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Zinc in PDB 2qyv: Crystal Structure of Putative Xaa-His Dipeptidase (YP_718209.1) From Haemophilus Somnus 129PT at 2.11 A Resolution

Enzymatic activity of Crystal Structure of Putative Xaa-His Dipeptidase (YP_718209.1) From Haemophilus Somnus 129PT at 2.11 A Resolution

All present enzymatic activity of Crystal Structure of Putative Xaa-His Dipeptidase (YP_718209.1) From Haemophilus Somnus 129PT at 2.11 A Resolution:
3.4.13.20;

Protein crystallography data

The structure of Crystal Structure of Putative Xaa-His Dipeptidase (YP_718209.1) From Haemophilus Somnus 129PT at 2.11 A Resolution, PDB code: 2qyv was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.84 / 2.11
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 173.922, 84.293, 123.204, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 24.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Putative Xaa-His Dipeptidase (YP_718209.1) From Haemophilus Somnus 129PT at 2.11 A Resolution (pdb code 2qyv). 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 Putative Xaa-His Dipeptidase (YP_718209.1) From Haemophilus Somnus 129PT at 2.11 A Resolution, PDB code: 2qyv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2qyv

Go back to Zinc Binding Sites List in 2qyv
Zinc binding site 1 out of 4 in the Crystal Structure of Putative Xaa-His Dipeptidase (YP_718209.1) From Haemophilus Somnus 129PT at 2.11 A Resolution


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 Putative Xaa-His Dipeptidase (YP_718209.1) From Haemophilus Somnus 129PT at 2.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:73.3
occ:1.00
 OD1 A:ASP169 2.1 74.0 1.0
OD1 A:ASP115 2.2 56.8 1.0
NE2 A:HIS76 2.3 66.3 1.0
OD2 A:ASP169 2.3 65.3 1.0
CG A:ASP169 2.5 69.8 1.0
CG A:ASP115 3.1 65.7 1.0
CD2 A:HIS76 3.1 65.2 1.0
CE1 A:HIS76 3.3 67.4 1.0
OD2 A:ASP115 3.4 68.1 1.0
ZN A:ZN502 3.7 0.7 1.0
OE1 A:GLU145 3.9 67.6 1.0
CB A:ASP169 4.0 67.7 1.0
CB A:ASN116 4.0 68.7 1.0
OE2 A:GLU146 4.1 68.9 1.0
OE2 A:GLU171 4.2 72.5 1.0
CG A:HIS76 4.3 67.2 1.0
CB A:ASP115 4.4 67.9 1.0
ND1 A:HIS76 4.4 69.0 1.0
CD A:GLU145 4.4 68.2 1.0
O A:ASP169 4.4 68.6 1.0
CG A:ASN116 4.5 67.3 1.0
OD1 A:ASN116 4.7 63.4 1.0
CA A:ASP169 4.7 67.5 1.0
OE2 A:GLU145 4.8 70.1 1.0
CA A:ASN116 4.8 69.2 1.0
C A:ASP115 4.8 69.0 1.0
N A:ASN116 4.8 70.0 1.0
CA A:ASP115 4.8 69.1 1.0
CD A:GLU146 4.9 72.2 1.0

Zinc binding site 2 out of 4 in 2qyv

Go back to Zinc Binding Sites List in 2qyv
Zinc binding site 2 out of 4 in the Crystal Structure of Putative Xaa-His Dipeptidase (YP_718209.1) From Haemophilus Somnus 129PT at 2.11 A Resolution


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 Putative Xaa-His Dipeptidase (YP_718209.1) From Haemophilus Somnus 129PT at 2.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:0.7
occ:1.00
 OD2 A:ASP115 2.1 68.1 1.0
OE2 A:GLU146 2.3 68.9 1.0
NE2 A:HIS458 2.4 86.0 1.0
OE1 A:GLU146 2.8 66.4 1.0
CD A:GLU146 2.9 72.2 1.0
CG A:ASP115 3.2 65.7 1.0
CE1 A:HIS458 3.3 85.6 1.0
CD2 A:HIS458 3.3 87.0 1.0
OD1 A:ASP115 3.5 56.8 1.0
ZN A:ZN501 3.7 73.3 1.0
OE1 A:GLU145 4.2 67.6 1.0
ND1 A:HIS458 4.4 87.1 1.0
CG A:GLU146 4.4 71.2 1.0
CG A:HIS458 4.4 87.3 1.0
CB A:ASP115 4.5 67.9 1.0
O2 A:SO4503 4.6 61.8 1.0
NE2 A:HIS76 4.6 66.3 1.0
O A:HOH645 4.7 62.0 1.0
OE2 A:GLU171 4.8 72.5 1.0
CG2 A:VAL80 4.9 75.4 1.0
CE1 A:HIS76 4.9 67.4 1.0

