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Zinc in PDB 5jf4: Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT019

Enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT019

All present enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT019:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT019, PDB code: 5jf4 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) 44.28 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.150, 65.710, 88.540, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT019 (pdb code 5jf4). 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 AT019, PDB code: 5jf4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5jf4

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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 AT019


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 AT019 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:21.0
occ:1.00
 OD3 A:OCS131 1.7 20.1 1.0
O2 A:6JT301 2.1 30.9 1.0
NE2 A:HIS174 2.1 8.0 1.0
NE2 A:HIS178 2.2 5.8 1.0
O4 A:6JT301 2.5 43.1 1.0
N1 A:6JT301 2.8 38.7 1.0
C3 A:6JT301 2.9 40.6 1.0
CD2 A:HIS174 2.9 7.3 1.0
CD2 A:HIS178 3.1 5.9 1.0
SG A:OCS131 3.1 19.6 1.0
CE1 A:HIS178 3.2 4.1 1.0
CE1 A:HIS174 3.3 2.8 1.0
OD2 A:OCS131 3.4 25.5 1.0
NE2 A:GLN77 3.5 11.3 1.0
O A:HOH473 3.9 17.1 1.0
OD1 A:OCS131 4.0 22.7 1.0
CD A:GLN77 4.0 11.7 1.0
OE1 A:GLN77 4.1 11.9 1.0
CB A:OCS131 4.1 17.5 1.0
CG A:HIS174 4.1 6.4 1.0
CG A:HIS178 4.2 4.1 1.0
ND1 A:HIS174 4.3 9.1 1.0
OE2 A:GLU175 4.3 14.2 1.0
C5 A:6JT301 4.3 41.8 1.0
ND1 A:HIS178 4.3 4.4 1.0
OE1 A:GLU175 4.3 12.6 1.0
CA A:OCS131 4.4 17.9 1.0
C6 A:6JT301 4.5 42.5 1.0
O A:GLY130 4.6 18.1 1.0
C7 A:6JT301 4.6 41.4 1.0
CD A:GLU175 4.7 11.5 1.0
O A:HOH454 4.8 10.2 1.0
N A:LEU132 4.9 16.6 1.0

Zinc binding site 2 out of 9 in 5jf4

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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 AT019


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 AT019 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:25.3
occ:1.00
 NE2 A:HIS55 2.1 13.4 1.0
CD2 A:HIS55 3.0 14.1 1.0
CE1 A:HIS55 3.2 14.4 1.0
CG A:HIS55 4.2 15.8 1.0
OE1 A:GLN51 4.2 26.1 1.0
ND1 A:HIS55 4.3 17.4 1.0
CG A:GLN51 4.6 18.0 1.0
CD A:GLN51 4.8 22.2 1.0
CG A:MET61 4.9 32.6 1.0

Zinc binding site 3 out of 9 in 5jf4

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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 AT019


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 AT019 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:29.8
occ:1.00
 NE2 A:HIS118 2.1 11.0 1.0
O A:HOH524 2.3 25.5 1.0
O A:HOH564 2.4 21.6 1.0
CE1 A:HIS118 3.1 10.6 1.0
CD2 A:HIS118 3.1 10.1 1.0
O A:HOH576 3.3 45.6 1.0
ND1 A:HIS118 4.2 11.2 1.0
CG A:HIS118 4.3 9.8 1.0
O A:HOH517 4.3 14.1 1.0
O A:HOH529 4.5 16.1 1.0
O A:HOH584 4.8 31.6 1.0
CE1 A:HIS145 5.0 8.3 1.0

Zinc binding site 4 out of 9 in 5jf4

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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 AT019


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 AT019 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:23.7
occ:1.00
 OE2 A:GLU190 1.9 32.2 1.0
O A:HOH415 2.2 21.4 1.0
CD A:GLU190 2.8 30.8 1.0
OE1 A:GLU190 3.1 29.9 1.0
O A:HOH438 3.9 28.6 1.0
O A:HOH429 4.0 13.5 1.0
O A:TYR185 4.0 16.1 1.0
CG A:GLU190 4.2 31.1 1.0
O A:ILE188 4.5 15.6 1.0
CA A:GLU190 4.6 31.2 1.0
CB A:GLU190 4.9 31.0 1.0

Zinc binding site 5 out of 9 in 5jf4

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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 AT019


