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Zinc in PDB 5jez: Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Ser

Enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Ser

All present enzymatic activity of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Ser:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Ser, PDB code: 5jez 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) 44.41 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.150, 65.550, 88.840, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 18.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Ser (pdb code 5jez). 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 Tripeptide Met-Ala-Ser, PDB code: 5jez:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5jez

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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 Tripeptide Met-Ala-Ser


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 Tripeptide Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:10.3
occ:1.00
 OD3 A:OCS131 1.8 15.7 1.0
O A:HOH447 2.0 11.7 1.0
NE2 A:HIS174 2.1 10.5 1.0
NE2 A:HIS178 2.1 10.6 1.0
O A:HOH620 2.4 4.6 1.0
CD2 A:HIS178 3.0 10.1 1.0
CD2 A:HIS174 3.0 9.6 1.0
CE1 A:HIS174 3.1 10.5 1.0
CE1 A:HIS178 3.2 10.1 1.0
SG A:OCS131 3.2 13.4 1.0
OD2 A:OCS131 3.5 12.5 1.0
NE2 A:GLN77 3.6 10.1 1.0
OE1 A:GLN77 3.9 10.7 1.0
CD A:GLN77 3.9 10.4 1.0
CA D:MET1 4.0 17.0 1.0
OD1 A:OCS131 4.1 16.2 1.0
O A:HOH537 4.1 13.8 1.0
CG A:HIS174 4.1 8.8 1.0
ND1 A:HIS174 4.2 9.7 1.0
CG A:HIS178 4.2 9.6 1.0
ND1 A:HIS178 4.2 10.2 1.0
CB A:OCS131 4.3 13.6 1.0
OE1 A:GLU175 4.3 15.4 1.0
CA A:OCS131 4.5 13.8 1.0
OE2 A:GLU175 4.6 18.5 1.0
O A:HOH533 4.7 10.4 1.0
CD A:GLU175 4.9 13.2 1.0
N A:LEU132 4.9 14.0 1.0
CB D:MET1 4.9 20.9 1.0
O A:GLY130 5.0 14.6 1.0

Zinc binding site 2 out of 8 in 5jez

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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 Tripeptide Met-Ala-Ser


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 Tripeptide Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:16.8
occ:1.00
 NE2 A:HIS55 2.1 14.9 1.0
O A:HOH642 2.1 21.7 1.0
CE1 A:HIS55 3.1 14.3 1.0
CD2 A:HIS55 3.1 14.4 1.0
NE2 A:GLN51 4.1 16.9 1.0
ND1 A:HIS55 4.2 14.2 1.0
O A:HOH662 4.2 37.2 1.0
CG A:HIS55 4.2 13.7 1.0
O A:HOH613 4.3 34.6 1.0
CG A:GLN51 4.7 14.6 1.0
CG A:MET61 4.7 23.3 1.0
CE A:MET61 4.8 24.1 1.0
CD A:GLN51 4.9 15.3 1.0

Zinc binding site 3 out of 8 in 5jez

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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 Tripeptide Met-Ala-Ser


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 Tripeptide Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:20.0
occ:1.00
 O A:HOH622 2.1 24.6 1.0
NE2 A:HIS118 2.1 14.9 1.0
O A:HOH624 2.2 27.7 1.0
O A:HOH654 2.2 27.2 1.0
CD2 A:HIS118 3.0 13.1 1.0
CE1 A:HIS118 3.1 15.2 1.0
O A:HOH682 4.0 33.4 1.0
ND1 A:HIS118 4.1 12.4 1.0
CG A:HIS118 4.2 11.3 1.0
O A:HOH627 4.3 15.9 1.0
O A:HOH619 4.4 21.2 1.0
O A:HOH698 4.4 42.0 1.0
O A:HOH727 4.4 28.3 1.0
CE1 A:HIS145 4.9 12.5 1.0

Zinc binding site 4 out of 8 in 5jez

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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 Tripeptide Met-Ala-Ser


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 Tripeptide Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:13.9
occ:1.00
 OE2 A:GLU190 1.8 21.1 1.0
O A:HOH484 2.0 13.0 1.0
CD A:GLU190 2.6 22.2 1.0
OE1 A:GLU190 2.7 22.6 1.0
O A:HOH413 3.8 27.8 1.0
CG A:GLU190 4.1 22.6 1.0
O A:TYR185 4.2 10.9 1.0
O A:ILE188 4.6 12.5 1.0
CA A:GLU190 4.6 21.1 1.0
CB A:GLU190 4.6 21.4 1.0
O A:HOH659 4.7 42.1 1.0

Zinc binding site 5 out of 8 in 5jez

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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 Tripeptide Met-Ala-Ser


