Atomistry » Cadmium » PDB 2eil-2mhu » 2ydq
Atomistry »
  Cadmium »
    PDB 2eil-2mhu »
      2ydq »

Cadmium in PDB 2ydq: Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide

Enzymatic activity of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide

All present enzymatic activity of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide:
3.2.1.169; 3.2.1.52;

Protein crystallography data

The structure of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide, PDB code: 2ydq was solved by M.Schimpl, V.S.Borodkin, L.J.Gray, D.M.F.Van Aalten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.70 / 2.60
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 118.210, 118.210, 148.210, 90.00, 90.00, 120.00
R / Rfree (%) 19.302 / 23.053

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide (pdb code 2ydq). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 19 binding sites of Cadmium where determined in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide, PDB code: 2ydq:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; 15; 16; 17; 18; 19;

Cadmium binding site 1 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 1 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1620

b:33.6
occ:1.00
OD1 A:ASP117 2.2 31.4 1.0
OE2 A:GLU145 2.3 29.2 1.0
O A:HOH2025 2.3 34.3 1.0
O A:HOH2022 2.5 32.7 1.0
CG A:ASP117 2.9 34.2 1.0
OD2 A:ASP117 3.0 35.2 1.0
CD A:GLU145 3.2 26.5 1.0
OE1 A:GLU145 3.5 28.5 1.0
O A:HOH2023 3.9 37.0 1.0
CB A:ASP117 4.4 33.9 1.0
OG1 A:THR124 4.4 30.7 1.0
CG A:GLU145 4.6 22.9 1.0
CD1 A:LEU120 4.7 28.2 1.0
CA A:VAL109 4.9 24.9 1.0
CA A:ASP117 4.9 33.9 1.0
CD A:CD1637 4.9 75.8 1.0
O A:VAL109 4.9 26.9 1.0

Cadmium binding site 2 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 2 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1621

b:39.7
occ:1.00
O A:HOH2031 2.2 10.2 1.0
OD2 A:ASP139 2.2 28.2 0.0
OD1 A:ASP139 2.6 28.1 0.0
CG A:ASP139 2.7 28.4 0.0
ND2 A:ASN138 3.8 26.5 0.0
CB A:ASP139 4.1 27.9 1.0
OD1 A:ASN138 4.3 26.5 0.0
O A:HOH2030 4.3 16.9 1.0
CG A:ASN138 4.5 26.6 0.0
O A:HOH2029 4.6 24.6 1.0

Cadmium binding site 3 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 3 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1622

b:26.4
occ:1.00
OE2 A:GLU282 2.1 29.8 1.0
OD2 A:ASP286 2.3 24.1 1.0
O A:HOH2059 2.3 24.9 1.0
OD1 A:ASP286 2.5 21.3 1.0
CG A:ASP286 2.7 22.5 1.0
CD A:GLU282 3.1 29.7 1.0
CG A:GLU282 3.6 26.0 1.0
CB A:ASP286 4.2 21.8 1.0
OE1 A:GLU282 4.3 31.4 1.0
O A:HOH2058 4.4 30.7 1.0
NZ A:LYS322 4.6 22.3 1.0
O A:GLU282 4.7 25.0 1.0

Cadmium binding site 4 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 4 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1623

b:41.7
occ:1.00
O A:HOH2007 2.0 19.0 1.0
O A:HOH2008 2.0 30.0 1.0
OD2 A:ASP58 2.2 31.6 1.0
OD1 A:ASP58 2.9 32.1 1.0
CG A:ASP58 2.9 30.4 1.0
O A:HOH2009 4.4 44.7 1.0
CB A:ASP58 4.4 28.6 1.0
NE2 A:GLN40 4.6 38.3 1.0

Cadmium binding site 5 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 5 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1624

b:95.9
occ:1.00
OD2 A:ASP266 2.3 44.0 1.0
NZ A:LYS306 3.0 44.6 1.0
CG A:ASP266 3.4 39.4 1.0
CE A:LYS306 3.5 41.4 1.0
OD1 A:ASP266 3.9 42.2 1.0
CB A:ASP266 4.7 35.8 1.0
CD A:LYS306 4.9 39.1 1.0

