Atomistry » Zinc » PDB 5jez-5jmx » 5jf2
Atomistry »
  Zinc »
    PDB 5jez-5jmx »
      5jf2 »

Zinc in PDB 5jf2: Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT002

Enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT002

All present enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT002:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT002, PDB code: 5jf2 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) 44.46 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.300, 65.540, 88.890, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 20

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT002 (pdb code 5jf2). 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 AT002, PDB code: 5jf2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5jf2

Go back to Zinc Binding Sites List in 5jf2
Zinc binding site 1 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT002


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 AT002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:15.5
occ:1.00
 OD3 A:OCS131 1.8 17.1 1.0
O2 A:SF7301 2.0 18.6 1.0
NE2 A:HIS178 2.0 6.7 1.0
NE2 A:HIS174 2.1 7.7 1.0
O4 A:SF7301 2.6 25.0 1.0
N1 A:SF7301 2.7 23.7 1.0
CD2 A:HIS174 2.9 7.2 1.0
CD2 A:HIS178 3.0 6.3 1.0
C3 A:SF7301 3.0 25.4 1.0
CE1 A:HIS178 3.1 9.7 1.0
SG A:OCS131 3.1 16.1 1.0
NE2 A:GLN77 3.1 10.4 1.0
CE1 A:HIS174 3.2 9.2 1.0
OD2 A:OCS131 3.4 17.8 1.0
O A:HOH480 3.6 14.1 1.0
CD A:GLN77 4.0 10.4 1.0
OD1 A:OCS131 4.0 21.4 1.0
CG A:HIS178 4.1 5.7 1.0
CG A:HIS174 4.2 5.8 1.0
ND1 A:HIS178 4.2 5.7 1.0
CB A:OCS131 4.2 15.3 1.0
OE2 A:GLU175 4.3 15.8 1.0
ND1 A:HIS174 4.3 5.8 1.0
OE1 A:GLN77 4.3 12.6 1.0
CA A:OCS131 4.3 15.6 1.0
C5 A:SF7301 4.4 27.3 1.0
OE1 A:GLU175 4.4 16.8 1.0
O A:HOH478 4.6 13.4 1.0
O A:GLY130 4.7 15.5 1.0
C6 A:SF7301 4.7 29.5 1.0
CD A:GLU175 4.8 12.7 1.0
C7 A:SF7301 4.8 28.0 1.0
N A:LEU132 4.8 16.5 1.0

Zinc binding site 2 out of 8 in 5jf2

Go back to Zinc Binding Sites List in 5jf2
Zinc binding site 2 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT002


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 AT002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:23.3
occ:1.00
 NE2 A:HIS55 2.2 18.4 1.0
CD2 A:HIS55 3.1 18.5 1.0
CE1 A:HIS55 3.2 18.9 1.0
O A:HOH615 3.5 35.2 1.0
NE2 A:GLN51 4.1 24.3 1.0
CG A:HIS55 4.2 14.6 1.0
ND1 A:HIS55 4.3 16.7 1.0
CG A:GLN51 4.6 17.5 1.0
O A:HOH617 4.6 38.8 1.0
CD A:GLN51 4.8 20.4 1.0
CG A:MET61 4.8 34.8 1.0
CE A:MET61 4.9 34.0 1.0

Zinc binding site 3 out of 8 in 5jf2

Go back to Zinc Binding Sites List in 5jf2
Zinc binding site 3 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT002


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 AT002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:24.2
occ:1.00
 NE2 A:HIS118 2.1 12.6 1.0
O A:HOH568 2.2 28.6 1.0
O A:HOH582 2.3 27.5 1.0
O A:HOH601 2.7 20.0 1.0
CD2 A:HIS118 3.0 9.7 1.0
CE1 A:HIS118 3.2 11.1 1.0
CG A:HIS118 4.2 9.4 1.0
O A:HOH560 4.2 13.9 1.0
ND1 A:HIS118 4.2 11.5 1.0
O A:HOH561 4.3 25.0 1.0
O A:HOH623 4.7 30.4 1.0

Zinc binding site 4 out of 8 in 5jf2

Go back to Zinc Binding Sites List in 5jf2
Zinc binding site 4 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT002


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 AT002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:17.0
occ:1.00
 OE1 A:GLU190 1.8 28.0 1.0
O A:HOH436 2.0 10.5 1.0
O A:HOH421 2.4 13.4 1.0
CD A:GLU190 2.6 27.4 1.0
OE2 A:GLU190 2.6 25.9 1.0
CG A:GLU190 4.0 27.9 1.0
O A:TYR185 4.1 11.8 1.0
O A:HOH438 4.2 15.0 1.0
O A:ILE188 4.5 15.5 1.0
CA A:GLU190 4.5 26.9 1.0
CB A:GLU190 4.6 27.6 1.0

