Zinc in PDB 3kl9: Crystal Structure of Pepa From Streptococcus Pneumoniae

All present enzymatic activity of Crystal Structure of Pepa From Streptococcus Pneumoniae:
3.4.11.7;

The structure of Crystal Structure of Pepa From Streptococcus Pneumoniae, PDB code: 3kl9 was solved by K.K.Kim, S.Lee, D.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.43 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	138.296, 118.344, 160.299, 90.00, 106.35, 90.00
R / Rfree (%)	20 / 24.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Pepa From Streptococcus Pneumoniae (pdb code 3kl9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Crystal Structure of Pepa From Streptococcus Pneumoniae, PDB code: 3kl9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in the Crystal Structure of Pepa From Streptococcus Pneumoniae


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 Pepa From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn355 b:63.4 occ:1.00 OD2 A:ASP236 2.2 27.1 1.0 OD1 A:ASP181 2.3 30.7 1.0 CE1 A:HIS66 2.5 21.1 1.0 OD1 A:ASP236 2.8 28.9 1.0 CG A:ASP236 2.9 27.6 1.0 CG A:ASP181 3.1 29.2 1.0 ZN A:ZN356 3.3 64.5 1.0 NE2 A:HIS66 3.3 20.4 1.0 OD2 A:ASP181 3.6 30.5 1.0 ND1 A:HIS66 3.6 21.3 1.0 OE1 A:GLU213 3.6 27.8 1.0 OE1 A:GLU214 3.8 27.4 1.0 OE2 A:GLU213 3.9 27.7 1.0 CD A:GLU213 4.0 27.0 1.0 CB A:ASN182 4.0 27.5 1.0 O A:CYS237 4.2 26.9 1.0 CB A:ASP181 4.3 27.5 1.0 CB A:ASP236 4.3 26.9 1.0 CG A:ASN182 4.4 28.6 1.0 CD2 A:HIS66 4.6 20.6 1.0 CD A:GLU214 4.6 26.8 1.0 OD1 A:ASN182 4.7 29.0 1.0 N A:CYS237 4.7 26.9 1.0 CA A:ASP181 4.7 27.3 1.0 CG A:HIS66 4.7 21.1 1.0 OE2 A:GLU214 4.9 27.6 1.0 C A:ASP181 4.9 27.3 1.0 CA A:ASN182 5.0 27.3 1.0

Zinc binding site 2 out of 24 in the Crystal Structure of Pepa From Streptococcus Pneumoniae


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 Pepa From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn356 b:64.5 occ:1.00 OD2 A:ASP181 2.2 30.5 1.0 OE1 A:GLU214 2.3 27.4 1.0 NE2 A:HIS318 2.4 26.1 1.0 OE2 A:GLU214 2.4 27.6 1.0 CD A:GLU214 2.7 26.8 1.0 CG A:ASP181 3.0 29.2 1.0 OD1 A:ASP181 3.1 30.7 1.0 ZN A:ZN355 3.3 63.4 1.0 CD2 A:HIS318 3.3 25.3 1.0 CE1 A:HIS318 3.3 25.9 1.0 OE1 A:GLU213 3.9 27.8 1.0 CG A:GLU214 4.2 25.1 1.0 ND1 A:HIS318 4.4 25.9 1.0 CB A:ASP181 4.5 27.5 1.0 CG A:HIS318 4.5 24.7 1.0 NE2 A:HIS66 4.7 20.4 1.0 CE1 A:HIS66 4.7 21.1 1.0 CD A:GLU213 4.8 27.0 1.0 CG1 A:VAL70 4.9 22.5 1.0 OE2 A:GLU213 4.9 27.7 1.0

Zinc binding site 3 out of 24 in the Crystal Structure of Pepa From Streptococcus Pneumoniae