Cadmium binding site 6 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 6 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1625

b:26.4
occ:1.00
OD2 A:ASP112 2.3 40.3 1.0
O A:HOH2020 2.3 19.1 1.0
CG A:ASP112 3.3 38.5 1.0
OD1 A:ASP112 3.7 40.5 1.0
CB A:ASP112 4.6 36.5 1.0

Cadmium binding site 7 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 7 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1626

b:69.9
occ:1.00
OE1 A:GLU581 2.5 38.1 0.0
CD A:GLU581 3.0 38.2 0.0
OE2 A:GLU581 3.4 38.1 0.0
CG A:GLU581 4.0 38.4 1.0
CB A:GLU581 4.9 38.3 1.0

Cadmium binding site 8 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 8 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1627

b:43.5
occ:1.00
O A:HOH2012 2.2 29.1 1.0
O A:LEU68 2.4 29.1 1.0
O A:HOH2014 2.4 20.9 1.0
OE2 A:GLU71 2.6 40.5 1.0
OE1 A:GLU71 2.6 38.7 1.0
CD A:GLU71 3.0 39.0 1.0
C A:LEU68 3.5 28.4 1.0
OE2 A:GLU72 3.8 49.0 1.0
CA A:VAL69 4.0 26.7 1.0
N A:VAL69 4.1 27.4 1.0
OE1 A:GLU72 4.4 47.6 1.0
CD A:GLU72 4.5 46.6 1.0
N A:GLY70 4.5 27.4 1.0
CG A:GLU71 4.5 35.3 1.0
O A:HOH2018 4.5 24.0 1.0
CA A:LEU68 4.6 28.4 1.0
CB A:LEU68 4.6 28.2 1.0
C A:VAL69 4.7 26.8 1.0
CG2 A:VAL69 4.9 25.4 1.0
CG A:LEU68 5.0 27.3 1.0
N A:LEU68 5.0 29.6 1.0

Cadmium binding site 9 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 9 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1628

b:34.0
occ:1.00
OE1 A:GLU108 2.1 32.7 1.0
O A:HOH2019 2.3 30.3 1.0
O A:GLU73 2.3 30.6 1.0
OD1 A:ASP111 2.3 33.5 1.0
O A:HOH2015 2.4 19.8 1.0
OD2 A:ASP111 2.8 33.9 1.0
CG A:ASP111 2.9 33.6 1.0
CD A:GLU108 3.3 28.2 1.0
C A:GLU73 3.5 31.5 1.0
CA A:ALA74 4.2 28.9 1.0
OE2 A:GLU108 4.2 27.1 1.0
CG A:GLU108 4.2 24.8 1.0
OD1 A:ASP110 4.2 29.8 1.0
N A:ALA74 4.3 30.0 1.0
C A:ALA74 4.3 28.7 1.0
CB A:GLU108 4.4 22.9 1.0
N A:ASP75 4.4 28.4 1.0
CB A:ASP111 4.4 31.9 1.0
CA A:GLU73 4.5 33.6 1.0
CB A:GLU73 4.7 34.9 1.0
O A:ALA74 4.8 28.1 1.0
N A:GLU108 4.9 22.5 1.0

Cadmium binding site 10 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 10 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1629

b:53.8
occ:1.00
OD1 A:ASP252 2.5 22.9 1.0
O A:HOH2033 2.8 8.2 1.0
O A:HOH2032 3.1 6.2 1.0
CG A:ASP252 3.3 21.0 1.0
OD2 A:ASP252 3.4 23.7 1.0
OD2 A:ASP150 3.5 29.6 1.0
OD1 A:ASP150 4.1 30.1 1.0
CG A:ASP150 4.2 25.2 1.0
O A:LYS250 4.5 17.6 1.0
CB A:ASP252 4.7 18.8 1.0

