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Zinc in PDB 5jf6: Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)

Enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)

All present enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47):
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47), PDB code: 5jf6 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) 44.15 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.920, 66.280, 88.290, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17.5

Other elements in 5jf6:

The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47) 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 6B (AB47) (pdb code 5jf6). 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 6B (AB47), PDB code: 5jf6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5jf6

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Zinc binding site 1 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)


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 6B (AB47) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:9.3
occ:1.00
 OD3 A:OCS131 2.0 13.4 1.0
O14 A:BB4301 2.0 11.8 1.0
NE2 A:HIS174 2.1 9.0 1.0
NE2 A:HIS178 2.1 8.4 1.0
O2 A:BB4301 2.2 16.1 1.0
C13 A:BB4301 2.6 18.2 1.0
N1 A:BB4301 2.7 15.8 1.0
CD2 A:HIS174 3.0 8.0 1.0
CD2 A:HIS178 3.0 8.9 1.0
CE1 A:HIS178 3.1 8.8 1.0
CE1 A:HIS174 3.1 8.4 1.0
SG A:OCS131 3.2 11.3 1.0
OD2 A:OCS131 3.4 11.4 1.0
NE2 A:GLN77 3.4 10.1 1.0
O A:HOH564 3.9 10.5 1.0
CD A:GLN77 4.0 10.0 1.0
C12 A:BB4301 4.1 15.4 1.0
OD1 A:OCS131 4.1 14.4 1.0
OE1 A:GLN77 4.1 10.1 1.0
CG A:HIS174 4.2 7.0 1.0
CG A:HIS178 4.2 7.8 1.0
ND1 A:HIS178 4.2 8.7 1.0
ND1 A:HIS174 4.2 8.1 1.0
CB A:OCS131 4.2 11.8 1.0
OE1 A:GLU175 4.3 11.5 1.0
CA A:OCS131 4.4 12.3 1.0
O A:HOH594 4.5 9.6 1.0
OE2 A:GLU175 4.6 11.6 1.0
O A:GLY130 4.6 14.2 1.0
C5 A:BB4301 4.7 18.1 1.0
CD A:GLU175 4.7 9.5 1.0
N A:LEU132 4.9 11.1 1.0

Zinc binding site 2 out of 8 in 5jf6

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Zinc binding site 2 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)


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 6B (AB47) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:15.1
occ:1.00
 NE2 A:HIS55 2.1 11.8 1.0
CD2 A:HIS55 3.0 11.5 1.0
CE1 A:HIS55 3.1 11.1 1.0
O A:HOH730 3.1 26.6 1.0
NE2 A:GLN51 4.0 13.8 1.0
O A:HOH643 4.1 30.9 1.0
ND1 A:HIS55 4.2 10.3 1.0
CG A:HIS55 4.2 10.3 1.0
CG A:GLN51 4.7 11.4 1.0
CG A:MET61 4.7 18.8 1.0
CD A:GLN51 4.8 12.6 1.0
CE A:MET61 4.9 20.4 1.0

Zinc binding site 3 out of 8 in 5jf6

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Zinc binding site 3 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)


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 6B (AB47) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:14.8
occ:1.00
 NE2 A:HIS118 2.1 11.0 1.0
O A:HOH632 2.1 18.1 1.0
O A:HOH667 2.1 16.6 1.0
O A:HOH648 2.2 20.4 1.0
CE1 A:HIS118 3.0 11.3 1.0
CD2 A:HIS118 3.0 10.0 1.0
ND1 A:HIS118 4.1 10.0 1.0
CG A:HIS118 4.2 8.7 1.0
O A:HOH647 4.3 12.8 1.0
O A:HOH727 4.4 33.9 1.0
O A:HOH749 4.4 26.1 1.0
O A:HOH624 4.4 19.6 1.0
CE1 A:HIS145 4.9 9.0 1.0

Zinc binding site 4 out of 8 in 5jf6

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Zinc binding site 4 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)


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 6B (AB47) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:11.9
occ:1.00
 OE2 A:GLU190 1.9 18.2 1.0
O A:HOH439 2.0 10.1 1.0
O A:HOH527 2.1 11.0 1.0
CD A:GLU190 2.6 20.7 1.0
OE1 A:GLU190 2.7 19.2 1.0
O A:HOH438 3.9 26.7 1.0
CG A:GLU190 4.1 19.2 1.0
O A:HOH458 4.1 9.0 1.0
O A:TYR185 4.2 8.3 1.0
O A:ILE188 4.5 10.1 1.0
CA A:GLU190 4.5 17.7 1.0
CB A:GLU190 4.6 17.9 1.0
O A:HOH652 4.6 40.5 1.0