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 Pepa From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn355 b:77.3 occ:1.00 OD2 B:ASP236 2.3 28.0 1.0 OD1 B:ASP181 2.3 29.0 1.0 OD1 B:ASP236 2.6 30.1 1.0 CE1 B:HIS66 2.7 24.0 1.0 CG B:ASP236 2.7 28.3 1.0 CG B:ASP181 3.1 26.9 1.0 OD2 B:ASP181 3.5 27.9 1.0 NE2 B:HIS66 3.5 24.1 1.0 ZN B:ZN356 3.5 57.9 1.0 OE2 B:GLU213 3.6 28.4 1.0 OE1 B:GLU213 3.7 27.6 1.0 ND1 B:HIS66 3.8 23.8 1.0 CD B:GLU213 3.8 27.7 1.0 O B:CYS237 3.9 26.2 1.0 CB B:ASN182 4.1 25.8 1.0 CB B:ASP236 4.2 27.0 1.0 CB B:ASP181 4.2 26.1 1.0 CG B:ASN182 4.6 25.9 1.0 N B:CYS237 4.7 26.6 1.0 CA B:ASP181 4.7 25.8 1.0 OE1 B:GLU214 4.8 29.4 1.0 CD2 B:HIS66 4.8 23.1 1.0 OE2 B:GLU214 4.9 28.0 1.0 CG B:HIS66 4.9 23.8 1.0 CG B:GLU213 4.9 26.3 1.0 OD1 B:ASN182 4.9 26.9 1.0 CA B:ASP236 5.0 26.8 1.0 C B:ASP181 5.0 25.8 1.0

Zinc binding site 4 out of 24 in the Crystal Structure of Pepa From Streptococcus Pneumoniae


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 Pepa From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn356 b:57.9 occ:1.00 OE2 B:GLU214 2.1 28.0 1.0 NE2 B:HIS318 2.2 25.9 1.0 OD2 B:ASP181 2.3 27.9 1.0 OE1 B:GLU214 2.7 29.4 1.0 CD B:GLU214 2.8 28.1 1.0 CE1 B:HIS318 3.1 25.9 1.0 CG B:ASP181 3.1 26.9 1.0 OD1 B:ASP181 3.2 29.0 1.0 CD2 B:HIS318 3.3 25.0 1.0 ZN B:ZN355 3.5 77.3 1.0 OE1 B:GLU213 3.7 27.6 1.0 O B:HOH371 4.0 22.4 1.0 CG B:GLU214 4.2 26.8 1.0 ND1 B:HIS318 4.3 25.1 1.0 CG B:HIS318 4.4 24.2 1.0 OE2 B:GLU213 4.5 28.4 1.0 CB B:ASP181 4.5 26.1 1.0 CD B:GLU213 4.6 27.7 1.0 CG1 B:VAL70 4.6 22.1 1.0 NE2 B:HIS66 4.7 24.1 1.0 CE1 B:HIS66 4.9 24.0 1.0 CB B:GLU214 4.9 26.3 1.0

Zinc binding site 5 out of 24 in the Crystal Structure of Pepa From Streptococcus Pneumoniae


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 Pepa From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn355 b:65.6 occ:1.00 OD1 C:ASP181 2.3 29.6 1.0 OD2 C:ASP236 2.5 29.6 1.0 CE1 C:HIS66 2.7 21.4 1.0 OD1 C:ASP236 2.7 29.8 1.0 CG C:ASP236 2.9 28.3 1.0 CG C:ASP181 3.2 27.6 1.0 ZN C:ZN356 3.3 66.7 1.0 NE2 C:HIS66 3.3 22.0 1.0 OE1 C:GLU213 3.4 24.0 1.0 OD2 C:ASP181 3.6 28.0 1.0 OE2 C:GLU213 3.7 26.0 1.0 ND1 C:HIS66 3.7 21.1 1.0 CD C:GLU213 3.8 24.6 1.0 OE1 C:GLU214 4.3 27.6 1.0 CB C:ASN182 4.3 26.9 1.0 O C:CYS237 4.3 27.5 1.0 OE2 C:GLU214 4.4 26.0 1.0 CB C:ASP181 4.4 26.7 1.0 CB C:ASP236 4.4 27.0 1.0 CD2 C:HIS66 4.6 21.2 1.0 CD C:GLU214 4.6 26.5 1.0 CG C:HIS66 4.8 21.9 1.0 CG C:ASN182 4.8 27.1 1.0 CG C:GLU213 4.9 24.8 1.0 CA C:ASP181 5.0 26.6 1.0