Cadmium binding site 11 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 11 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1630

b:30.1
occ:1.00
O A:HOH2011 2.1 28.0 1.0
O A:HOH2030 2.3 16.9 1.0
OE1 A:GLU170 2.4 25.7 1.0
O A:HOH2010 2.5 27.9 1.0
OE2 A:GLU170 2.6 27.8 1.0
CD A:GLU170 2.8 25.7 1.0
OD1 A:ASP139 3.9 28.1 0.0
N A:ASP58 4.2 27.2 1.0
OD1 A:ASN138 4.3 26.5 0.0
CG A:GLU170 4.3 24.2 1.0
O A:GLY59 4.5 27.6 1.0
CA A:GLY57 4.5 25.9 1.0
N A:ASP139 4.6 27.8 1.0
N A:GLY59 4.8 27.6 1.0
C A:GLY57 4.8 26.7 1.0
CA A:ASP139 5.0 28.8 1.0

Cadmium binding site 12 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 12 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1631

b:37.7
occ:1.00
OE2 A:GLU362 2.3 27.9 1.0
O A:HOH2081 2.3 28.8 1.0
OE1 A:GLU362 2.3 26.2 1.0
OD2 A:ASP424 2.4 32.2 1.0
O A:HOH2073 2.6 15.9 1.0
OD1 A:ASP424 2.6 31.3 1.0
CD A:GLU362 2.6 27.2 1.0
CG A:ASP424 2.8 30.0 1.0
O A:HOH2068 4.1 31.8 1.0
CG A:GLU362 4.2 26.3 1.0
CB A:ASP424 4.3 27.5 1.0
O A:ASN390 4.3 22.8 1.0
O A:HOH2069 4.4 25.1 1.0
CB A:ASN390 4.7 24.1 1.0

Cadmium binding site 13 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 13 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1632

b:38.9
occ:1.00
OE2 A:GLU51 1.7 33.7 1.0
OD1 A:ASP452 2.1 32.8 1.0
O A:HOH2086 2.4 28.4 1.0
CD A:GLU51 2.4 30.7 1.0
OD1 A:ASN450 2.5 22.7 1.0
OE1 A:GLU51 2.7 32.6 1.0
CG A:ASP452 3.1 29.2 1.0
OD2 A:ASP452 3.3 34.3 1.0
CG A:ASN450 3.4 21.5 1.0
CG A:GLU51 3.8 27.9 1.0
ND2 A:ASN450 3.9 20.0 1.0
N A:ASP452 4.4 24.9 1.0
CB A:ASP452 4.4 25.8 1.0
N A:ASN453 4.5 24.0 1.0
CB A:ASN450 4.5 22.0 1.0
CA A:ASN450 4.5 21.6 1.0
C A:ASN450 4.6 22.3 1.0
CB A:ASN453 4.6 23.0 1.0
O A:HOH2005 4.7 31.3 1.0
N A:MET451 4.8 22.9 1.0
CA A:ASP452 4.8 25.3 1.0
CB A:GLU51 4.9 23.6 1.0
OG1 A:THR178 5.0 19.2 1.0

Cadmium binding site 14 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 14 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 14 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1633

b:55.9
occ:1.00
OD2 A:ASP474 2.4 25.0 1.0
OE1 A:GLU534 2.6 43.2 1.0
OD1 A:ASP474 2.6 26.6 1.0
CG A:ASP474 2.8 25.0 1.0
OE2 A:GLU534 2.9 41.4 1.0
CD A:GLU534 3.1 40.1 1.0
NH1 A:ARG531 3.3 43.8 1.0
ND2 A:ASN538 4.0 27.5 1.0
CZ A:ARG531 4.2 44.3 1.0
CB A:ASP474 4.3 24.4 1.0
CG A:ASN538 4.4 27.1 1.0
CB A:ASN538 4.4 24.9 1.0
NH2 A:ARG531 4.5 43.0 1.0
CG A:GLU534 4.6 32.9 1.0
CA A:ALA535 4.6 25.1 1.0
O A:HOH2092 4.7 20.1 1.0
O A:GLU534 5.0 27.5 1.0
N A:ALA535 5.0 26.2 1.0