Zinc binding site 5 out of 8 in 5jf6

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Zinc binding site 5 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)


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 6B (AB47) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:10.7
occ:1.00
 O A:ACT302 2.0 10.5 1.0
NE2 A:HIS145 2.0 7.8 1.0
O A:HOH647 2.1 12.8 1.0
C A:ACT302 2.7 10.5 1.0
OXT A:ACT302 2.9 11.2 1.0
CD2 A:HIS145 3.0 7.5 1.0
CE1 A:HIS145 3.0 9.0 1.0
O A:HOH574 3.7 18.4 1.0
ND1 A:HIS145 4.1 7.8 1.0
CG A:HIS145 4.1 8.0 1.0
O A:HOH632 4.2 18.1 1.0
CH3 A:ACT302 4.2 10.6 1.0
O A:HOH450 4.3 21.5 1.0
CD2 A:HIS118 4.6 10.0 1.0
O A:HOH702 4.6 18.9 1.0
NE2 A:HIS118 4.8 11.0 1.0
CG1 A:VAL115 5.0 7.2 1.0

Zinc binding site 6 out of 8 in 5jf6

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Zinc binding site 6 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)


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 6B (AB47) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:33.9
occ:1.00
 O A:HOH412 2.1 20.7 1.0
NE2 A:HIS12 2.1 18.2 1.0
O A:HOH493 2.1 10.7 1.0
OD1 A:ASP18 2.2 11.5 1.0
OD2 A:ASP18 2.3 13.4 1.0
CG A:ASP18 2.5 12.6 1.0
CE1 A:HIS12 2.9 19.7 1.0
CD2 A:HIS12 3.2 19.1 1.0
O A:HOH743 3.3 13.2 1.0
O A:HOH707 3.8 26.8 1.0
OD1 A:ASP15 3.8 13.1 1.0
O A:LEU13 3.9 11.7 1.0
ND1 A:HIS12 4.0 18.2 1.0
CB A:ASP18 4.1 11.5 1.0
O A:HOH722 4.2 32.8 1.0
CG A:HIS12 4.2 16.5 1.0
O A:HOH481 4.3 28.3 1.0
CG A:ASP15 4.4 14.2 1.0
OD2 A:ASP15 4.4 16.0 1.0
N A:ASP15 4.5 11.3 1.0
N A:ASP18 4.6 11.3 1.0
CA A:ASP18 4.7 11.6 1.0
O A:HOH540 4.8 30.1 1.0
CA A:ILE14 4.8 12.0 1.0
O A:HOH418 4.8 22.1 1.0
O A:HOH681 4.9 13.7 1.0
C A:LEU13 4.9 11.9 1.0

Zinc binding site 7 out of 8 in 5jf6

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Zinc binding site 7 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)


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 6B (AB47) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:26.3
occ:1.00
 O A:HOH578 2.1 30.0 1.0
OE2 A:GLU47 2.1 17.2 1.0
O A:HOH441 2.1 30.3 1.0
OE2 A:GLU43 2.2 27.1 1.0
O A:HOH606 2.2 32.4 1.0
CD A:GLU47 2.9 17.3 1.0
CD A:GLU43 3.1 24.6 1.0
OE1 A:GLU47 3.2 19.6 1.0
CG A:GLU43 3.7 18.1 1.0
NZ A:LYS155 4.0 24.8 1.0
OE1 A:GLU43 4.0 26.2 1.0
O A:HOH435 4.1 35.6 1.0
CG A:GLU47 4.3 13.2 1.0
O A:HOH669 4.3 38.2 1.0
CE A:LYS155 4.3 23.2 1.0
O A:HOH402 4.9 28.5 1.0

Zinc binding site 8 out of 8 in 5jf6

Go back to Zinc Binding Sites List in 5jf6
Zinc binding site 8 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor 6B (AB47)


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 6B (AB47) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn310

b:16.4
occ:1.00
 OE2 A:GLU151 2.1 13.4 1.0
CD A:GLU151 2.8 12.3 1.0
O A:HOH586 2.9 16.6 1.0
OE1 A:GLU151 2.9 13.9 1.0
O A:HOH423 3.8 42.0 1.0
NH2 A:ARG161 3.9 13.7 1.0
NE A:ARG161 4.0 13.2 1.0
NZ A:LYS159 4.1 18.6 1.0
CG A:GLU151 4.2 11.1 1.0
CZ A:ARG161 4.3 14.1 1.0
O A:HOH723 4.5 42.5 1.0
CE A:LYS159 4.7 15.6 1.0
CG1 A:VAL116 4.7 10.2 1.0
CD A:ARG161 4.9 12.1 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: Thu Aug 21 03:48:54 2025

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