Zinc binding site 6 out of 24 in the Crystal Structure of Pepa From Streptococcus Pneumoniae


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 Pepa From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn356 b:66.7 occ:1.00 OE2 C:GLU214 2.2 26.0 1.0 NE2 C:HIS318 2.3 26.3 1.0 OD2 C:ASP181 2.4 28.0 1.0 OE1 C:GLU214 2.6 27.6 1.0 CD C:GLU214 2.7 26.5 1.0 CG C:ASP181 3.2 27.6 1.0 ZN C:ZN355 3.3 65.6 1.0 OD1 C:ASP181 3.3 29.6 1.0 CD2 C:HIS318 3.3 26.2 1.0 CE1 C:HIS318 3.3 26.4 1.0 OE1 C:GLU213 4.0 24.0 1.0 CG C:GLU214 4.2 25.6 1.0 ND1 C:HIS318 4.4 26.0 1.0 CG C:HIS318 4.4 25.7 1.0 CB C:ASP181 4.7 26.7 1.0 CG1 C:VAL70 4.7 21.0 1.0 NE2 C:HIS66 4.8 22.0 1.0 CD C:GLU213 4.9 24.6 1.0 CB C:GLU214 5.0 25.0 1.0 OE2 C:GLU213 5.0 26.0 1.0

Zinc binding site 7 out of 24 in the Crystal Structure of Pepa From Streptococcus Pneumoniae


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 Pepa From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn355 b:61.6 occ:1.00 NE2 D:HIS318 2.1 25.7 1.0 OD2 D:ASP181 2.2 29.4 1.0 OE1 D:GLU214 2.5 26.8 1.0 OE2 D:GLU214 2.6 26.1 1.0 CD D:GLU214 2.9 25.4 1.0 CE1 D:HIS318 3.1 26.0 1.0 CD2 D:HIS318 3.1 24.6 1.0 CG D:ASP181 3.2 28.6 1.0 ZN D:ZN356 3.3 73.5 1.0 OD1 D:ASP181 3.5 29.2 1.0 OE1 D:GLU213 4.1 28.8 1.0 ND1 D:HIS318 4.2 25.4 1.0 CG D:HIS318 4.3 24.0 1.0 CG D:GLU214 4.4 25.1 1.0 CB D:ASP181 4.5 27.7 1.0 NE2 D:HIS66 4.8 25.2 1.0 CG1 D:VAL70 4.8 22.3 1.0 CE1 D:HIS66 4.9 25.6 1.0 CD D:GLU213 5.0 27.6 1.0 OE2 D:GLU213 5.0 29.3 1.0

Zinc binding site 8 out of 24 in the Crystal Structure of Pepa From Streptococcus Pneumoniae


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 Pepa From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn356 b:73.5 occ:1.00 OD1 D:ASP181 2.4 29.2 1.0 OD2 D:ASP236 2.6 28.5 1.0 CE1 D:HIS66 2.8 25.6 1.0 OD1 D:ASP236 3.1 29.1 1.0 CG D:ASP236 3.1 28.0 1.0 CG D:ASP181 3.3 28.6 1.0 ZN D:ZN355 3.3 61.6 1.0 OD2 D:ASP181 3.5 29.4 1.0 OE1 D:GLU213 3.6 28.8 1.0 NE2 D:HIS66 3.6 25.2 1.0 ND1 D:HIS66 3.8 25.4 1.0 OE2 D:GLU213 3.8 29.3 1.0 CD D:GLU213 3.8 27.6 1.0 OE1 D:GLU214 4.0 26.8 1.0 O D:CYS237 4.1 27.2 1.0 CB D:ASP236 4.5 27.0 1.0 CB D:ASP181 4.6 27.7 1.0 CB D:ASN182 4.6 27.9 1.0 CD D:GLU214 4.8 25.4 1.0 CD2 D:HIS66 4.8 25.1 1.0 CG D:GLU213 4.9 25.8 1.0 CG D:HIS66 4.9 25.2 1.0 CG D:ASN182 5.0 28.5 1.0