Cadmium binding site 15 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 15 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 15 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1634

b:40.3
occ:1.00
OE2 A:GLU272 2.1 35.6 1.0
NE2 A:HIS276 2.5 30.1 1.0
CD A:GLU272 3.3 34.3 1.0
CD2 A:HIS276 3.4 28.1 1.0
CE1 A:HIS276 3.5 31.1 1.0
CG A:GLU272 4.0 31.4 1.0
OE1 A:GLU272 4.3 34.6 1.0
CD A:ARG228 4.6 23.3 1.0
ND1 A:HIS276 4.6 30.4 1.0
CG A:HIS276 4.6 27.6 1.0

Cadmium binding site 16 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 16 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 16 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1635

b:48.9
occ:1.00
NE2 A:HIS413 2.2 25.3 1.0
CE1 A:HIS413 3.0 26.3 1.0
CD2 A:HIS413 3.4 24.8 1.0
ND1 A:HIS413 4.2 26.0 1.0
CG A:HIS413 4.4 23.7 1.0
OE1 A:GLU496 4.4 44.4 1.0
CA A:ARG495 4.5 25.6 1.0
N A:GLU496 4.5 27.7 1.0
O A:GLY494 4.6 23.6 1.0
CD A:GLU496 5.0 43.8 1.0

Cadmium binding site 17 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 17 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 17 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1636

b:64.7
occ:1.00
O A:LYS404 2.5 21.9 1.0
NE2 A:HIS433 2.6 19.0 1.0
O A:HOH2075 2.7 23.0 1.0
C A:LYS404 3.5 21.5 1.0
O A:HOH2099 3.5 26.9 1.0
CE1 A:HIS433 3.6 21.1 1.0
CD2 A:HIS433 3.6 19.7 1.0
CA A:LYS404 3.9 21.5 1.0
CB A:LYS404 4.0 21.3 1.0
OG1 A:THR400 4.4 18.3 1.0
O A:LYS406 4.6 19.5 1.0
N A:GLY405 4.7 21.1 1.0
ND1 A:HIS433 4.7 22.4 1.0
CG A:LYS404 4.7 23.2 1.0
CG A:HIS433 4.8 21.5 1.0
CD2 A:LEU407 4.8 17.0 1.0
CE2 A:PHE601 4.9 27.6 1.0
CZ A:PHE601 5.0 27.9 1.0

Cadmium binding site 18 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 18 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 18 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1637

b:75.8
occ:1.00
OD2 A:ASP117 3.2 35.2 1.0
CG A:ASP117 4.1 34.2 1.0
OD1 A:ASP112 4.4 40.5 1.0
OD1 A:ASP117 4.7 31.4 1.0
O A:HOH2022 4.8 32.7 1.0
CB A:ASP117 4.9 33.9 1.0
CD A:CD1620 4.9 33.6 1.0

Cadmium binding site 19 out of 19 in 2ydq

Go back to Cadmium Binding Sites List in 2ydq
Cadmium binding site 19 out of 19 in the Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 19 of Cpoga D298N in Complex with Hoga-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cd1409

b:47.1
occ:1.00
NE2 T:HIS404 2.3 43.2 1.0
CD2 T:HIS404 3.2 42.3 1.0
CE1 T:HIS404 3.3 42.9 1.0
CG T:HIS404 4.4 43.3 1.0
ND1 T:HIS404 4.4 42.5 1.0
O A:HOH2076 4.9 28.6 1.0

Reference:

M.Schimpl, V.S.Borodkin, L.J.Gray, D.M.F.Van Aalten. Synergy of Peptide and Sugar in O-Glcnacase Substrate Recognition. Chem.Biol. V. 19 173 2012.
ISSN: ISSN 1074-5521
PubMed: 22365600
DOI: 10.1016/J.CHEMBIOL.2012.01.011
Page generated: Fri Aug 28 13:17:02 2020
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy