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Zinc in PDB 3s2s: The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159

Enzymatic activity of The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159

All present enzymatic activity of The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159:
3.5.1.19;

Protein crystallography data

The structure of The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159, PDB code: 3s2s was solved by X.-D.Su, X.Liu, H.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.490, 80.120, 130.960, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.1

Other elements in 3s2s:

The structure of The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159 also contains other interesting chemical elements:

Arsenic (As) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159 (pdb code 3s2s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159, PDB code: 3s2s:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3s2s

Go back to Zinc Binding Sites List in 3s2s
Zinc binding site 1 out of 4 in the The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn184

b:25.5
occ:0.80
 OD2 A:ASP53 2.0 28.4 1.0
OE1 A:GLU64 2.1 26.3 1.0
O A:HOH401 2.1 35.8 1.0
NE2 A:HIS55 2.2 25.9 1.0
NE2 A:HIS71 2.2 24.8 1.0
O A:HOH299 2.3 27.3 1.0
CD A:GLU64 3.0 26.4 1.0
CG A:ASP53 3.1 32.5 1.0
CE1 A:HIS71 3.1 27.2 1.0
CD2 A:HIS55 3.1 25.3 1.0
CE1 A:HIS55 3.1 27.9 1.0
OE2 A:GLU64 3.3 27.6 1.0
CD2 A:HIS71 3.3 24.3 1.0
OD1 A:ASP53 3.5 27.2 1.0
ND1 A:HIS71 4.2 25.2 1.0
ND1 A:HIS55 4.2 27.1 1.0
O A:HOH586 4.3 33.6 1.0
CG A:HIS55 4.3 25.0 1.0
CB A:ASP53 4.3 22.7 1.0
CG A:HIS71 4.4 26.9 1.0
CG A:GLU64 4.4 26.4 1.0
CZ A:PHE14 4.7 23.7 1.0
CE1 A:TYR106 4.8 20.8 1.0
O A:ARG104 5.0 17.3 1.0

Zinc binding site 2 out of 4 in 3s2s

Go back to Zinc Binding Sites List in 3s2s
Zinc binding site 2 out of 4 in the The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn184

b:29.1
occ:0.80
 O B:HOH216 2.0 24.8 1.0
OE1 B:GLU64 2.1 27.2 1.0
NE2 B:HIS71 2.2 29.1 1.0
NE2 B:HIS55 2.3 30.8 1.0
OD2 B:ASP53 2.3 30.7 1.0
OD1 B:ASP53 2.8 28.5 1.0
CG B:ASP53 2.8 27.5 1.0
CD B:GLU64 3.0 33.1 1.0
CE1 B:HIS71 3.1 27.2 1.0
CE1 B:HIS55 3.2 34.5 1.0
CD2 B:HIS71 3.2 25.4 1.0
CD2 B:HIS55 3.2 30.9 1.0
OE2 B:GLU64 3.2 34.4 1.0
O B:HOH307 4.1 33.8 1.0
O B:HOH306 4.1 29.8 1.0
ND1 B:HIS71 4.2 29.8 1.0
CB B:ASP53 4.3 23.0 1.0
CG B:HIS71 4.3 28.5 1.0
ND1 B:HIS55 4.3 34.3 1.0
CG B:HIS55 4.4 34.0 1.0
CG B:GLU64 4.4 25.9 1.0
O B:HOH224 4.5 28.3 1.0
CZ B:PHE14 4.6 30.2 1.0
CB B:GLU64 4.8 30.2 1.0

Zinc binding site 3 out of 4 in 3s2s

Go back to Zinc Binding Sites List in 3s2s
Zinc binding site 3 out of 4 in the The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn184

b:25.1
occ:0.60
 O C:HOH207 1.8 26.4 1.0
OE1 C:GLU64 2.2 26.2 1.0
NE2 C:HIS55 2.2 39.7 1.0
NE2 C:HIS71 2.2 31.2 1.0
OD2 C:ASP53 2.3 30.9 1.0
OD1 C:ASP53 2.8 31.0 1.0
CG C:ASP53 2.8 28.8 1.0
CE1 C:HIS55 3.0 46.4 1.0
CD C:GLU64 3.1 30.4 1.0
CE1 C:HIS71 3.1 27.2 1.0
CD2 C:HIS71 3.3 27.8 1.0
CD2 C:HIS55 3.3 32.8 1.0
OE2 C:GLU64 3.3 32.5 1.0
O C:HOH430 3.9 30.6 1.0
O C:HOH548 4.1 43.4 1.0
ND1 C:HIS71 4.2 30.5 1.0
ND1 C:HIS55 4.2 42.2 1.0
CB C:ASP53 4.3 20.7 1.0
CG C:HIS71 4.3 29.1 1.0
CG C:HIS55 4.4 31.4 1.0
O C:HOH225 4.4 30.8 1.0
CG C:GLU64 4.5 27.3 1.0
CZ C:PHE14 4.6 27.6 1.0
CB C:GLU64 4.9 35.5 1.0

Zinc binding site 4 out of 4 in 3s2s

Go back to Zinc Binding Sites List in 3s2s
Zinc binding site 4 out of 4 in the The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Pyrazinamidase/Nicotinamidase From Streptococcus Mutans UA159 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn184

b:28.1
occ:0.80
 O D:HOH204 1.9 24.4 1.0
OE1 D:GLU64 2.2 25.6 1.0
NE2 D:HIS71 2.2 29.7 1.0
NE2 D:HIS55 2.3 32.8 1.0
OD2 D:ASP53 2.3 32.6 1.0
OD1 D:ASP53 2.8 28.1 1.0
CG D:ASP53 2.8 27.3 1.0
CE1 D:HIS71 3.0 28.2 1.0
CD D:GLU64 3.1 27.5 1.0
CD2 D:HIS55 3.2 33.7 1.0
CD2 D:HIS71 3.2 28.5 1.0
CE1 D:HIS55 3.2 37.9 1.0
OE2 D:GLU64 3.3 31.1 1.0
ND1 D:HIS71 4.1 30.2 1.0
O D:HOH260 4.2 32.4 1.0
O D:HOH315 4.2 29.6 1.0
CB D:ASP53 4.3 21.2 1.0
CG D:HIS71 4.3 30.1 1.0
ND1 D:HIS55 4.4 36.3 1.0
CG D:HIS55 4.4 32.8 1.0
CZ D:PHE14 4.5 30.3 1.0
CG D:GLU64 4.5 27.3 1.0
O D:HOH218 4.5 27.8 1.0
CB D:GLU64 4.9 32.3 1.0
ND2 D:ASN72 5.0 34.2 1.0

Reference:

X.Liu, H.Zhang, X.J.Wang, L.F.Li, X.-D.Su. Get Phases From Arsenic Anomalous Scattering: De Novo Sad Phasing of Two Protein Structures Crystallized in Cacodylate Buffer Plos One V. 6 24227 2011.
ISSN: ESSN 1932-6203
PubMed: 21912678
DOI: 10.1371/JOURNAL.PONE.0024227
Page generated: Wed Dec 16 04:49:21 2020

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