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Cadmium in PDB 2ydr: Cpoga D298N in Complex with P53-Derived O-Glcnac Peptide

Enzymatic activity of Cpoga D298N in Complex with P53-Derived O-Glcnac Peptide

All present enzymatic activity of Cpoga D298N in Complex with P53-Derived O-Glcnac Peptide:
3.2.1.52;

Protein crystallography data

The structure of Cpoga D298N in Complex with P53-Derived O-Glcnac Peptide, PDB code: 2ydr 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) 25.00 / 2.75
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 117.950, 117.950, 148.121, 90.00, 90.00, 120.00
R / Rfree (%) 18.507 / 21.881

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Cpoga D298N in Complex with P53-Derived O-Glcnac Peptide (pdb code 2ydr). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 18 binding sites of Cadmium where determined in the Cpoga D298N in Complex with P53-Derived O-Glcnac Peptide, PDB code: 2ydr:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; 15; 16; 17; 18;

Cadmium binding site 1 out of 18 in 2ydr

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Cadmium binding site 1 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1620

b:47.2
occ:1.00
O A:HOH2008 2.4 21.9 1.0
O A:LEU68 2.4 33.6 1.0
OE1 A:GLU71 2.5 44.2 1.0
OE2 A:GLU71 3.0 45.3 1.0
CD A:GLU71 3.1 43.8 1.0
C A:LEU68 3.4 33.3 1.0
OE2 A:GLU72 3.6 46.3 1.0
CA A:VAL69 4.1 32.6 1.0
N A:VAL69 4.2 33.0 1.0
CD A:GLU72 4.3 45.3 1.0
OE1 A:GLU72 4.4 44.0 1.0
CA A:LEU68 4.5 33.4 1.0
CB A:LEU68 4.5 33.5 1.0
N A:GLY70 4.6 33.5 1.0
CG A:GLU71 4.6 39.9 1.0
C A:VAL69 4.8 33.1 1.0
N A:LEU68 4.9 34.0 1.0
CG A:LEU68 4.9 32.8 1.0

Cadmium binding site 2 out of 18 in 2ydr

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Cadmium binding site 2 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1621

b:38.8
occ:1.00
OE1 A:GLU108 2.1 35.1 1.0
O A:GLU73 2.3 35.5 1.0
OD1 A:ASP111 2.4 35.9 1.0
OD2 A:ASP111 2.8 34.5 1.0
CG A:ASP111 3.0 35.0 1.0
CD A:GLU108 3.3 31.7 1.0
C A:GLU73 3.5 35.6 1.0
OD1 A:ASP110 4.0 34.6 1.0
CA A:ALA74 4.1 32.0 1.0
CG A:GLU108 4.2 28.2 1.0
N A:ALA74 4.2 33.9 1.0
OE2 A:GLU108 4.2 30.3 1.0
O A:HOH2009 4.3 26.9 1.0
C A:ALA74 4.3 31.3 1.0
CB A:GLU108 4.4 27.1 1.0
N A:ASP75 4.4 30.7 1.0
CB A:ASP111 4.5 35.4 1.0
CA A:GLU73 4.5 37.1 1.0
CB A:GLU73 4.7 38.3 1.0
O A:ALA74 4.8 30.8 1.0
N A:GLU108 4.9 26.5 1.0

Cadmium binding site 3 out of 18 in 2ydr

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Cadmium binding site 3 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1622

b:33.6
occ:1.00
OD2 A:ASP112 2.2 44.1 1.0
CG A:ASP112 3.2 42.7 1.0
OD1 A:ASP112 3.5 45.2 1.0
CB A:ASP112 4.6 40.9 1.0

Cadmium binding site 4 out of 18 in 2ydr

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Cadmium binding site 4 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1623

b:40.9
occ:1.00
OD1 A:ASP117 2.3 37.7 1.0
OE2 A:GLU145 2.4 34.2 1.0
OD2 A:ASP117 2.9 39.2 1.0
CG A:ASP117 2.9 38.0 1.0
CD A:GLU145 3.1 30.1 1.0
OE1 A:GLU145 3.2 29.0 1.0
OG1 A:THR124 4.1 32.5 1.0
O A:HOH2015 4.3 18.3 1.0
CB A:ASP117 4.4 37.7 1.0
CG A:GLU145 4.6 25.6 1.0
CD1 A:LEU120 4.7 32.8 1.0
CA A:ASP117 4.8 37.6 1.0

Cadmium binding site 5 out of 18 in 2ydr

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Cadmium binding site 5 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1624

b:40.9
occ:1.00
OD2 A:ASP139 2.6 28.2 0.0
OD1 A:ASP139 2.7 28.2 0.0
CG A:ASP139 2.8 28.3 0.0
ND2 A:ASN138 3.0 25.8 0.0
CB A:ASP139 4.1 28.2 1.0
CG A:ASN138 4.2 26.0 0.0
OD1 A:ASN138 4.7 25.8 0.0

