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Zinc in PDB 2bgn: Hiv-1 Tat Protein Derived N-Terminal Nonapeptide TRP2-Tat (1-9) Bound to the Active Site of Dipeptidyl Peptidase IV (CD26)

Enzymatic activity of Hiv-1 Tat Protein Derived N-Terminal Nonapeptide TRP2-Tat (1-9) Bound to the Active Site of Dipeptidyl Peptidase IV (CD26)

All present enzymatic activity of Hiv-1 Tat Protein Derived N-Terminal Nonapeptide TRP2-Tat (1-9) Bound to the Active Site of Dipeptidyl Peptidase IV (CD26):
3.4.14.5; 3.5.4.4;

Protein crystallography data

The structure of Hiv-1 Tat Protein Derived N-Terminal Nonapeptide TRP2-Tat (1-9) Bound to the Active Site of Dipeptidyl Peptidase IV (CD26), PDB code: 2bgn was solved by W.A.Weihofen, J.Liu, W.Reutter, W.Saenger, H.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.945, 170.273, 239.200, 90.00, 100.93, 90.00
R / Rfree (%) 22.7 / 24.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Hiv-1 Tat Protein Derived N-Terminal Nonapeptide TRP2-Tat (1-9) Bound to the Active Site of Dipeptidyl Peptidase IV (CD26) (pdb code 2bgn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Hiv-1 Tat Protein Derived N-Terminal Nonapeptide TRP2-Tat (1-9) Bound to the Active Site of Dipeptidyl Peptidase IV (CD26), PDB code: 2bgn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2bgn

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Zinc binding site 1 out of 4 in the Hiv-1 Tat Protein Derived N-Terminal Nonapeptide TRP2-Tat (1-9) Bound to the Active Site of Dipeptidyl Peptidase IV (CD26)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hiv-1 Tat Protein Derived N-Terminal Nonapeptide TRP2-Tat (1-9) Bound to the Active Site of Dipeptidyl Peptidase IV (CD26) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:66.3
occ:1.00
 NE2 E:HIS214 2.0 81.7 1.0
NE2 E:HIS17 2.1 81.3 1.0
NE2 E:HIS15 2.1 80.9 1.0
OD1 E:ASP295 2.2 71.4 1.0
CE1 E:HIS214 2.8 82.2 1.0
CE1 E:HIS15 2.9 81.0 1.0
CD2 E:HIS17 2.9 81.4 1.0
CG E:ASP295 3.1 71.7 1.0
CD2 E:HIS214 3.1 82.8 1.0
CE1 E:HIS17 3.1 81.3 1.0
CD2 E:HIS15 3.2 81.1 1.0
OD2 E:ASP295 3.3 68.5 1.0
NE2 E:HIS238 3.9 71.7 1.0
ND1 E:HIS214 4.0 82.3 1.0
ND1 E:HIS15 4.1 80.6 1.0
CG E:HIS17 4.1 80.7 1.0
CG E:HIS214 4.2 82.6 1.0
ND1 E:HIS17 4.2 80.8 1.0
CG E:HIS15 4.2 80.9 1.0
CB E:ASP295 4.5 73.3 1.0
CD2 E:HIS238 4.6 73.0 1.0
CD E:ARG101 4.7 82.3 1.0
OD1 E:ASP296 4.8 74.1 1.0
CA E:ASP295 4.8 73.5 1.0
CE1 E:HIS238 5.0 72.0 1.0

Zinc binding site 2 out of 4 in 2bgn

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Zinc binding site 2 out of 4 in the Hiv-1 Tat Protein Derived N-Terminal Nonapeptide TRP2-Tat (1-9) Bound to the Active Site of Dipeptidyl Peptidase IV (CD26)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hiv-1 Tat Protein Derived N-Terminal Nonapeptide TRP2-Tat (1-9) Bound to the Active Site of Dipeptidyl Peptidase IV (CD26) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:83.2
occ:1.00
 NE2 F:HIS214 2.1 81.9 1.0
NE2 F:HIS15 2.1 81.1 1.0
NE2 F:HIS17 2.1 81.6 1.0
OD1 F:ASP295 2.2 78.4 1.0
CE1 F:HIS214 2.9 82.2 1.0
CE1 F:HIS15 3.0 81.0 1.0
CD2 F:HIS17 3.0 81.4 1.0
CG F:ASP295 3.1 78.7 1.0
CD2 F:HIS214 3.1 82.9 1.0
CD2 F:HIS15 3.2 81.2 1.0
CE1 F:HIS17 3.2 81.4 1.0
OD2 F:ASP295 3.3 77.7 1.0
ND1 F:HIS214 4.1 82.4 1.0
ND1 F:HIS15 4.1 80.6 1.0
CG F:HIS17 4.2 80.7 1.0
CG F:HIS214 4.2 82.7 1.0
CG F:HIS15 4.2 81.0 1.0
ND1 F:HIS17 4.3 80.8 1.0
CB F:ASP295 4.5 79.2 1.0
NE2 F:HIS238 4.6 82.2 1.0
CD2 F:HIS238 4.6 82.3 1.0
O F:ASP295 4.7 79.4 1.0
CD F:ARG101 4.8 82.3 1.0
CA F:ASP295 4.8 79.4 1.0
OD1 F:ASP296 5.0 78.8 1.0

