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Zinc in PDB 1w1i: Crystal Structure of Dipeptidyl Peptidase IV (Dppiv or CD26) in Complex with Adenosine Deaminase

Enzymatic activity of Crystal Structure of Dipeptidyl Peptidase IV (Dppiv or CD26) in Complex with Adenosine Deaminase

All present enzymatic activity of Crystal Structure of Dipeptidyl Peptidase IV (Dppiv or CD26) in Complex with Adenosine Deaminase:
3.4.14.5; 3.5.4.4;

Protein crystallography data

The structure of Crystal Structure of Dipeptidyl Peptidase IV (Dppiv or CD26) in Complex with Adenosine Deaminase, PDB code: 1w1i 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 / 3.03
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.065, 168.504, 236.842, 90.00, 100.54, 90.00
R / Rfree (%) 22.4 / 25.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Dipeptidyl Peptidase IV (Dppiv or CD26) in Complex with Adenosine Deaminase (pdb code 1w1i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Dipeptidyl Peptidase IV (Dppiv or CD26) in Complex with Adenosine Deaminase, PDB code: 1w1i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1w1i

Go back to Zinc Binding Sites List in 1w1i
Zinc binding site 1 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV (Dppiv or CD26) in Complex with Adenosine Deaminase


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 Dipeptidyl Peptidase IV (Dppiv or CD26) in Complex with Adenosine Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:53.0
occ:1.00
 NE2 E:HIS15 2.0 55.8 1.0
NE2 E:HIS17 2.1 56.7 1.0
NE2 E:HIS214 2.1 61.4 1.0
OD1 E:ASP295 2.2 58.7 1.0
CE1 E:HIS214 2.9 62.6 1.0
CD2 E:HIS15 3.0 55.5 1.0
CG E:ASP295 3.0 59.3 1.0
CE1 E:HIS15 3.0 55.7 1.0
CD2 E:HIS17 3.0 56.4 1.0
OD2 E:ASP295 3.0 58.9 1.0
CE1 E:HIS17 3.0 56.4 1.0
CD2 E:HIS214 3.1 63.1 1.0
NE2 E:HIS238 4.0 51.7 1.0
ND1 E:HIS214 4.1 63.3 1.0
ND1 E:HIS15 4.1 55.6 1.0
CG E:HIS15 4.1 55.4 1.0
ND1 E:HIS17 4.1 56.2 1.0
CG E:HIS17 4.2 56.1 1.0
CG E:HIS214 4.2 63.6 1.0
CB E:ASP295 4.5 60.3 1.0
OD2 E:ASP296 4.6 62.8 1.0
CD2 E:HIS238 4.6 52.5 1.0
CD E:ARG101 4.8 52.3 1.0
CA E:ASP295 4.9 61.1 1.0

Zinc binding site 2 out of 4 in 1w1i

Go back to Zinc Binding Sites List in 1w1i
Zinc binding site 2 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV (Dppiv or CD26) in Complex with Adenosine Deaminase


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 Dipeptidyl Peptidase IV (Dppiv or CD26) in Complex with Adenosine Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:62.9
occ:1.00
 NE2 F:HIS214 2.1 61.7 1.0
NE2 F:HIS15 2.1 56.2 1.0
NE2 F:HIS17 2.1 57.1 1.0
OD1 F:ASP295 2.2 59.0 1.0
OD2 F:ASP295 2.9 59.0 1.0
CG F:ASP295 3.0 59.5 1.0
CE1 F:HIS214 3.0 62.6 1.0
CD2 F:HIS15 3.0 55.6 1.0
CD2 F:HIS17 3.1 56.5 1.0
CE1 F:HIS15 3.1 55.7 1.0
CD2 F:HIS214 3.1 63.0 1.0
CE1 F:HIS17 3.1 56.5 1.0
NE2 F:HIS238 3.8 73.6 1.0
ND1 F:HIS214 4.1 63.4 1.0
CD2 F:HIS238 4.2 73.6 1.0
ND1 F:HIS15 4.2 55.6 1.0
CG F:HIS15 4.2 55.5 1.0
CG F:HIS214 4.2 63.8 1.0
ND1 F:HIS17 4.2 56.3 1.0
CG F:HIS17 4.2 56.1 1.0
CB F:ASP295 4.4 60.4 1.0
OD2 F:ASP296 4.5 62.8 1.0
CE1 F:HIS238 4.9 73.5 1.0
CD F:ARG101 4.9 52.4 1.0
CA F:ASP295 4.9 61.2 1.0