Cadmium binding site 6 out of 18 in 2ydr

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Cadmium binding site 6 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1625

b:64.6
occ:1.00
OD1 A:ASP252 2.4 32.4 1.0
CG A:ASP252 3.2 27.8 1.0
O A:HOH2021 3.3 14.7 1.0
OD2 A:ASP252 3.4 32.1 1.0
OD2 A:ASP150 3.7 28.6 1.0
O A:HOH2044 3.7 12.8 1.0
OD1 A:ASP150 4.0 31.1 1.0
CG A:ASP150 4.2 26.1 1.0
O A:LYS250 4.4 20.7 1.0
CB A:ASP252 4.7 22.7 1.0

Cadmium binding site 7 out of 18 in 2ydr

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Cadmium binding site 7 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1626

b:32.8
occ:1.00
OE1 A:GLU170 2.1 26.0 1.0
OE2 A:GLU170 2.6 27.2 1.0
CD A:GLU170 2.7 25.2 1.0
O A:HOH2005 2.9 7.0 1.0
OD1 A:ASP139 3.8 28.2 0.0
OD1 A:ASN138 3.9 25.8 0.0
N A:ASP58 4.1 30.6 1.0
CG A:GLU170 4.2 22.5 1.0
CA A:GLY57 4.3 28.6 1.0
O A:GLY59 4.5 32.0 1.0
N A:ASP139 4.5 27.9 1.0
CG A:ASN138 4.7 26.0 0.0
N A:GLY59 4.7 31.9 1.0
C A:GLY57 4.7 29.7 1.0
CB A:GLU170 4.9 20.6 1.0
CG A:ASP139 5.0 28.3 0.0

Cadmium binding site 8 out of 18 in 2ydr

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Cadmium binding site 8 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1627

b:43.7
occ:1.00
O A:HOH2046 1.9 10.8 1.0
O A:HOH2047 2.1 24.2 1.0
OE2 A:GLU272 2.5 39.6 1.0
NE2 A:HIS276 2.6 29.9 1.0
CD A:GLU272 3.4 36.5 1.0
CD2 A:HIS276 3.5 28.4 1.0
CE1 A:HIS276 3.6 30.1 1.0
CG A:GLU272 3.9 34.1 1.0
OE1 A:GLU272 4.3 36.1 1.0
NH2 A:ARG264 4.7 39.8 1.0
CG A:HIS276 4.7 28.4 1.0
CD A:ARG228 4.7 25.9 1.0
ND1 A:HIS276 4.7 30.1 1.0
OD1 A:ASP273 5.0 32.7 1.0

Cadmium binding site 9 out of 18 in 2ydr

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Cadmium binding site 9 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1628

b:29.7
occ:1.00
OE2 A:GLU282 2.2 29.0 1.0
OD1 A:ASP286 2.4 21.0 1.0
OD2 A:ASP286 2.6 24.8 1.0
CG A:ASP286 2.8 20.9 1.0
CD A:GLU282 3.2 29.9 1.0
CG A:GLU282 3.6 26.0 1.0
CB A:ASP286 4.3 20.6 1.0
OE1 A:GLU282 4.4 30.2 1.0
O A:GLU282 4.7 22.5 1.0
NZ A:LYS322 4.7 27.7 1.0

Cadmium binding site 10 out of 18 in 2ydr

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Cadmium binding site 10 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1629

b:42.1
occ:1.00
OD2 A:ASP424 2.1 31.1 1.0
OE2 A:GLU362 2.3 32.4 1.0
OE1 A:GLU362 2.6 32.3 1.0
OD1 A:ASP424 2.8 32.4 1.0
CG A:ASP424 2.8 30.0 1.0
CD A:GLU362 2.8 30.5 1.0
O A:HOH2062 3.1 34.4 1.0
O A:HOH2057 3.6 18.5 1.0
CB A:ASP424 4.2 28.0 1.0
CG A:GLU362 4.3 27.7 1.0
O A:ASN390 4.4 24.3 1.0
O A:HOH2064 4.4 39.9 1.0
CB A:ASN390 4.8 25.9 1.0

Cadmium binding site 11 out of 18 in 2ydr

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Cadmium binding site 11 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1630

b:50.6
occ:1.00
NE2 A:HIS413 2.3 24.8 1.0
CE1 A:HIS413 3.1 24.7 1.0
CD2 A:HIS413 3.4 24.1 1.0
ND1 A:HIS413 4.3 24.3 1.0
CG A:HIS413 4.5 22.9 1.0
CG A:GLU496 4.5 35.1 1.0
CA A:ARG495 4.5 27.6 1.0
N A:GLU496 4.6 28.6 1.0
CD A:GLU496 4.6 41.9 1.0
O A:GLY494 4.8 26.4 1.0
OE2 A:GLU496 4.9 43.0 1.0
OE1 A:GLU496 5.0 43.2 1.0