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 Tripeptide Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:13.3
occ:1.00
 O A:ACT301 2.1 13.1 1.0
NE2 A:HIS145 2.1 10.5 1.0
O A:HOH627 2.2 15.9 1.0
C A:ACT301 2.7 14.3 1.0
OXT A:ACT301 2.9 13.1 1.0
CD2 A:HIS145 3.0 10.4 1.0
CE1 A:HIS145 3.0 12.5 1.0
O A:HOH618 3.9 20.9 1.0
O A:HOH622 4.1 24.6 1.0
ND1 A:HIS145 4.1 11.5 1.0
CG A:HIS145 4.1 10.3 1.0
O A:HOH444 4.1 21.0 1.0
CH3 A:ACT301 4.2 12.7 1.0
CD2 A:HIS118 4.6 13.1 1.0
O A:HOH688 4.8 24.7 1.0
NE2 A:HIS118 4.8 14.9 1.0
CG1 A:VAL115 5.0 9.9 1.0

Zinc binding site 6 out of 8 in 5jez

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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 Tripeptide Met-Ala-Ser


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 Tripeptide Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:31.9
occ:1.00
 O A:HOH418 2.1 23.2 1.0
NE2 A:HIS12 2.1 23.1 1.0
O A:HOH436 2.2 17.6 1.0
OD1 A:ASP18 2.2 15.7 1.0
O A:HOH424 2.4 32.1 1.0
OD2 A:ASP18 2.4 17.9 1.0
O A:HOH626 2.5 34.6 1.0
CG A:ASP18 2.6 16.6 1.0
CE1 A:HIS12 2.9 23.1 1.0
O A:HOH714 3.2 16.0 1.0
CD2 A:HIS12 3.3 23.3 1.0
O A:HOH693 3.7 30.7 1.0
OD1 A:ASP15 3.8 16.6 1.0
O A:LEU13 3.9 14.6 1.0
CB A:ASP18 4.1 15.1 1.0
ND1 A:HIS12 4.1 23.5 1.0
CG A:ASP15 4.2 17.0 1.0
OD2 A:ASP15 4.3 18.6 1.0
O A:HOH746 4.3 43.3 1.0
CG A:HIS12 4.3 21.5 1.0
N A:ASP15 4.4 14.1 1.0
O A:HOH439 4.6 27.9 1.0
N A:ASP18 4.7 14.8 1.0
CA A:ASP18 4.8 15.2 1.0
O A:HOH665 4.8 14.7 1.0
CA A:ILE14 4.8 14.2 1.0
C A:LEU13 4.8 15.1 1.0

Zinc binding site 7 out of 8 in 5jez

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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 Tripeptide Met-Ala-Ser


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 Tripeptide Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:34.6
occ:1.00
 O A:HOH525 2.0 30.8 1.0
OE2 A:GLU47 2.2 23.4 1.0
OE1 A:GLU43 2.3 35.8 1.0
CD A:GLU47 3.0 23.1 1.0
CD A:GLU43 3.1 31.0 1.0
OE1 A:GLU47 3.1 25.3 1.0
CG A:GLU43 3.7 24.0 1.0
OE2 A:GLU43 4.0 33.3 1.0
NZ A:LYS155 4.1 32.2 1.0
O A:HOH441 4.2 33.1 1.0
CG A:GLU47 4.4 18.0 1.0
CE A:LYS155 4.4 30.6 1.0

Zinc binding site 8 out of 8 in 5jez

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Zinc binding site 8 out of 8 in the Crystal Structure of Type 2 Pdf From Streptococcus Agalactiae in Complex with Tripeptide Met-Ala-Ser


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 Tripeptide Met-Ala-Ser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:22.9
occ:1.00
 OE2 A:GLU151 2.1 17.0 1.0
O A:HOH641 2.1 24.0 1.0
O A:HOH617 2.7 24.4 1.0
CD A:GLU151 2.8 16.7 1.0
O A:HOH636 2.8 24.9 1.0
OE1 A:GLU151 2.9 19.2 1.0
O A:HOH481 3.9 34.9 1.0
NZ A:LYS159 3.9 21.7 1.0
NH2 A:ARG161 3.9 18.2 1.0
NE A:ARG161 4.0 16.3 1.0
O A:HOH739 4.1 35.1 1.0
CG A:GLU151 4.3 14.3 1.0
CZ A:ARG161 4.3 17.5 1.0
CG1 A:VAL116 4.6 14.1 1.0
CE A:LYS159 4.7 19.0 1.0
CD A:ARG161 4.9 15.9 1.0
O A:HOH606 5.0 30.7 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: Sun Oct 27 18:48:28 2024

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