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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

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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

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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

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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 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

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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

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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

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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

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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

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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: Thu Aug 21 03:48:54 2025

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