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Zinc in PDB 5jf5: Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT020

Enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT020

All present enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT020:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT020, PDB code: 5jf5 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) 44.24 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.000, 65.270, 88.470, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor AT020 (pdb code 5jf5). 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 AT020, PDB code: 5jf5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5jf5

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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 AT020


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 AT020 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:17.3
occ:1.00
 OD3 A:OCS131 1.8 20.9 1.0
NE2 A:HIS178 2.1 11.7 1.0
NE2 A:HIS174 2.1 13.5 1.0
O2 A:7JT301 2.2 18.1 1.0
O4 A:7JT301 2.3 29.5 1.0
C3 A:7JT301 2.9 28.3 1.0
N1 A:7JT301 2.9 26.4 1.0
CD2 A:HIS178 2.9 10.9 1.0
CD2 A:HIS174 2.9 9.7 1.0
SG A:OCS131 3.0 18.4 1.0
CE1 A:HIS178 3.1 11.4 1.0
OD2 A:OCS131 3.2 19.6 1.0
CE1 A:HIS174 3.2 10.3 1.0
NE2 A:GLN77 3.3 13.2 1.0
O A:HOH496 3.8 17.8 1.0
OD1 A:OCS131 3.9 23.3 1.0
CD A:GLN77 4.0 15.4 1.0
CB A:OCS131 4.1 18.5 1.0
CG A:HIS178 4.1 10.7 1.0
CG A:HIS174 4.1 9.8 1.0
OE1 A:GLN77 4.2 14.1 1.0
ND1 A:HIS178 4.2 9.8 1.0
ND1 A:HIS174 4.2 10.6 1.0
CA A:OCS131 4.3 18.5 1.0
OE2 A:GLU175 4.4 17.5 1.0
C5 A:7JT301 4.4 29.0 1.0
OE1 A:GLU175 4.5 16.7 1.0
O A:HOH507 4.5 14.9 1.0
O A:GLY130 4.7 19.3 1.0
N A:LEU132 4.7 18.0 1.0
C6 A:7JT301 4.8 30.4 1.0
CD A:GLU175 4.8 13.2 1.0
C7 A:7JT301 4.9 29.2 1.0

Zinc binding site 2 out of 9 in 5jf5

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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 AT020


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 AT020 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:21.9
occ:1.00
 NE2 A:HIS55 2.0 20.4 1.0
O A:HOH535 2.1 22.0 1.0
CD2 A:HIS55 3.0 19.2 1.0
CE1 A:HIS55 3.1 20.3 1.0
NE2 A:GLN51 4.0 21.8 1.0
CG A:HIS55 4.1 19.5 1.0
ND1 A:HIS55 4.1 19.2 1.0
CG A:GLN51 4.6 19.3 1.0
O A:HOH604 4.6 38.6 1.0
CG A:MET61 4.6 30.4 1.0
CD A:GLN51 4.8 21.3 1.0
CE A:MET61 4.9 32.1 1.0

Zinc binding site 3 out of 9 in 5jf5

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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 AT020


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 AT020 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:25.2
occ:1.00
 NE2 A:HIS118 2.1 14.1 1.0
O A:HOH578 2.2 31.0 1.0
O A:HOH575 2.2 27.7 1.0
O A:HOH587 2.4 29.0 1.0
CD2 A:HIS118 3.0 13.3 1.0
CE1 A:HIS118 3.1 14.3 1.0
CG A:HIS118 4.2 10.2 1.0
ND1 A:HIS118 4.2 12.1 1.0
O A:HOH589 4.2 43.2 1.0
O A:HOH572 4.4 19.6 1.0
O A:HOH563 4.4 25.3 1.0
O A:HOH622 4.6 30.4 1.0
CE1 A:HIS145 4.9 11.3 1.0

Zinc binding site 4 out of 9 in 5jf5

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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 AT020


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 AT020 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:20.6
occ:1.00
 O A:HOH426 2.1 18.6 1.0
OE2 A:GLU190 2.1 29.3 1.0
O A:HOH566 2.2 23.5 1.0
CD A:GLU190 2.8 28.6 1.0
OE1 A:GLU190 2.8 27.4 1.0
O A:HOH435 3.9 31.1 1.0
O A:TYR185 4.2 14.5 1.0
CG A:GLU190 4.3 27.7 1.0
O A:ILE188 4.5 16.3 1.0
CA A:GLU190 4.6 26.8 1.0
O A:HOH567 4.7 45.2 1.0
CB A:GLU190 4.8 26.7 1.0