Cadmium binding site 12 out of 18 in 2ydr

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Cadmium binding site 12 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1631

b:60.1
occ:1.00
O A:LYS404 2.6 22.7 1.0
NE2 A:HIS433 2.7 22.9 1.0
O A:HOH2096 3.0 20.0 1.0
O A:HOH2097 3.3 32.0 1.0
CD2 A:HIS433 3.5 23.6 1.0
C A:LYS404 3.6 21.5 1.0
CE1 A:HIS433 3.7 23.9 1.0
CA A:LYS404 3.9 21.6 1.0
OG1 A:THR400 4.0 17.4 1.0
CB A:LYS404 4.1 22.2 1.0
O A:LYS406 4.7 20.3 1.0
CG A:HIS433 4.7 23.7 1.0
N A:GLY405 4.7 20.9 1.0
CG A:LYS404 4.8 23.7 1.0
ND1 A:HIS433 4.8 24.5 1.0
CG A:GLU432 4.8 26.7 1.0
OE2 A:GLU432 4.9 32.6 1.0
CD2 A:LEU407 4.9 20.4 1.0
CD A:GLU432 5.0 30.9 1.0

Cadmium binding site 13 out of 18 in 2ydr

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Cadmium binding site 13 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1632

b:43.4
occ:1.00
OE2 A:GLU51 1.9 34.3 1.0
OD1 A:ASP452 2.2 35.1 1.0
OD1 A:ASN450 2.5 25.1 1.0
CD A:GLU51 2.5 34.0 1.0
OE1 A:GLU51 2.6 35.2 1.0
CG A:ASP452 3.1 30.6 1.0
OD2 A:ASP452 3.3 33.9 1.0
CG A:ASN450 3.5 23.3 1.0
CG A:GLU51 4.0 30.3 1.0
ND2 A:ASN450 4.0 23.6 1.0
O A:HOH2026 4.2 24.5 1.0
N A:ASN453 4.5 25.0 1.0
CB A:ASP452 4.5 26.3 1.0
N A:ASP452 4.6 25.3 1.0
CB A:ASN453 4.6 25.0 1.0
CA A:ASN450 4.6 22.8 1.0
CB A:ASN450 4.6 23.1 1.0
C A:ASN450 4.7 23.0 1.0
N A:MET451 4.8 23.4 1.0
OG1 A:THR178 4.9 21.7 1.0
CA A:ASP452 4.9 25.9 1.0

Cadmium binding site 14 out of 18 in 2ydr

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Cadmium binding site 14 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1633

b:0.7
occ:1.00
OE1 A:GLU581 2.7 48.2 0.0
CD A:GLU581 3.1 48.2 0.0
OE2 A:GLU581 3.5 48.2 0.0
CG A:GLU581 4.1 48.4 1.0

Cadmium binding site 15 out of 18 in 2ydr

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Cadmium binding site 15 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1634

b:42.0
occ:1.00
OD2 A:ASP58 2.1 34.4 1.0
O A:HOH2006 2.2 17.3 1.0
CG A:ASP58 2.8 34.1 1.0
OD1 A:ASP58 2.8 35.8 1.0
NE2 A:GLN40 3.8 40.8 1.0
CB A:ASP58 4.2 32.1 1.0
CD A:GLN40 4.7 39.7 1.0
CG A:GLN40 4.8 36.9 1.0

Cadmium binding site 16 out of 18 in 2ydr

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Cadmium binding site 16 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1635

b:0.0
occ:1.00
OD2 A:ASP266 2.7 42.0 1.0
NZ A:LYS306 2.8 39.9 1.0
CG A:ASP266 3.7 40.7 1.0
CE A:LYS306 4.1 37.2 1.0
OD1 A:ASP266 4.2 42.7 1.0
CB A:ASP266 4.8 37.8 1.0

Cadmium binding site 17 out of 18 in 2ydr

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Cadmium binding site 17 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1636

b:62.5
occ:1.00
OD2 A:ASP474 2.4 29.7 1.0
OE1 A:GLU534 2.6 42.2 1.0
OD1 A:ASP474 2.7 28.4 1.0
CG A:ASP474 2.8 28.1 1.0
OE2 A:GLU534 3.2 42.8 1.0
CD A:GLU534 3.3 40.5 1.0
NH1 A:ARG531 3.3 39.6 1.0
ND2 A:ASN538 4.0 25.1 1.0
NH2 A:ARG531 4.1 38.7 1.0
CZ A:ARG531 4.1 39.8 1.0
CB A:ASP474 4.4 26.2 1.0
CB A:ASN538 4.4 26.1 1.0
CG A:ASN538 4.4 25.6 1.0
O A:HOH2079 4.6 22.5 1.0
CA A:ALA535 4.7 27.3 1.0
CG A:GLU534 4.8 34.0 1.0
O A:GLU534 4.8 28.6 1.0

Cadmium binding site 18 out of 18 in 2ydr

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Cadmium binding site 18 out of 18 in the Cpoga D298N in Complex with P53-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 P53-Derived O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1637

b:81.2
occ:1.00
OD2 A:ASP117 3.7 39.2 1.0
CG A:ASP117 4.0 38.0 1.0
O A:HOH2015 4.1 18.3 1.0
OD1 A:ASP117 4.3 37.7 1.0
OD1 A:ASP112 4.5 45.2 1.0
O A:ILE113 4.8 40.3 1.0
CB A:ASP117 4.8 37.7 1.0
CA A:PRO114 4.9 40.9 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: Wed Oct 28 10:00:42 2020
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