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 AT019 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:21.6
occ:1.00
 O A:HOH517 2.0 14.1 1.0
O A:ACT302 2.2 20.8 1.0
NE2 A:HIS145 2.2 8.4 1.0
C A:ACT302 3.0 20.8 1.0
OXT A:ACT302 3.1 21.2 1.0
CE1 A:HIS145 3.2 8.3 1.0
CD2 A:HIS145 3.2 4.9 1.0
O A:HOH524 4.0 25.5 1.0
O A:HOH549 4.3 21.4 1.0
ND1 A:HIS145 4.3 10.6 1.0
CG A:HIS145 4.4 8.2 1.0
CH3 A:ACT302 4.4 21.9 1.0
CD2 A:HIS118 4.7 10.1 1.0
NE2 A:HIS118 5.0 11.0 1.0

Zinc binding site 6 out of 9 in 5jf4

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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 AT019


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 AT019 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:62.5
occ:1.00
 NE2 A:HIS12 2.4 30.5 1.0
OD1 A:ASP18 2.5 27.8 1.0
OD2 A:ASP18 2.7 27.2 1.0
CE1 A:HIS12 2.8 31.2 1.0
CG A:ASP18 2.9 26.6 1.0
O A:HOH578 3.0 19.3 1.0
CD2 A:HIS12 3.6 29.1 1.0
OD1 A:ASP15 3.8 27.3 1.0
O A:LEU13 3.9 24.0 1.0
ND1 A:HIS12 4.0 30.3 1.0
OD2 A:ASP15 4.2 31.1 1.0
CG A:ASP15 4.2 27.4 1.0
CB A:ASP18 4.3 23.4 1.0
CG A:HIS12 4.5 29.4 1.0
O A:HOH408 4.5 42.2 1.0
N A:ASP15 4.6 23.4 1.0
N A:ASP18 4.7 23.4 1.0
CA A:ASP18 4.9 22.9 1.0
C A:LEU13 4.9 24.1 1.0
O A:HOH507 4.9 14.3 1.0
CA A:ILE14 5.0 22.9 1.0

Zinc binding site 7 out of 9 in 5jf4

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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 AT019


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 AT019 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn310

b:62.0
occ:1.00
 OE1 A:GLU47 2.4 37.0 1.0
OE1 A:GLU43 2.9 41.5 1.0
O A:HOH555 2.9 43.5 1.0
CD A:GLU47 3.1 33.8 1.0
OE2 A:GLU47 3.2 37.4 1.0
CD A:GLU43 3.5 39.4 1.0
NZ A:LYS155 3.9 34.0 1.0
CG A:GLU43 4.1 29.4 1.0
OE2 A:GLU43 4.2 43.1 1.0
CE A:LYS155 4.3 29.2 1.0
O A:HOH404 4.4 37.8 1.0
CG A:GLU47 4.6 22.3 1.0
O A:HOH514 4.9 36.8 1.0

Zinc binding site 8 out of 9 in 5jf4

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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 AT019


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 AT019 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn311

b:38.7
occ:1.00
 OE1 A:GLU151 1.9 23.9 1.0
O A:HOH556 2.7 22.4 1.0
CD A:GLU151 2.8 19.5 1.0
OE2 A:GLU151 3.0 21.5 1.0
O A:HOH552 3.4 29.5 1.0
NZ A:LYS159 3.8 20.6 1.0
O A:HOH580 3.8 32.0 1.0
O A:HOH403 3.9 31.5 1.0
NH2 A:ARG161 4.1 17.2 1.0
NE A:ARG161 4.1 20.4 1.0
CG A:GLU151 4.2 15.4 1.0
CZ A:ARG161 4.4 18.9 1.0
CG1 A:VAL116 4.5 8.9 1.0
CE A:LYS159 4.7 20.1 1.0

Zinc binding site 9 out of 9 in 5jf4

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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 AT019


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 AT019 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn312

b:77.4
occ:1.00
 OE1 A:GLU32 2.0 41.6 1.0
N3 A:IMD303 2.3 33.7 1.0
O A:HOH550 2.5 33.4 1.0
C2 A:IMD303 2.9 30.5 1.0
CD A:GLU32 3.0 34.2 1.0
O A:HOH401 3.0 40.6 1.0
C4 A:IMD303 3.5 33.0 1.0
O A:HOH470 3.7 21.3 1.0
OE2 A:GLU32 3.7 36.1 1.0
CG A:GLU32 3.9 26.3 1.0
N1 A:IMD303 4.2 30.0 1.0
C5 A:IMD303 4.5 31.0 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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