Atomistry » Zinc » PDB 5wpb-5x51 » 5wvu
Atomistry »
  Zinc »
    PDB 5wpb-5x51 »
      5wvu »

Zinc in PDB 5wvu: Crystal Structure of Carboxypeptidase From Thermus Thermophilus

Enzymatic activity of Crystal Structure of Carboxypeptidase From Thermus Thermophilus

All present enzymatic activity of Crystal Structure of Carboxypeptidase From Thermus Thermophilus:
3.4.17.19;

Protein crystallography data

The structure of Crystal Structure of Carboxypeptidase From Thermus Thermophilus, PDB code: 5wvu was solved by M.Okai, K.Nagata, M.Tanokura, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.25 / 2.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 170.100, 233.700, 124.400, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Carboxypeptidase From Thermus Thermophilus (pdb code 5wvu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Carboxypeptidase From Thermus Thermophilus, PDB code: 5wvu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5wvu

Go back to Zinc Binding Sites List in 5wvu
Zinc binding site 1 out of 3 in the Crystal Structure of Carboxypeptidase From Thermus Thermophilus


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 Carboxypeptidase From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn804

b:53.1
occ:1.00
NE2 A:HIS280 2.3 31.5 1.0
OE1 A:GLU306 2.4 35.5 1.0
NE2 A:HIS276 2.5 32.6 1.0
CE1 A:HIS280 3.2 28.3 1.0
CD2 A:HIS276 3.3 29.6 1.0
CD A:GLU306 3.3 33.5 1.0
CD2 A:HIS280 3.4 28.0 1.0
CE1 A:HIS276 3.5 35.8 1.0
OE2 A:GLU306 3.5 45.4 1.0
OG A:SER309 3.8 33.5 1.0
CB A:SER309 4.2 28.6 1.0
ND1 A:HIS280 4.4 29.4 1.0
CG A:HIS280 4.5 32.1 1.0
CG A:HIS276 4.5 30.8 1.0
ND1 A:HIS276 4.5 35.1 1.0
CG A:GLU306 4.7 35.6 1.0

Zinc binding site 2 out of 3 in 5wvu

Go back to Zinc Binding Sites List in 5wvu
Zinc binding site 2 out of 3 in the Crystal Structure of Carboxypeptidase From Thermus Thermophilus


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 Carboxypeptidase From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:83.7
occ:1.00
OE1 B:GLU306 2.3 54.7 1.0
NE2 B:HIS280 2.5 49.5 1.0
CE1 B:HIS276 2.6 53.6 1.0
CD B:GLU306 3.2 56.7 1.0
NE2 B:HIS276 3.2 51.5 1.0
CE1 B:HIS280 3.4 45.1 1.0
OE2 B:GLU306 3.4 59.1 1.0
CD2 B:HIS280 3.5 48.1 1.0
ND1 B:HIS276 3.6 53.4 1.0
OG B:SER309 3.9 50.8 1.0
CD2 B:HIS276 4.4 48.5 1.0
CB B:SER309 4.4 45.6 1.0
ND1 B:HIS280 4.5 47.5 1.0
CG B:GLU306 4.6 52.8 1.0
CG B:HIS280 4.6 48.9 1.0
CG B:HIS276 4.6 46.9 1.0
OE2 B:GLU277 4.9 53.4 1.0

Zinc binding site 3 out of 3 in 5wvu

Go back to Zinc Binding Sites List in 5wvu
Zinc binding site 3 out of 3 in the Crystal Structure of Carboxypeptidase From Thermus Thermophilus


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 Carboxypeptidase From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:61.3
occ:1.00
NE2 C:HIS280 2.0 41.6 1.0
NE2 C:HIS276 2.5 54.0 1.0
OE1 C:GLU306 2.6 50.0 1.0
OE2 C:GLU306 2.7 57.4 1.0
CE1 C:HIS280 2.7 41.6 1.0
CD C:GLU306 3.0 49.7 1.0
CD2 C:HIS280 3.1 45.4 1.0
CD2 C:HIS276 3.3 51.0 1.0
CE1 C:HIS276 3.6 50.7 1.0
CE1 C:TYR430 3.6 48.1 1.0
OG C:SER309 3.8 44.6 1.0
ND1 C:HIS280 3.9 42.9 1.0
OH C:TYR430 4.0 44.5 1.0
CG C:HIS280 4.2 44.6 1.0
CB C:SER309 4.3 44.2 1.0
CZ C:TYR430 4.3 48.7 1.0
CG C:HIS276 4.4 54.8 1.0
CG C:GLU306 4.5 41.2 1.0
ND1 C:HIS276 4.5 58.3 1.0
CD1 C:TYR430 4.6 47.9 1.0
OH C:TYR426 4.8 52.7 1.0
OE2 C:GLU277 4.9 39.2 1.0

Reference:

M.Okai, A.Yamamura, K.Hayakawa, S.Tsutsui, K.I.Miyazono, W.C.Lee, K.Nagata, Y.Inoue, M.Tanokura. Insight Into the Transition Between the Open and Closed Conformations of Thermus Thermophilus Carboxypeptidase. Biochem. Biophys. Res. V. 484 787 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 28161633
DOI: 10.1016/J.BBRC.2017.01.167
Page generated: Mon Oct 28 14:38:47 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy