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Zinc in PDB 5jex: Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Imidazole Buffer

Enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Imidazole Buffer

All present enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Imidazole Buffer:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Imidazole Buffer, PDB code: 5jex 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) 44.37 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.320, 65.550, 88.710, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 20.8

Zinc Binding Sites:

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

Zinc binding site 1 out of 9 in 5jex

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Zinc binding site 1 out of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Imidazole Buffer


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, Crystallized in Imidazole Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:7.2
occ:1.00
 OD3 A:OCS131 1.8 12.9 1.0
O A:HOH421 2.0 4.3 1.0
NE2 A:HIS178 2.0 3.7 1.0
NE2 A:HIS174 2.1 4.3 1.0
CD2 A:HIS174 2.9 2.0 1.0
CD2 A:HIS178 3.0 2.8 1.0
CE1 A:HIS178 3.1 3.4 1.0
SG A:OCS131 3.1 9.7 1.0
CE1 A:HIS174 3.2 3.9 1.0
O A:HOH445 3.3 22.0 1.0
O A:HOH562 3.5 12.0 1.0
OD1 A:OCS131 3.6 12.7 1.0
NE2 A:GLN77 3.7 2.5 1.0
O A:HOH515 3.7 5.3 1.0
OE1 A:GLU175 3.9 9.0 1.0
OE1 A:GLN77 3.9 4.1 1.0
OD2 A:OCS131 3.9 10.8 1.0
CD A:GLN77 4.0 4.2 1.0
CG A:HIS174 4.1 3.2 1.0
CG A:HIS178 4.1 3.2 1.0
ND1 A:HIS178 4.2 3.0 1.0
OE2 A:GLU175 4.2 11.0 1.0
ND1 A:HIS174 4.2 3.0 1.0
CB A:OCS131 4.3 9.2 1.0
CD A:GLU175 4.4 6.5 1.0
O A:HOH502 4.6 3.4 1.0
O A:HOH444 4.6 18.5 1.0
CA A:OCS131 4.7 8.6 1.0
O A:GLY130 4.7 11.1 1.0

Zinc binding site 2 out of 9 in 5jex

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Zinc binding site 2 out of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Imidazole Buffer


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, Crystallized in Imidazole Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:12.2
occ:1.00
 NE2 A:HIS55 2.2 6.8 1.0
O A:HOH590 2.2 11.2 1.0
CD2 A:HIS55 3.1 6.4 1.0
CE1 A:HIS55 3.2 5.9 1.0
NE2 A:GLN51 4.2 10.6 1.0
CG A:HIS55 4.2 5.1 1.0
ND1 A:HIS55 4.3 5.5 1.0
CG A:MET61 4.6 15.7 1.0
CG A:GLN51 4.7 7.2 1.0
O A:HOH687 4.7 31.0 1.0
CD A:GLN51 4.9 9.2 1.0
CE A:MET61 4.9 16.0 1.0

Zinc binding site 3 out of 9 in 5jex

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Zinc binding site 3 out of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Imidazole Buffer


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, Crystallized in Imidazole Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:16.8
occ:1.00
 O A:HOH554 2.0 14.4 1.0
O A:HOH594 2.0 8.5 1.0
NE2 A:HIS118 2.0 8.3 1.0
O A:HOH650 2.7 34.6 1.0
CD2 A:HIS118 3.0 4.4 1.0
CE1 A:HIS118 3.1 8.7 1.0
CG A:HIS118 4.1 4.6 1.0
ND1 A:HIS118 4.1 6.8 1.0
O A:HOH592 4.4 12.0 1.0
O A:HOH701 4.7 25.7 1.0
CE1 A:HIS145 4.9 2.6 1.0

Zinc binding site 4 out of 9 in 5jex

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Zinc binding site 4 out of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Imidazole Buffer


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, Crystallized in Imidazole Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:9.2
occ:1.00
 OE2 A:GLU190 1.9 13.2 1.0
O A:HOH438 2.1 2.2 1.0
O A:HOH428 2.3 7.1 1.0
CD A:GLU190 2.6 14.1 1.0
OE1 A:GLU190 2.7 14.0 1.0
O A:HOH431 3.8 24.4 1.0
CG A:GLU190 4.1 14.8 1.0
O A:TYR185 4.1 5.9 1.0
O A:HOH442 4.2 4.1 1.0
O A:ILE188 4.4 5.8 1.0
CA A:GLU190 4.6 13.9 1.0
CB A:GLU190 4.6 13.7 1.0

Zinc binding site 5 out of 9 in 5jex

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Zinc binding site 5 out of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Imidazole Buffer


