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Zinc in PDB 5jf7: Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor SMP289

Enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor SMP289

All present enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor SMP289:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor SMP289, PDB code: 5jf7 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) 44.66 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.470, 65.970, 89.320, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 21.1

Other elements in 5jf7:

The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor SMP289 also contains other interesting chemical elements:

Bromine (Br) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor SMP289 (pdb code 5jf7). 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 SMP289, PDB code: 5jf7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5jf7

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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 SMP289


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 SMP289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:18.8
occ:1.00
 OD3 A:OCS131 1.9 23.2 1.0
O14 A:6JU301 2.0 28.3 1.0
NE2 A:HIS174 2.1 15.3 1.0
NE2 A:HIS178 2.2 12.1 1.0
N1 A:6JU301 2.7 40.9 1.0
O2 A:6JU301 2.9 46.2 1.0
CD2 A:HIS174 2.9 15.1 1.0
C13 A:6JU301 3.1 48.6 1.0
CD2 A:HIS178 3.1 12.8 1.0
CE1 A:HIS178 3.1 12.9 1.0
CE1 A:HIS174 3.2 16.1 1.0
SG A:OCS131 3.2 23.6 1.0
OD2 A:OCS131 3.5 23.6 1.0
NE2 A:GLN77 3.5 14.6 1.0
OD1 A:OCS131 3.8 27.8 1.0
O A:HOH482 3.9 14.8 1.0
CB A:OCS131 3.9 23.0 1.0
CD A:GLN77 4.1 14.7 1.0
OE1 A:GLN77 4.1 15.2 1.0
CG A:HIS174 4.1 15.1 1.0
ND1 A:HIS174 4.2 15.8 1.0
ND1 A:HIS178 4.3 13.0 1.0
CG A:HIS178 4.3 12.6 1.0
OE1 A:GLU175 4.3 21.4 1.0
OE2 A:GLU175 4.3 22.9 1.0
CA A:OCS131 4.4 20.9 1.0
C12 A:6JU301 4.5 55.1 1.0
O A:HOH504 4.5 17.7 1.0
C10 A:6JU301 4.6 58.4 1.0
N3 A:6JU301 4.7 63.5 1.0
C11 A:6JU301 4.7 62.8 1.0
CD A:GLU175 4.7 18.1 1.0
O A:GLY130 4.7 26.3 1.0

Zinc binding site 2 out of 9 in 5jf7

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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 SMP289


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 SMP289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:26.1
occ:1.00
 NE2 A:HIS55 2.2 18.1 1.0
CD2 A:HIS55 3.1 18.6 1.0
CE1 A:HIS55 3.3 18.5 1.0
NE2 A:GLN51 4.2 26.4 1.0
CG A:HIS55 4.3 17.3 1.0
ND1 A:HIS55 4.3 19.0 1.0
O A:HOH606 4.4 51.1 1.0
CG A:GLN51 4.7 21.3 1.0
CG A:MET61 4.9 34.7 1.0
CD A:GLN51 5.0 22.8 1.0

Zinc binding site 3 out of 9 in 5jf7

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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 SMP289


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 SMP289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:29.2
occ:1.00
 O A:HOH554 2.1 26.4 1.0
NE2 A:HIS118 2.1 16.9 1.0
O A:HOH564 2.2 22.5 1.0
O A:HOH577 2.2 46.4 1.0
CD2 A:HIS118 3.1 16.1 1.0
CE1 A:HIS118 3.2 16.5 1.0
ND1 A:HIS118 4.2 17.1 1.0
CG A:HIS118 4.2 15.5 1.0
O A:HOH561 4.3 19.0 1.0
O A:HOH562 4.4 24.1 1.0
O A:HOH612 4.8 35.2 1.0
CE1 A:HIS145 4.9 13.7 1.0

Zinc binding site 4 out of 9 in 5jf7

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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 SMP289


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 SMP289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:21.4
occ:1.00
 OE1 A:GLU190 1.8 27.0 1.0
O A:HOH416 2.1 17.5 1.0
O A:HOH566 2.3 29.1 1.0
O A:HOH422 2.3 22.4 1.0
CD A:GLU190 2.7 27.6 1.0
OE2 A:GLU190 2.8 29.3 1.0
CG A:GLU190 4.1 30.2 1.0
O A:TYR185 4.1 16.0 1.0
O A:HOH435 4.2 13.0 1.0
O A:ILE188 4.4 18.2 1.0
CB A:GLU190 4.7 28.5 1.0
CA A:GLU190 4.7 29.0 1.0

Zinc binding site 5 out of 9 in 5jf7

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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 SMP289


