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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

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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

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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: Wed Aug 20 08:53:20 2025

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