:14.8
occ:1.00
|
NE2
|
A:HIS118
|
2.1
|
11.0
|
1.0
|
O
|
A:HOH632
|
2.1
|
18.1
|
1.0
|
O
|
A:HOH667
|
2.1
|
16.6
|
1.0
|
O
|
A:HOH648
|
2.2
|
20.4
|
1.0
|
CE1
|
A:HIS118
|
3.0
|
11.3
|
1.0
|
CD2
|
A:HIS118
|
3.0
|
10.0
|
1.0
|
ND1
|
A:HIS118
|
4.1
|
10.0
|
1.0
|
CG
|
A:HIS118
|
4.2
|
8.7
|
1.0
|
O
|
A:HOH647
|
4.3
|
12.8
|
1.0
|
O
|
A:HOH727
|
4.4
|
33.9
|
1.0
|
O
|
A:HOH749
|
4.4
|
26.1
|
1.0
|
O
|
A:HOH624
|
4.4
|
19.6
|
1.0
|
CE1
|
A:HIS145
|
4.9
|
9.0
|
1.0
|
|
Zinc binding site 4 out
of 8 in 5jf6
Go back to
Zinc Binding Sites List in 5jf6
Zinc binding site 4 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)
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 6B (AB47) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn306
b:11.9
occ:1.00
|
OE2
|
A:GLU190
|
1.9
|
18.2
|
1.0
|
O
|
A:HOH439
|
2.0
|
10.1
|
1.0
|
O
|
A:HOH527
|
2.1
|
11.0
|
1.0
|
CD
|
A:GLU190
|
2.6
|
20.7
|
1.0
|
OE1
|
A:GLU190
|
2.7
|
19.2
|
1.0
|
O
|
A:HOH438
|
3.9
|
26.7
|
1.0
|
CG
|
A:GLU190
|
4.1
|
19.2
|
1.0
|
O
|
A:HOH458
|
4.1
|
9.0
|
1.0
|
O
|
A:TYR185
|
4.2
|
8.3
|
1.0
|
O
|
A:ILE188
|
4.5
|
10.1
|
1.0
|
CA
|
A:GLU190
|
4.5
|
17.7
|
1.0
|
CB
|
A:GLU190
|
4.6
|
17.9
|
1.0
|
O
|
A:HOH652
|
4.6
|
40.5
|
1.0
|
|
Zinc binding site 5 out
of 8 in 5jf6
Go back to
Zinc Binding Sites List in 5jf6
Zinc binding site 5 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)
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 6B (AB47) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn307
b:10.7
occ:1.00
|
O
|
A:ACT302
|
2.0
|
10.5
|
1.0
|
NE2
|
A:HIS145
|
2.0
|
7.8
|
1.0
|
O
|
A:HOH647
|
2.1
|
12.8
|
1.0
|
C
|
A:ACT302
|
2.7
|
10.5
|
1.0
|
OXT
|
A:ACT302
|
2.9
|
11.2
|
1.0
|
CD2
|
A:HIS145
|
3.0
|
7.5
|
1.0
|
CE1
|
A:HIS145
|
3.0
|
9.0
|
1.0
|
O
|
A:HOH574
|
3.7
|
18.4
|
1.0
|
ND1
|
A:HIS145
|
4.1
|
7.8
|
1.0
|
CG
|
A:HIS145
|
4.1
|
8.0
|
1.0
|
O
|
A:HOH632
|
4.2
|
18.1
|
1.0
|
CH3
|
A:ACT302
|
4.2
|
10.6
|
1.0
|
O
|
A:HOH450
|
4.3
|
21.5
|
1.0
|
CD2
|
A:HIS118
|
4.6
|
10.0
|
1.0
|
O
|
A:HOH702
|
4.6
|
18.9
|
1.0
|
NE2
|
A:HIS118
|
4.8
|
11.0
|
1.0
|
CG1
|
A:VAL115
|
5.0
|
7.2
|
1.0
|
|
Zinc binding site 6 out
of 8 in 5jf6
Go back to
Zinc Binding Sites List in 5jf6
Zinc binding site 6 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)
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 6B (AB47) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn308
b:33.9
occ:1.00
|
O
|
A:HOH412
|
2.1
|
20.7
|
1.0
|
NE2
|
A:HIS12
|
2.1
|
18.2
|
1.0
|
O
|
A:HOH493
|
2.1
|
10.7
|
1.0
|
OD1
|
A:ASP18
|
2.2
|
11.5
|