Zinc binding site 3 out of 4 in 1w1i

Go back to Zinc Binding Sites List in 1w1i
Zinc binding site 3 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV (Dppiv or CD26) in Complex with Adenosine Deaminase


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 Dipeptidyl Peptidase IV (Dppiv or CD26) in Complex with Adenosine Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn501

b:58.2
occ:1.00
 NE2 G:HIS17 2.1 56.9 1.0
NE2 G:HIS15 2.1 56.1 1.0
NE2 G:HIS214 2.1 61.6 1.0
OD1 G:ASP295 2.2 59.0 1.0
CE1 G:HIS214 3.0 62.6 1.0
CG G:ASP295 3.0 59.4 1.0
OD2 G:ASP295 3.0 59.0 1.0
CD2 G:HIS15 3.0 55.6 1.0
CD2 G:HIS17 3.0 56.4 1.0
CE1 G:HIS17 3.1 56.4 1.0
CE1 G:HIS15 3.1 55.7 1.0
CD2 G:HIS214 3.1 63.1 1.0
NE2 G:HIS238 3.7 68.6 1.0
ND1 G:HIS214 4.1 63.4 1.0
ND1 G:HIS17 4.2 56.3 1.0
ND1 G:HIS15 4.2 55.6 1.0
CG G:HIS15 4.2 55.4 1.0
CG G:HIS17 4.2 56.2 1.0
CG G:HIS214 4.2 63.7 1.0
CB G:ASP295 4.4 60.4 1.0
CD2 G:HIS238 4.5 68.2 1.0
OD2 G:ASP296 4.5 62.9 1.0
CE1 G:HIS238 4.7 68.5 1.0
CD G:ARG101 4.9 52.4 1.0
CA G:ASP295 4.9 61.1 1.0

Zinc binding site 4 out of 4 in 1w1i

Go back to Zinc Binding Sites List in 1w1i
Zinc binding site 4 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV (Dppiv or CD26) in Complex with Adenosine Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Dipeptidyl Peptidase IV (Dppiv or CD26) in Complex with Adenosine Deaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn501

b:58.5
occ:1.00
 NE2 H:HIS214 2.1 61.7 1.0
NE2 H:HIS15 2.1 56.1 1.0
NE2 H:HIS17 2.1 56.9 1.0
OD1 H:ASP295 2.2 59.0 1.0
OD2 H:ASP295 3.0 59.0 1.0
CG H:ASP295 3.0 59.4 1.0
CE1 H:HIS214 3.0 62.6 1.0
CD2 H:HIS15 3.0 55.6 1.0
CE1 H:HIS15 3.1 55.7 1.0
CD2 H:HIS17 3.1 56.5 1.0
CE1 H:HIS17 3.1 56.5 1.0
CD2 H:HIS214 3.1 63.1 1.0
NE2 H:HIS238 3.2 67.7 1.0
CD2 H:HIS238 4.1 68.0 1.0
CE1 H:HIS238 4.1 67.8 1.0
ND1 H:HIS214 4.1 63.4 1.0
ND1 H:HIS15 4.2 55.7 1.0
CG H:HIS15 4.2 55.5 1.0
ND1 H:HIS17 4.2 56.3 1.0
CG H:HIS214 4.2 63.7 1.0
CG H:HIS17 4.2 56.2 1.0
CB H:ASP295 4.5 60.4 1.0
OD2 H:ASP296 4.5 62.8 1.0
CD H:ARG101 4.9 52.5 1.0
CA H:ASP295 4.9 61.1 1.0

Reference:

W.A.Weihofen, J.Liu, W.Reutter, W.Saenger, H.Fan. Crystal Structure of CD26/Dipeptidyl-Peptidase IV in Complex with Adenosine Deaminase Reveals A Highly Amphiphilic Interface. J. Biol. Chem. V. 279 43330 2004.
ISSN: ISSN 0021-9258
PubMed: 15213224
DOI: 10.1074/JBC.M405001200
Page generated: Wed Oct 16 19:53:42 2024

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