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Zinc in PDB 5jf8: Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor RAS358 (21)

Enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor RAS358 (21)

All present enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor RAS358 (21):
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor RAS358 (21), PDB code: 5jf8 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) 44.32 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.470, 65.760, 88.640, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Inhibitor RAS358 (21) (pdb code 5jf8). 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 RAS358 (21), PDB code: 5jf8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5jf8

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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 RAS358 (21)


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 RAS358 (21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:15.5
occ:1.00
 OD3 A:OCS131 2.0 20.0 1.0
NE2 A:HIS178 2.1 14.4 1.0
NE2 A:HIS174 2.1 11.8 1.0
O2 A:PN3301 2.1 18.6 1.0
O4 A:PN3301 2.3 32.3 1.0
C1 A:PN3301 2.7 27.7 1.0
N3 A:PN3301 2.8 32.8 1.0
CD2 A:HIS178 3.0 12.8 1.0
CD2 A:HIS174 3.0 10.0 1.0
CE1 A:HIS178 3.2 13.1 1.0
SG A:OCS131 3.2 17.9 1.0
CE1 A:HIS174 3.2 11.3 1.0
NE2 A:GLN77 3.4 15.5 1.0
OD2 A:OCS131 3.5 15.8 1.0
O A:HOH532 3.8 19.1 1.0
OD1 A:OCS131 3.9 20.9 1.0
CD A:GLN77 3.9 15.1 1.0
OE1 A:GLN77 4.0 13.7 1.0
C5 A:PN3301 4.1 30.6 1.0
CG A:HIS178 4.2 12.9 1.0
CG A:HIS174 4.2 9.7 1.0
ND1 A:HIS178 4.2 11.9 1.0
ND1 A:HIS174 4.3 12.5 1.0
N14 A:PN3301 4.3 30.6 1.0
OE2 A:GLU175 4.4 22.1 1.0
C6 A:PN3301 4.4 32.3 1.0
CB A:OCS131 4.5 17.3 1.0
CA A:OCS131 4.5 16.6 1.0
OE1 A:GLU175 4.5 18.0 1.0
O A:GLY130 4.6 18.9 1.0
O A:HOH498 4.6 13.5 1.0
CD A:GLU175 4.8 18.4 1.0

Zinc binding site 2 out of 9 in 5jf8

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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 RAS358 (21)


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 RAS358 (21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:31.4
occ:1.00
 O A:HOH515 2.0 29.1 1.0
NE2 A:HIS55 2.1 20.7 1.0
CD2 A:HIS55 2.9 17.8 1.0
CE1 A:HIS55 3.2 18.7 1.0
O A:HOH642 3.6 36.9 1.0
NE2 A:GLN51 3.9 24.6 1.0
CG A:HIS55 4.2 17.4 1.0
ND1 A:HIS55 4.2 17.5 1.0
CG A:GLN51 4.5 16.3 1.0
CD A:GLN51 4.6 21.0 1.0

Zinc binding site 3 out of 9 in 5jf8

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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 RAS358 (21)


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 RAS358 (21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:29.9
occ:1.00
 NE2 A:HIS118 2.0 18.4 1.0
O A:HOH545 2.1 30.8 1.0
O A:HOH596 2.5 35.1 1.0
O A:HOH591 2.6 42.0 1.0
O A:HOH615 2.6 37.6 1.0
CE1 A:HIS118 3.0 15.7 1.0
CD2 A:HIS118 3.0 16.3 1.0
ND1 A:HIS118 4.1 13.8 1.0
CG A:HIS118 4.2 11.3 1.0
O A:HOH585 4.3 16.5 1.0
O A:HOH582 4.4 21.6 1.0
O A:HOH637 4.9 35.1 1.0
CE1 A:HIS145 5.0 14.0 1.0

Zinc binding site 4 out of 9 in 5jf8

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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 RAS358 (21)


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 RAS358 (21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:20.8
occ:1.00
 O A:HOH433 2.1 15.6 1.0
OE2 A:GLU190 2.2 30.5 1.0
O A:HOH463 2.2 15.2 1.0
OE1 A:GLU190 2.5 27.9 1.0
CD A:GLU190 2.7 29.3 1.0
O A:HOH467 3.8 36.3 1.0
O A:TYR185 4.1 14.1 1.0
CG A:GLU190 4.2 26.8 1.0
O A:ILE188 4.5 15.3 1.0
CA A:GLU190 4.8 25.0 1.0
CB A:GLU190 4.8 25.1 1.0

Zinc binding site 5 out of 9 in 5jf8

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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 RAS358 (21)