Zinc binding site 3 out of 4 in 2qyv

Go back to Zinc Binding Sites List in 2qyv
Zinc binding site 3 out of 4 in the Crystal Structure of Putative Xaa-His Dipeptidase (YP_718209.1) From Haemophilus Somnus 129PT at 2.11 A Resolution


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 Putative Xaa-His Dipeptidase (YP_718209.1) From Haemophilus Somnus 129PT at 2.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:95.7
occ:1.00
 OD1 B:ASP169 2.1 73.8 1.0
NE2 B:HIS76 2.3 68.5 1.0
OD1 B:ASP115 2.3 58.3 1.0
OD2 B:ASP169 2.5 68.8 1.0
CG B:ASP169 2.6 70.5 1.0
CD2 B:HIS76 3.0 66.7 1.0
CG B:ASP115 3.2 67.2 1.0
OD2 B:ASP115 3.4 66.8 1.0
CE1 B:HIS76 3.4 67.1 1.0
ZN B:ZN502 3.5 0.2 1.0
OE1 B:GLU145 3.7 68.7 1.0
O B:HOH638 3.8 62.4 1.0
CB B:ASN116 4.0 68.6 1.0
CB B:ASP169 4.1 67.9 1.0
CG B:HIS76 4.2 67.5 1.0
OE1 B:GLU146 4.4 69.5 1.0
CD B:GLU145 4.4 69.8 1.0
ND1 B:HIS76 4.4 69.2 1.0
CG B:ASN116 4.5 67.7 1.0
OE2 B:GLU171 4.5 71.4 1.0
O B:ASP169 4.5 68.0 1.0
CB B:ASP115 4.6 68.1 1.0
OD1 B:ASN116 4.7 62.8 1.0
CA B:ASN116 4.8 69.0 1.0
N B:ASN116 4.8 69.3 1.0
CA B:ASP169 4.8 67.8 1.0
C B:ASP115 4.9 68.6 1.0
CA B:ASP115 5.0 68.8 1.0
OE2 B:GLU145 5.0 69.6 1.0

Zinc binding site 4 out of 4 in 2qyv

Go back to Zinc Binding Sites List in 2qyv
Zinc binding site 4 out of 4 in the Crystal Structure of Putative Xaa-His Dipeptidase (YP_718209.1) From Haemophilus Somnus 129PT at 2.11 A Resolution


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 Putative Xaa-His Dipeptidase (YP_718209.1) From Haemophilus Somnus 129PT at 2.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:0.2
occ:1.00
 OD2 B:ASP115 2.2 66.8 1.0
OE2 B:GLU146 2.6 70.2 1.0
OE1 B:GLU146 2.6 69.5 1.0
CE1 B:HIS458 2.8 87.5 1.0
CD B:GLU146 2.9 72.6 1.0
CG B:ASP115 3.1 67.2 1.0
NE2 B:HIS458 3.3 88.4 1.0
OD1 B:ASP115 3.5 58.3 1.0
ZN B:ZN501 3.5 95.7 1.0
ND1 B:HIS458 3.6 88.4 1.0
OE1 B:GLU145 4.1 68.7 1.0
CD2 B:HIS458 4.3 88.4 1.0
CG B:GLU146 4.3 71.5 1.0
NE2 B:HIS76 4.4 68.5 1.0
CB B:ASP115 4.4 68.1 1.0
CG B:HIS458 4.4 88.3 1.0
CE1 B:HIS76 4.6 67.1 1.0
OE2 B:GLU171 4.9 71.4 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Wed Aug 20 05:31:35 2025

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