Zinc binding site 5 out of 8 in 5jf2

Go back to Zinc Binding Sites List in 5jf2
Zinc binding site 5 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT002


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 AT002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:16.1
occ:1.00
 O A:ACT302 2.0 16.6 1.0
NE2 A:HIS145 2.0 9.7 1.0
O A:HOH560 2.1 13.9 1.0
C A:ACT302 2.9 17.7 1.0
OXT A:ACT302 3.0 17.9 1.0
CE1 A:HIS145 3.0 10.7 1.0
CD2 A:HIS145 3.0 7.6 1.0
ND1 A:HIS145 4.1 9.8 1.0
O A:HOH582 4.2 27.5 1.0
CG A:HIS145 4.2 8.5 1.0
O A:HOH593 4.2 25.8 1.0
CH3 A:ACT302 4.3 17.5 1.0
O A:HOH511 4.4 27.0 1.0
CD2 A:HIS118 4.9 9.7 1.0

Zinc binding site 6 out of 8 in 5jf2

Go back to Zinc Binding Sites List in 5jf2
Zinc binding site 6 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT002


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 AT002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:44.7
occ:1.00
 OD2 A:ASP18 2.2 22.2 1.0
NE2 A:HIS12 2.2 28.4 1.0
O A:HOH497 2.6 43.5 1.0
OD1 A:ASP18 2.7 23.2 1.0
O A:HOH577 2.7 36.5 1.0
CG A:ASP18 2.8 21.6 1.0
CE1 A:HIS12 2.8 27.9 1.0
O A:HOH453 2.9 37.6 1.0
O A:HOH620 3.3 22.6 1.0
CD2 A:HIS12 3.3 28.5 1.0
O A:LEU13 3.8 21.1 1.0
OD1 A:ASP15 3.9 24.4 1.0
ND1 A:HIS12 4.0 28.6 1.0
OD2 A:ASP15 4.1 27.2 1.0
CG A:ASP15 4.2 24.1 1.0
CB A:ASP18 4.2 20.6 1.0
CG A:HIS12 4.3 28.0 1.0
O A:HOH567 4.4 20.0 1.0
N A:ASP15 4.5 18.7 1.0
O A:HOH414 4.5 23.3 1.0
CA A:ILE14 4.7 18.8 1.0
C A:LEU13 4.8 21.7 1.0
N A:ASP18 4.8 21.2 1.0
CA A:ASP18 4.9 20.3 1.0
O A:HOH590 4.9 27.9 1.0

Zinc binding site 7 out of 8 in 5jf2

Go back to Zinc Binding Sites List in 5jf2
Zinc binding site 7 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT002


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 AT002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn310

b:49.0
occ:1.00
 O A:HOH562 2.2 36.6 1.0
OE1 A:GLU43 2.2 40.2 1.0
OE2 A:GLU47 2.3 29.6 1.0
O A:HOH496 2.4 33.0 1.0
OE1 A:GLU47 3.0 27.9 1.0
CD A:GLU47 3.1 23.0 1.0
CD A:GLU43 3.2 37.5 1.0
CG A:GLU43 3.7 28.7 1.0
NZ A:LYS155 4.1 26.7 1.0
OE2 A:GLU43 4.3 41.4 1.0
CG A:GLU47 4.6 19.0 1.0
O A:HOH534 4.9 38.4 1.0

Zinc binding site 8 out of 8 in 5jf2

Go back to Zinc Binding Sites List in 5jf2
Zinc binding site 8 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT002


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 AT002 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn311

b:29.6
occ:1.00
 OE2 A:GLU151 2.0 17.2 1.0
O A:HOH571 2.8 41.7 1.0
CD A:GLU151 2.9 18.1 1.0
OE1 A:GLU151 3.0 18.6 1.0
NZ A:LYS159 3.7 22.4 1.0
O A:HOH454 4.0 38.8 1.0
NE A:ARG161 4.1 19.2 1.0
NH2 A:ARG161 4.2 25.3 1.0
CG A:GLU151 4.3 15.2 1.0
CZ A:ARG161 4.4 24.1 1.0
CG1 A:VAL116 4.6 15.0 1.0
CE A:LYS159 4.7 18.3 1.0
O A:HOH527 4.8 37.3 1.0
CD A:ARG161 5.0 20.3 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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy