Zinc in PDB 4ebb: Structure of DPP2

Enzymatic activity of Structure of DPP2

All present enzymatic activity of Structure of DPP2:
3.4.14.2;

Protein crystallography data

The structure of Structure of DPP2, PDB code: 4ebb was solved by L.M.Shewchuk, A.H.Hassell, S.M.Sweitzer, T.D.Sweitzer, P.J.Mcdevitt, K.M.Kennedy-Wilson, K.O.Johanson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.77 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.089, 96.447, 192.137, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of DPP2 (pdb code 4ebb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of DPP2, PDB code: 4ebb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4ebb

Go back to Zinc Binding Sites List in 4ebb
Zinc binding site 1 out of 3 in the Structure of DPP2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of DPP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:41.3
occ:1.00
NE2 A:HIS125 2.1 35.8 1.0
CE1 A:HIS125 3.0 34.5 1.0
CD2 A:HIS125 3.1 33.5 1.0
OE1 A:GLN119 3.7 36.3 1.0
ND1 A:HIS125 4.2 33.6 1.0
CG A:HIS125 4.2 32.5 1.0
O A:ARG123 4.5 33.2 1.0
OE1 A:GLN122 4.5 37.7 1.0
CD A:GLN119 4.6 35.0 1.0
CB A:GLN119 4.9 31.7 1.0

Zinc binding site 2 out of 3 in 4ebb

Go back to Zinc Binding Sites List in 4ebb
Zinc binding site 2 out of 3 in the Structure of DPP2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of DPP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:31.2
occ:1.00
OE1 A:GLU453 2.0 32.8 1.0
ND1 A:HIS451 2.2 28.8 1.0
CD A:GLU453 2.8 33.8 1.0
OE2 A:GLU453 3.0 35.6 1.0
CE1 A:HIS451 3.1 28.9 1.0
CG A:HIS451 3.2 29.0 1.0
CB A:HIS451 3.6 28.6 1.0
CB A:TYR276 4.1 27.2 1.0
CG A:GLU453 4.2 32.8 1.0
CD A:PRO452 4.2 30.2 1.0
NE2 A:HIS451 4.2 29.1 1.0
CG A:TYR276 4.2 26.9 1.0
CD2 A:HIS451 4.3 28.9 1.0
CA A:HIS451 4.5 28.8 1.0
CD1 A:TYR276 4.6 27.1 1.0
CD2 A:TYR276 4.7 27.0 1.0
N A:PRO452 4.7 30.1 1.0
CB A:GLU453 4.8 31.8 1.0
N A:GLU453 4.9 31.3 1.0
C A:HIS451 5.0 29.3 1.0

Zinc binding site 3 out of 3 in 4ebb

Go back to Zinc Binding Sites List in 4ebb
Zinc binding site 3 out of 3 in the Structure of DPP2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of DPP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:48.0
occ:1.00
OD2 A:ASP251 2.2 33.7 1.0
CG A:ASP251 3.1 32.7 1.0
OD1 A:ASP251 3.3 31.7 1.0
OD2 A:ASP254 4.1 29.7 1.0
OD1 A:ASP254 4.2 28.5 1.0
CG A:ASP254 4.5 29.0 1.0
CB A:ASP251 4.5 32.6 1.0

Reference:

G.A.Bezerra, E.Dobrovetsky, A.Dong, A.Seitova, L.Crombett, L.M.Shewchuk, A.M.Hassell, S.M.Sweitzer, T.D.Sweitzer, P.J.Mcdevitt, K.O.Johanson, K.M.Kennedy-Wilson, D.Cossar, A.Bochkarev, K.Gruber, S.Dhe-Paganon. Structures of Human DPP7 Reveal the Molecular Basis of Specific Inhibition and the Architectural Diversity of Proline-Specific Peptidases. Plos One V. 7 43019 2012.
ISSN: ESSN 1932-6203
PubMed: 22952628
DOI: 10.1371/JOURNAL.PONE.0043019
Page generated: Wed Dec 16 05:15:58 2020

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