Zinc binding site 9 out of 24 in the Crystal Structure of Pepa From Streptococcus Pneumoniae


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 Pepa From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn355 b:63.2 occ:1.00 OE2 E:GLU214 2.2 27.0 1.0 OD2 E:ASP181 2.3 29.4 1.0 NE2 E:HIS318 2.3 23.3 1.0 OE1 E:GLU214 2.9 29.9 1.0 CD E:GLU214 2.9 28.0 1.0 CG E:ASP181 3.2 27.9 1.0 CE1 E:HIS318 3.2 23.7 1.0 CD2 E:HIS318 3.3 23.4 1.0 OD1 E:ASP181 3.3 30.3 1.0 ZN E:ZN356 3.4 75.4 1.0 OE1 E:GLU213 4.0 29.7 1.0 CG E:GLU214 4.3 26.9 1.0 ND1 E:HIS318 4.4 23.6 1.0 CG E:HIS318 4.4 23.7 1.0 CB E:ASP181 4.5 26.4 1.0 CG1 E:VAL70 4.6 22.5 1.0 OE2 E:GLU213 4.6 30.9 1.0 CD E:GLU213 4.7 29.9 1.0 NE2 E:HIS66 4.8 20.9 1.0 CE1 E:HIS66 4.8 21.2 1.0 CB E:GLU214 5.0 26.5 1.0

Zinc binding site 10 out of 24 in the Crystal Structure of Pepa From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Pepa From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn356 b:75.4 occ:1.00 OD1 E:ASP181 2.2 30.3 1.0 OD2 E:ASP236 2.5 26.1 1.0 OD1 E:ASP236 2.7 27.8 1.0 CE1 E:HIS66 2.7 21.2 1.0 CG E:ASP236 2.9 26.1 1.0 CG E:ASP181 3.2 27.9 1.0 ZN E:ZN355 3.4 63.2 1.0 OE2 E:GLU213 3.4 30.9 1.0 NE2 E:HIS66 3.6 20.9 1.0 OD2 E:ASP181 3.7 29.4 1.0 OE1 E:GLU213 3.7 29.7 1.0 CD E:GLU213 3.7 29.9 1.0 ND1 E:HIS66 3.7 20.0 1.0 O E:CYS237 4.2 25.8 1.0 OE1 E:GLU214 4.4 29.9 1.0 CB E:ASN182 4.4 26.1 1.0 CB E:ASP236 4.4 25.4 1.0 CB E:ASP181 4.5 26.4 1.0 OE2 E:GLU214 4.7 27.0 1.0 CD E:GLU214 4.7 28.0 1.0 CG E:GLU213 4.8 28.1 1.0 CG E:ASN182 4.8 26.8 1.0 CD2 E:HIS66 4.8 20.9 1.0 CG E:HIS66 4.9 21.1 1.0

D.Kim, B.H.San, S.H.Moh, H.J.Park, D.Y.Kim, S.Lee, K.K.Kim. Structural Basis For the Substrate Specificity of Pepa From Streptococcus Pneumoniae, A Dodecameric Tetrahedral Protease Biochem.Biophys.Res.Commun. V. 391 431 2010.
ISSN: ISSN 0006-291X
PubMed: 19914209
DOI: 10.1016/J.BBRC.2009.11.075