Atomistry » Zinc » PDB 3eb6-3ejt » 3ee6
Atomistry »
  Zinc »
    PDB 3eb6-3ejt »
      3ee6 »

Zinc in PDB 3ee6: Crystal Structure Analysis of Tripeptidyl Peptidase -I

Enzymatic activity of Crystal Structure Analysis of Tripeptidyl Peptidase -I

All present enzymatic activity of Crystal Structure Analysis of Tripeptidyl Peptidase -I:
3.4.14.9;

Protein crystallography data

The structure of Crystal Structure Analysis of Tripeptidyl Peptidase -I, PDB code: 3ee6 was solved by A.Pal, R.Kraetzner, M.Grapp, T.Gruene, K.Schreiber, M.Granborg, H.Urlaub, A.R.Asif, S.Becker, J.Gartner, G.M.Sheldrick, R.Steinfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.21 / 2.35
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 113.450, 128.930, 100.500, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 26.2

Other elements in 3ee6:

The structure of Crystal Structure Analysis of Tripeptidyl Peptidase -I also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure Analysis of Tripeptidyl Peptidase -I (pdb code 3ee6). 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 Analysis of Tripeptidyl Peptidase -I, PDB code: 3ee6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3ee6

Go back to Zinc Binding Sites List in 3ee6
Zinc binding site 1 out of 8 in the Crystal Structure Analysis of Tripeptidyl Peptidase -I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of Tripeptidyl Peptidase -I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn576

b:91.4
occ:1.00
 OD2 A:ASP457 2.1 64.0 1.0
OE1 B:GLU529 2.4 73.5 1.0
CE1 A:HIS197 2.5 90.8 1.0
CG A:ASP457 2.8 64.1 1.0
OD1 A:ASP457 2.8 64.7 1.0
ND1 A:HIS197 2.9 90.2 1.0
OE2 B:GLU529 3.0 73.1 1.0
NE2 A:HIS197 3.0 91.3 1.0
CD B:GLU529 3.0 73.5 1.0
CG A:HIS197 3.5 88.2 1.0
CD2 A:HIS197 3.6 90.0 1.0
CB A:ASP457 4.3 63.6 1.0
OG A:SER392 4.4 68.9 1.0
O A:HOH583 4.5 51.9 1.0
CG B:GLU529 4.5 72.8 1.0
CB A:HIS197 4.6 86.3 1.0

Zinc binding site 2 out of 8 in 3ee6

Go back to Zinc Binding Sites List in 3ee6
Zinc binding site 2 out of 8 in the Crystal Structure Analysis of Tripeptidyl Peptidase -I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of Tripeptidyl Peptidase -I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn577

b:71.3
occ:0.50
 OE2 A:GLU137 1.8 61.2 1.0
NE2 A:HIS155 2.4 65.4 1.0
CD A:GLU137 2.7 61.6 1.0
OE1 A:GLU137 2.9 60.4 1.0
CD2 A:HIS155 3.0 63.7 1.0
CE1 A:HIS155 3.6 64.8 1.0
CG A:GLU137 4.1 60.9 1.0
CG A:HIS155 4.2 63.5 1.0
NE2 A:HIS139 4.5 62.1 1.0
ND1 A:HIS155 4.5 63.8 1.0
CB A:GLU137 4.5 60.4 1.0

Zinc binding site 3 out of 8 in 3ee6

Go back to Zinc Binding Sites List in 3ee6
Zinc binding site 3 out of 8 in the Crystal Structure Analysis of Tripeptidyl Peptidase -I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of Tripeptidyl Peptidase -I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn578

b:83.8
occ:1.00
 OE1 A:GLU45 2.3 66.2 1.0
NE2 A:HIS149 2.7 69.0 1.0
CD2 A:HIS140 2.9 68.4 1.0
CE1 A:HIS149 2.9 68.8 1.0
CD A:GLU45 3.0 66.8 1.0
OE2 A:GLU45 3.0 67.9 1.0
CG A:HIS140 3.1 66.6 1.0
CB A:HIS140 3.5 66.3 1.0
NE2 A:HIS140 3.6 69.4 1.0
ND1 A:HIS140 3.9 68.5 1.0
CD2 A:HIS149 4.0 69.0 1.0
CE1 A:HIS140 4.1 69.2 1.0
ND1 A:HIS149 4.2 70.3 1.0
CG2 A:VAL151 4.3 64.1 1.0
CG A:GLU45 4.4 66.5 1.0
CG A:HIS149 4.8 71.3 1.0

Zinc binding site 4 out of 8 in 3ee6

Go back to Zinc Binding Sites List in 3ee6
Zinc binding site 4 out of 8 in the Crystal Structure Analysis of Tripeptidyl Peptidase -I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of Tripeptidyl Peptidase -I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn579

b:0.1
occ:1.00
 NE2 A:HIS511 1.9 73.6 1.0
OE2 A:GLU424 2.7 73.8 1.0
CE1 A:HIS511 2.8 73.5 1.0
OE1 A:GLU424 2.8 74.7 1.0
CD A:GLU424 3.0 73.5 1.0
CD2 A:HIS511 3.0 73.2 1.0
O A:HOH618 3.3 71.1 1.0
ND1 A:HIS511 3.9 74.0 1.0
CG A:HIS511 4.0 73.1 1.0
CG A:GLU424 4.3 71.4 1.0
O A:HOH611 4.5 69.7 1.0