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 RAS358 (21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:15.7
occ:1.00
 NE2 A:HIS145 2.0 15.1 1.0
O A:ACT302 2.0 16.9 1.0
O A:HOH585 2.3 16.5 1.0
C A:ACT302 2.9 18.1 1.0
OXT A:ACT302 2.9 18.0 1.0
CD2 A:HIS145 3.0 10.8 1.0
CE1 A:HIS145 3.0 14.0 1.0
O A:HOH565 3.8 27.7 1.0
O A:HOH545 4.1 30.8 1.0
ND1 A:HIS145 4.1 15.3 1.0
CG A:HIS145 4.1 12.4 1.0
CH3 A:ACT302 4.3 18.5 1.0
O A:HOH492 4.3 23.2 1.0
CD2 A:HIS118 4.6 16.3 1.0
NE2 A:HIS118 4.8 18.4 1.0
O A:HOH621 4.8 34.7 1.0
NH2 A:ARG187 5.0 22.6 1.0

Zinc binding site 6 out of 9 in 5jf8

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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 RAS358 (21)


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 RAS358 (21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:52.1
occ:1.00
 NE2 A:HIS12 2.2 27.1 1.0
OD1 A:ASP18 2.4 18.7 1.0
OD2 A:ASP18 2.5 22.1 1.0
CG A:ASP18 2.7 20.0 1.0
CE1 A:HIS12 3.1 25.6 1.0
O A:HOH633 3.1 20.3 1.0
CD2 A:HIS12 3.3 24.9 1.0
OD1 A:ASP15 3.7 22.2 1.0
O A:LEU13 3.9 20.2 1.0
CB A:ASP18 4.2 18.9 1.0
CG A:ASP15 4.2 23.3 1.0
ND1 A:HIS12 4.3 27.9 1.0
O A:HOH638 4.3 29.3 1.0
OD2 A:ASP15 4.3 26.3 1.0
CG A:HIS12 4.4 25.6 1.0
N A:ASP15 4.6 19.8 1.0
O A:HOH408 4.6 24.3 1.0
N A:ASP18 4.7 20.1 1.0
CA A:ASP18 4.8 19.4 1.0
C A:LEU13 4.9 21.3 1.0
CA A:ILE14 4.9 19.1 1.0

Zinc binding site 7 out of 9 in 5jf8

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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 RAS358 (21)


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 RAS358 (21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn310

b:52.9
occ:1.00
 OE2 A:GLU47 2.2 30.2 1.0
O A:HOH559 2.4 37.4 1.0
OE2 A:GLU43 2.6 39.5 1.0
CD A:GLU47 3.0 25.0 1.0
OE1 A:GLU47 3.1 28.0 1.0
O A:HOH581 3.2 43.9 1.0
CD A:GLU43 3.2 34.9 1.0
CG A:GLU43 3.8 25.1 1.0
NZ A:LYS155 3.9 29.5 1.0
OE1 A:GLU43 4.0 38.0 1.0
O A:HOH442 4.3 36.3 1.0
CG A:GLU47 4.5 19.4 1.0
CE A:LYS155 4.5 26.7 1.0

Zinc binding site 8 out of 9 in 5jf8

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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 RAS358 (21)


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 RAS358 (21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn311

b:50.3
occ:1.00
 OE2 A:GLU151 2.2 23.8 1.0
O A:HOH609 2.4 26.0 1.0
CD A:GLU151 2.8 21.1 1.0
OE1 A:GLU151 2.8 20.9 1.0
O A:HOH524 3.0 29.9 1.0
O A:HOH530 3.6 36.3 1.0
NZ A:LYS159 3.6 28.0 1.0
NH2 A:ARG161 4.2 29.4 1.0
NE A:ARG161 4.2 27.0 1.0
CG A:GLU151 4.2 17.1 1.0
CG1 A:VAL116 4.5 13.2 1.0
CE A:LYS159 4.5 24.4 1.0
CZ A:ARG161 4.6 28.6 1.0
O A:HOH409 4.8 34.0 1.0

Zinc binding site 9 out of 9 in 5jf8

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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 RAS358 (21)


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 RAS358 (21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn312

b:92.5
occ:1.00
 OE1 A:GLU32 2.0 35.1 1.0
N3 A:IMD303 2.5 32.1 1.0
O A:HOH589 2.5 45.0 1.0
C2 A:IMD303 2.7 32.2 1.0
CD A:GLU32 3.0 27.7 1.0
OE2 A:GLU32 3.5 28.6 1.0
C4 A:IMD303 3.8 32.3 1.0
N1 A:IMD303 4.1 32.2 1.0
O A:HOH508 4.1 18.9 1.0
CG A:GLU32 4.2 22.3 1.0
O A:HOH636 4.2 40.6 1.0
C5 A:IMD303 4.6 33.7 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 03:50:28 2025

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