Zinc binding site 5 out of 9 in 5jf5

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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 AT020


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 AT020 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:18.6
occ:1.00
 O A:HOH572 2.0 19.6 1.0
NE2 A:HIS145 2.0 12.6 1.0
O A:ACT302 2.1 18.1 1.0
CD2 A:HIS145 2.9 9.6 1.0
C A:ACT302 3.0 17.8 1.0
OXT A:ACT302 3.0 17.7 1.0
CE1 A:HIS145 3.1 11.3 1.0
O A:HOH575 4.0 27.7 1.0
O A:HOH586 4.0 31.2 1.0
CG A:HIS145 4.1 11.9 1.0
ND1 A:HIS145 4.2 11.5 1.0
O A:HOH441 4.2 33.5 1.0
CH3 A:ACT302 4.4 19.6 1.0
CD2 A:HIS118 4.7 13.3 1.0
NE2 A:HIS118 5.0 14.1 1.0
CG1 A:VAL115 5.0 8.7 1.0

Zinc binding site 6 out of 9 in 5jf5

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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 AT020


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 AT020 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:66.1
occ:1.00
 NE2 A:HIS12 2.3 25.5 1.0
OD2 A:ASP18 2.5 24.2 1.0
OD1 A:ASP18 2.7 19.7 1.0
O A:HOH579 2.8 47.4 1.0
O A:HOH619 2.9 11.8 1.0
CG A:ASP18 2.9 22.1 1.0
CE1 A:HIS12 3.1 25.4 1.0
O A:HOH425 3.2 32.3 1.0
CD2 A:HIS12 3.4 27.6 1.0
OD1 A:ASP15 3.7 23.7 1.0
O A:LEU13 3.9 20.4 1.0
OD2 A:ASP15 4.1 27.3 1.0
CG A:ASP15 4.1 22.3 1.0
O A:HOH624 4.1 37.3 1.0
O A:HOH405 4.1 32.3 1.0
ND1 A:HIS12 4.2 28.4 1.0
O A:HOH614 4.2 32.8 1.0
CB A:ASP18 4.4 20.6 1.0
CG A:HIS12 4.4 25.9 1.0
N A:ASP15 4.6 19.7 1.0
N A:ASP18 4.7 20.8 1.0
O A:HOH592 4.9 11.2 1.0
CA A:ASP18 4.9 20.6 1.0
C A:LEU13 5.0 21.7 1.0

Zinc binding site 7 out of 9 in 5jf5

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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 AT020


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 AT020 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn310

b:48.0
occ:1.00
 OE2 A:GLU47 2.1 29.7 1.0
O A:HOH551 2.5 39.8 1.0
OE1 A:GLU43 2.5 35.6 1.0
CD A:GLU47 2.9 25.6 1.0
OE1 A:GLU47 3.1 27.6 1.0
CD A:GLU43 3.2 33.6 1.0
CG A:GLU43 3.6 24.1 1.0
NZ A:LYS155 3.7 31.8 1.0
O A:HOH539 3.7 49.1 1.0
OE2 A:GLU43 4.1 37.5 1.0
O A:HOH407 4.1 47.6 1.0
CE A:LYS155 4.3 28.1 1.0
O A:HOH569 4.3 39.4 1.0
CG A:GLU47 4.3 20.2 1.0
O A:HOH401 5.0 36.9 1.0

Zinc binding site 8 out of 9 in 5jf5

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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 AT020


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 AT020 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn311

b:28.2
occ:1.00
 OE1 A:GLU102 2.0 28.5 1.0
CD A:GLU102 2.7 28.1 1.0
OE2 A:GLU102 2.7 30.5 1.0
O A:HOH443 3.7 42.1 1.0
CG A:GLU102 4.1 26.7 1.0

Zinc binding site 9 out of 9 in 5jf5

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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 AT020


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 AT020 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn312

b:48.9
occ:1.00
 OE2 A:GLU32 1.8 36.0 1.0
O A:HOH593 2.3 32.8 1.0
N3 A:IMD303 2.4 34.2 1.0
O A:HOH410 2.5 38.4 1.0
C2 A:IMD303 2.8 32.9 1.0
CD A:GLU32 2.8 25.4 1.0
O A:HOH544 3.3 20.2 1.0
OE1 A:GLU32 3.4 28.1 1.0
O A:HOH458 3.5 40.5 1.0
C4 A:IMD303 3.7 33.4 1.0
CG A:GLU32 3.9 22.3 1.0
N1 A:IMD303 4.1 33.9 1.0
C5 A:IMD303 4.5 34.1 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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