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 SMP289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:18.2
occ:1.00
 O A:ACT302 2.1 20.0 1.0
O A:HOH561 2.1 19.0 1.0
NE2 A:HIS145 2.1 14.0 1.0
C A:ACT302 2.8 21.7 1.0
OXT A:ACT302 2.9 20.6 1.0
CD2 A:HIS145 3.0 12.8 1.0
CE1 A:HIS145 3.2 13.7 1.0
O A:HOH564 4.0 22.5 1.0
O A:HOH415 4.1 28.6 1.0
O A:HOH575 4.2 25.9 1.0
CG A:HIS145 4.2 12.6 1.0
CH3 A:ACT302 4.2 22.8 1.0
ND1 A:HIS145 4.3 13.0 1.0
CD2 A:HIS118 4.6 16.1 1.0
NE2 A:HIS118 4.9 16.9 1.0
CG1 A:VAL115 4.9 16.7 1.0

Zinc binding site 6 out of 9 in 5jf7

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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 SMP289


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 SMP289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:55.1
occ:1.00
 NE2 A:HIS12 2.3 28.0 1.0
O A:HOH418 2.3 41.6 1.0
OD2 A:ASP18 2.5 29.1 1.0
OD1 A:ASP18 2.5 24.7 1.0
O A:HOH539 2.6 38.3 1.0
O A:HOH574 2.7 38.9 1.0
O A:HOH414 2.7 38.2 1.0
CG A:ASP18 2.8 25.5 1.0
CE1 A:HIS12 3.0 27.4 1.0
O A:HOH613 3.3 20.9 1.0
CD2 A:HIS12 3.4 27.9 1.0
O A:LEU13 3.8 21.8 1.0
OD1 A:ASP15 3.9 26.8 1.0
OD2 A:ASP15 4.2 30.1 1.0
CG A:ASP15 4.2 25.2 1.0
ND1 A:HIS12 4.2 26.8 1.0
CB A:ASP18 4.2 24.2 1.0
CG A:HIS12 4.4 26.4 1.0
N A:ASP15 4.6 20.9 1.0
O A:HOH420 4.6 30.4 1.0
N A:ASP18 4.8 22.3 1.0
C A:LEU13 4.9 22.3 1.0
CA A:ILE14 4.9 21.4 1.0
CA A:ASP18 4.9 22.8 1.0

Zinc binding site 7 out of 9 in 5jf7

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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 SMP289


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 SMP289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn310

b:55.9
occ:1.00
 O A:HOH568 2.2 45.5 1.0
OE1 A:GLU43 2.2 47.3 1.0
OE2 A:GLU47 2.3 41.0 1.0
O A:HOH507 2.7 47.6 1.0
OE1 A:GLU47 3.0 30.6 1.0
CD A:GLU47 3.0 32.1 1.0
CD A:GLU43 3.3 39.8 1.0
O A:HOH493 3.3 53.3 1.0
CG A:GLU43 3.8 31.9 1.0
NZ A:LYS155 4.0 36.4 1.0
OE2 A:GLU43 4.4 44.0 1.0
CE A:LYS155 4.4 33.7 1.0
CG A:GLU47 4.5 25.5 1.0
O A:HOH494 4.6 47.3 1.0

Zinc binding site 8 out of 9 in 5jf7

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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 SMP289


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 SMP289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn311

b:34.8
occ:1.00
 OE2 A:GLU151 2.1 23.3 1.0
O A:HOH583 2.4 31.6 1.0
O A:HOH556 2.8 33.0 1.0
CD A:GLU151 2.8 23.9 1.0
OE1 A:GLU151 2.9 25.2 1.0
NZ A:LYS159 3.9 25.0 1.0
NH2 A:ARG161 4.0 24.9 1.0
NE A:ARG161 4.0 21.4 1.0
CG A:GLU151 4.3 22.0 1.0
CZ A:ARG161 4.4 23.9 1.0
CE A:LYS159 4.5 22.8 1.0
O A:HOH543 4.8 40.8 1.0
CG1 A:VAL116 4.8 21.5 1.0
CD A:ARG161 4.9 20.4 1.0

Zinc binding site 9 out of 9 in 5jf7

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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 SMP289


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 SMP289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn312

b:59.0
occ:1.00
 OE2 A:GLU32 2.0 41.2 1.0
O A:HOH405 2.3 32.1 1.0
N3 A:IMD303 2.4 29.4 1.0
C2 A:IMD303 2.8 30.1 1.0
CD A:GLU32 3.1 30.5 1.0
O A:HOH477 3.3 43.3 1.0
O A:HOH522 3.4 23.4 1.0
C4 A:IMD303 3.7 28.4 1.0
OE1 A:GLU32 3.8 33.7 1.0
N1 A:IMD303 4.1 32.6 1.0
CG A:GLU32 4.2 28.0 1.0
C5 A:IMD303 4.5 29.6 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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