Zinc binding site 3 out of 4 in 2bgn

Go back to Zinc Binding Sites List in 2bgn
Zinc binding site 3 out of 4 in the Hiv-1 Tat Protein Derived N-Terminal Nonapeptide TRP2-Tat (1-9) Bound to the Active Site of Dipeptidyl Peptidase IV (CD26)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hiv-1 Tat Protein Derived N-Terminal Nonapeptide TRP2-Tat (1-9) Bound to the Active Site of Dipeptidyl Peptidase IV (CD26) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn501

b:85.3
occ:1.00
 NE2 G:HIS15 2.1 81.1 1.0
NE2 G:HIS17 2.1 81.5 1.0
NE2 G:HIS214 2.1 81.9 1.0
OD1 G:ASP295 2.2 81.5 1.0
CD2 G:HIS17 2.9 81.4 1.0
CE1 G:HIS214 2.9 82.2 1.0
CE1 G:HIS15 3.0 81.0 1.0
CG G:ASP295 3.1 82.0 1.0
CD2 G:HIS15 3.1 81.2 1.0
CD2 G:HIS214 3.2 82.9 1.0
CE1 G:HIS17 3.2 81.3 1.0
OD2 G:ASP295 3.2 80.7 1.0
NE2 G:HIS238 3.9 86.9 1.0
ND1 G:HIS15 4.1 80.6 1.0
ND1 G:HIS214 4.1 82.4 1.0
CG G:HIS17 4.1 80.7 1.0
CG G:HIS15 4.2 81.0 1.0
ND1 G:HIS17 4.2 80.9 1.0
CG G:HIS214 4.3 82.7 1.0
CB G:ASP295 4.5 82.2 1.0
CD2 G:HIS238 4.6 85.9 1.0
OD1 G:ASP296 4.7 84.9 1.0
CD G:ARG101 4.7 82.3 1.0
CA G:ASP295 4.9 82.2 1.0
CE1 G:HIS238 5.0 86.8 1.0

Zinc binding site 4 out of 4 in 2bgn

Go back to Zinc Binding Sites List in 2bgn
Zinc binding site 4 out of 4 in the Hiv-1 Tat Protein Derived N-Terminal Nonapeptide TRP2-Tat (1-9) Bound to the Active Site of Dipeptidyl Peptidase IV (CD26)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Hiv-1 Tat Protein Derived N-Terminal Nonapeptide TRP2-Tat (1-9) Bound to the Active Site of Dipeptidyl Peptidase IV (CD26) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn501

b:84.0
occ:1.00
 NE2 H:HIS15 2.1 81.1 1.0
NE2 H:HIS214 2.1 81.9 1.0
NE2 H:HIS17 2.1 81.5 1.0
OD1 H:ASP295 2.2 84.5 1.0
CE1 H:HIS214 2.9 82.2 1.0
CE1 H:HIS15 2.9 81.0 1.0
CD2 H:HIS17 2.9 81.4 1.0
CG H:ASP295 3.1 82.3 1.0
CD2 H:HIS15 3.1 81.1 1.0
CD2 H:HIS214 3.2 82.9 1.0
CE1 H:HIS17 3.2 81.4 1.0
OD2 H:ASP295 3.3 83.1 1.0
NE2 H:HIS238 3.8 86.0 1.0
ND1 H:HIS15 4.0 80.6 1.0
ND1 H:HIS214 4.1 82.4 1.0
CG H:HIS17 4.1 80.7 1.0
CG H:HIS15 4.2 80.9 1.0
CG H:HIS214 4.2 82.7 1.0
ND1 H:HIS17 4.2 80.9 1.0
CB H:ASP295 4.4 81.1 1.0
CD2 H:HIS238 4.5 85.8 1.0
OD1 H:ASP296 4.6 80.0 1.0
CA H:ASP295 4.7 80.8 1.0
CD H:ARG101 4.7 82.3 1.0
CE1 H:HIS238 4.8 86.3 1.0

Reference:

W.A.Weihofen, J.Liu, W.Reutter, W.Saenger, H.Fan. Crystal Structures of Hiv-1 Tat-Derived Nonapeptides Tat-(1-9) and TRP2-Tat-(1-9) Bound to the Active Site of Dipeptidyl-Peptidase IV (CD26) J.Biol.Chem. V. 280 14911 2005.
ISSN: ISSN 0021-9258
PubMed: 15695814
DOI: 10.1074/JBC.M413400200
Page generated: Wed Dec 16 03:18:29 2020

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