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, Crystallized in Imidazole Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:8.2
occ:1.00
 NE2 A:HIS145 2.1 3.0 1.0
O A:HOH622 2.8 5.0 1.0
CD2 A:HIS145 3.0 0.6 1.0
CE1 A:HIS145 3.1 2.6 1.0
O A:HOH643 3.9 9.3 1.0
O A:HOH656 4.0 17.6 1.0
O A:HOH594 4.1 8.5 1.0
O A:HOH705 4.2 17.7 1.0
ND1 A:HIS145 4.2 1.8 1.0
CG A:HIS145 4.2 2.6 1.0
CD2 A:HIS118 4.6 4.4 1.0
O A:HOH679 4.7 25.1 1.0
NE2 A:HIS118 4.8 8.3 1.0
CG1 A:VAL115 5.0 3.6 1.0

Zinc binding site 6 out of 9 in 5jex

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Zinc binding site 6 out of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Imidazole Buffer


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, Crystallized in Imidazole Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:43.5
occ:1.00
 O A:HOH463 2.2 13.0 1.0
NE2 A:HIS12 2.2 14.5 1.0
OD1 A:ASP18 2.4 9.7 1.0
OD2 A:ASP18 2.5 10.8 1.0
O A:HOH539 2.7 32.7 1.0
CG A:ASP18 2.8 10.1 1.0
CE1 A:HIS12 2.8 12.3 1.0
O A:HOH443 3.1 35.2 1.0
O A:HOH695 3.2 12.8 1.0
CD2 A:HIS12 3.4 14.1 1.0
O A:LEU13 3.7 8.1 1.0
OD1 A:ASP15 3.8 11.1 1.0
ND1 A:HIS12 4.0 14.1 1.0
CG A:ASP15 4.2 11.8 1.0
OD2 A:ASP15 4.2 13.9 1.0
CB A:ASP18 4.3 10.3 1.0
CG A:HIS12 4.3 12.9 1.0
O A:HOH681 4.4 31.8 1.0
N A:ASP15 4.5 9.2 1.0
O A:HOH418 4.6 14.9 1.0
C A:LEU13 4.8 8.7 1.0
N A:ASP18 4.8 10.1 1.0
CA A:ILE14 4.8 8.4 1.0
CA A:ASP18 5.0 10.0 1.0

Zinc binding site 7 out of 9 in 5jex

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Zinc binding site 7 out of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Imidazole Buffer


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, Crystallized in Imidazole Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:33.7
occ:1.00
 OE2 A:GLU43 2.1 26.3 1.0
OE2 A:GLU47 2.1 15.6 1.0
O A:HOH601 2.2 41.6 1.0
O A:HOH525 2.3 34.7 1.0
CD A:GLU47 2.9 13.9 1.0
OE1 A:GLU47 3.0 13.6 1.0
CD A:GLU43 3.1 22.9 1.0
NZ A:LYS155 3.7 21.3 1.0
CG A:GLU43 3.7 14.2 1.0
OE1 A:GLU43 4.1 25.1 1.0
O A:HOH651 4.1 44.3 1.0
CE A:LYS155 4.3 17.1 1.0
CG A:GLU47 4.3 7.3 1.0
O A:HOH577 4.7 42.5 1.0

Zinc binding site 8 out of 9 in 5jex

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Zinc binding site 8 out of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Imidazole Buffer


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, Crystallized in Imidazole Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:23.5
occ:1.00
 OE2 A:GLU151 2.0 8.2 1.0
O A:HOH644 2.6 21.3 1.0
CD A:GLU151 2.8 9.2 1.0
OE1 A:GLU151 2.9 10.2 1.0
O A:HOH574 3.0 22.5 1.0
NZ A:LYS159 3.9 12.2 1.0
NE A:ARG161 4.0 9.7 1.0
NH1 A:ARG161 4.0 12.9 1.0
CG A:GLU151 4.2 6.0 1.0
CZ A:ARG161 4.4 12.5 1.0
CE A:LYS159 4.6 10.9 1.0
CG1 A:VAL116 4.6 7.2 1.0
CD A:ARG161 5.0 9.7 1.0

Zinc binding site 9 out of 9 in 5jex

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Zinc binding site 9 out of 9 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae, Crystallized in Imidazole Buffer


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, Crystallized in Imidazole Buffer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn310

b:44.8
occ:1.00
 OE2 A:GLU32 1.7 25.6 1.0
O A:HOH420 2.3 20.0 1.0
N3 A:IMD301 2.3 16.2 1.0
O A:HOH670 2.7 30.1 1.0
CD A:GLU32 2.8 17.0 1.0
C2 A:IMD301 2.9 14.2 1.0
O A:HOH475 3.3 24.8 1.0
O A:HOH542 3.4 6.3 1.0
OE1 A:GLU32 3.4 15.7 1.0
C4 A:IMD301 3.6 15.8 1.0
CG A:GLU32 4.0 13.0 1.0
N1 A:IMD301 4.1 14.9 1.0
C5 A:IMD301 4.4 15.4 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 18:46:54 2024

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