Zinc binding site 5 out of 8 in 3ee6

Go back to Zinc Binding Sites List in 3ee6
Zinc binding site 5 out of 8 in the Crystal Structure Analysis of Tripeptidyl Peptidase -I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure Analysis of Tripeptidyl Peptidase -I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn576

b:87.1
occ:0.50
 OE1 B:GLU137 2.1 71.1 1.0
OE2 B:GLU137 2.3 71.4 1.0
CD B:GLU137 2.4 69.9 1.0
NE2 B:HIS155 2.5 65.3 1.0
CD2 B:HIS155 2.9 65.3 1.0
CE1 B:HIS155 3.6 66.5 1.0
CG B:GLU137 3.8 67.6 1.0
CG B:HIS155 4.1 64.7 1.0
CE1 B:HIS139 4.3 65.6 1.0
ND1 B:HIS155 4.4 65.3 1.0
CB B:GLU137 4.4 66.1 1.0

Zinc binding site 6 out of 8 in 3ee6

Go back to Zinc Binding Sites List in 3ee6
Zinc binding site 6 out of 8 in the Crystal Structure Analysis of Tripeptidyl Peptidase -I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure Analysis of Tripeptidyl Peptidase -I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn577

b:94.5
occ:1.00
 OE1 A:GLU529 2.2 71.7 1.0
OD2 B:ASP457 2.2 65.8 1.0
ND1 B:HIS197 2.3 82.3 1.0
CD A:GLU529 2.8 70.7 1.0
OE2 A:GLU529 2.9 70.5 1.0
CE1 B:HIS197 3.0 82.5 1.0
CG B:ASP457 3.0 65.1 1.0
OD1 B:ASP457 3.1 67.5 1.0
CG B:HIS197 3.5 80.5 1.0
CB B:HIS197 4.1 77.8 1.0
CG A:GLU529 4.1 70.7 1.0
NE2 B:HIS197 4.2 83.2 1.0
CB B:ASP457 4.4 64.9 1.0
CD2 B:HIS197 4.4 82.3 1.0
O B:HOH612 4.6 64.6 1.0
OG B:SER392 4.7 68.3 1.0
O B:HOH606 4.8 62.6 1.0
N B:HIS197 4.8 77.5 1.0

Zinc binding site 7 out of 8 in 3ee6

Go back to Zinc Binding Sites List in 3ee6
Zinc binding site 7 out of 8 in the Crystal Structure Analysis of Tripeptidyl Peptidase -I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure Analysis of Tripeptidyl Peptidase -I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn578

b:90.4
occ:1.00
 OE1 B:GLU45 2.4 58.8 1.0
NE2 B:HIS149 2.5 73.0 1.0
ND1 B:HIS140 2.8 66.7 1.0
CE1 B:HIS149 2.8 73.7 1.0
CD B:GLU45 3.2 62.3 1.0
CG B:HIS140 3.3 66.4 1.0
CB B:HIS140 3.4 66.6 1.0
OE2 B:GLU45 3.4 61.9 1.0
CE1 B:HIS140 3.7 67.7 1.0
CD2 B:HIS149 3.8 73.3 1.0
ND1 B:HIS149 4.1 74.3 1.0
CD2 B:HIS140 4.3 67.3 1.0
NE2 B:HIS140 4.5 67.5 1.0
CG2 B:VAL151 4.5 66.5 1.0
CG B:GLU45 4.5 63.2 1.0
CG B:HIS149 4.6 74.1 1.0
CA B:HIS140 4.9 66.4 1.0

Zinc binding site 8 out of 8 in 3ee6

Go back to Zinc Binding Sites List in 3ee6
Zinc binding site 8 out of 8 in the Crystal Structure Analysis of Tripeptidyl Peptidase -I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure Analysis of Tripeptidyl Peptidase -I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn579

b:0.1
occ:1.00
 NE2 B:HIS511 2.0 75.0 1.0
OE2 B:GLU424 2.2 74.8 1.0
OE1 B:GLU424 2.8 77.4 1.0
O B:HOH645 2.8 67.4 1.0
CE1 B:HIS511 2.8 75.2 1.0
CD B:GLU424 2.8 74.8 1.0
CD2 B:HIS511 2.9 73.1 1.0
ND1 B:HIS511 3.9 74.8 1.0
CG B:HIS511 3.9 73.3 1.0
CG B:GLU424 4.3 72.0 1.0

Reference:

A.Pal, R.Kraetzner, T.Gruene, M.Grapp, K.Schreiber, M.Gronborg, H.Urlaub, S.Becker, A.R.Asif, J.Gartner, G.M.Sheldrick, R.Steinfeld. Structure of Tripeptidyl-Peptidase I Provides Insight Into the Molecular Basis of Late Infantile Neuronal Ceroid Lipofuscinosis J.Biol.Chem. V. 284 3976 2009.
ISSN: ISSN 0021-9258
PubMed: 19038966
DOI: 10.1074/JBC.M806947200
Page generated: Thu Oct 24 12:46:12 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