1.0
|
OD2
|
A:ASP18
|
2.3
|
13.4
|
1.0
|
CG
|
A:ASP18
|
2.5
|
12.6
|
1.0
|
CE1
|
A:HIS12
|
2.9
|
19.7
|
1.0
|
CD2
|
A:HIS12
|
3.2
|
19.1
|
1.0
|
O
|
A:HOH743
|
3.3
|
13.2
|
1.0
|
O
|
A:HOH707
|
3.8
|
26.8
|
1.0
|
OD1
|
A:ASP15
|
3.8
|
13.1
|
1.0
|
O
|
A:LEU13
|
3.9
|
11.7
|
1.0
|
ND1
|
A:HIS12
|
4.0
|
18.2
|
1.0
|
CB
|
A:ASP18
|
4.1
|
11.5
|
1.0
|
O
|
A:HOH722
|
4.2
|
32.8
|
1.0
|
CG
|
A:HIS12
|
4.2
|
16.5
|
1.0
|
O
|
A:HOH481
|
4.3
|
28.3
|
1.0
|
CG
|
A:ASP15
|
4.4
|
14.2
|
1.0
|
OD2
|
A:ASP15
|
4.4
|
16.0
|
1.0
|
N
|
A:ASP15
|
4.5
|
11.3
|
1.0
|
N
|
A:ASP18
|
4.6
|
11.3
|
1.0
|
CA
|
A:ASP18
|
4.7
|
11.6
|
1.0
|
O
|
A:HOH540
|
4.8
|
30.1
|
1.0
|
CA
|
A:ILE14
|
4.8
|
12.0
|
1.0
|
O
|
A:HOH418
|
4.8
|
22.1
|
1.0
|
O
|
A:HOH681
|
4.9
|
13.7
|
1.0
|
C
|
A:LEU13
|
4.9
|
11.9
|
1.0
|
|
Zinc binding site 7 out
of 8 in 5jf6
Go back to
Zinc Binding Sites List in 5jf6
Zinc binding site 7 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)
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 6B (AB47) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn309
b:26.3
occ:1.00
|
O
|
A:HOH578
|
2.1
|
30.0
|
1.0
|
OE2
|
A:GLU47
|
2.1
|
17.2
|
1.0
|
O
|
A:HOH441
|
2.1
|
30.3
|
1.0
|
OE2
|
A:GLU43
|
2.2
|
27.1
|
1.0
|
O
|
A:HOH606
|
2.2
|
32.4
|
1.0
|
CD
|
A:GLU47
|
2.9
|
17.3
|
1.0
|
CD
|
A:GLU43
|
3.1
|
24.6
|
1.0
|
OE1
|
A:GLU47
|
3.2
|
19.6
|
1.0
|
CG
|
A:GLU43
|
3.7
|
18.1
|
1.0
|
NZ
|
A:LYS155
|
4.0
|
24.8
|
1.0
|
OE1
|
A:GLU43
|
4.0
|
26.2
|
1.0
|
O
|
A:HOH435
|
4.1
|
35.6
|
1.0
|
CG
|
A:GLU47
|
4.3
|
13.2
|
1.0
|
O
|
A:HOH669
|
4.3
|
38.2
|
1.0
|
CE
|
A:LYS155
|
4.3
|
23.2
|
1.0
|
O
|
A:HOH402
|
4.9
|
28.5
|
1.0
|
|
Zinc binding site 8 out
of 8 in 5jf6
Go back to
Zinc Binding Sites List in 5jf6
Zinc binding site 8 out
of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)
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 6B (AB47) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn310
b:16.4
occ:1.00
|
OE2
|
A:GLU151
|
2.1
|
13.4
|
1.0
|
CD
|
A:GLU151
|
2.8
|
12.3
|
1.0
|
O
|
A:HOH586
|
2.9
|
16.6
|
1.0
|
OE1
|
A:GLU151
|
2.9
|
13.9
|
1.0
|
O
|
A:HOH423
|
3.8
|
42.0
|
1.0
|
NH2
|
A:ARG161
|
3.9
|
13.7
|
1.0
|
NE
|
A:ARG161
|
4.0
|
13.2
|
1.0
|
NZ
|
A:LYS159
|
4.1
|
18.6
|
1.0
|
CG
|
A:GLU151
|
4.2
|
11.1
|
1.0
|
CZ
|
A:ARG161
|
4.3
|
14.1
|
1.0
|
O
|
A:HOH723
|
4.5
|
42.5
|
1.0
|
CE
|
A:LYS159
|
4.7
|
15.6
|
1.0
|
CG1
|
A:VAL116
|
4.7
|
10.2
|
1.0
|
CD
|
A:ARG161
|
4.9
|
12.1
|
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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