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Cadmium in PDB 4zxl: Cpoga D298N in Complex with Drosophila Hcf -Derived Thr-O-Glcnac Peptide

Enzymatic activity of Cpoga D298N in Complex with Drosophila Hcf -Derived Thr-O-Glcnac Peptide

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

Protein crystallography data

The structure of Cpoga D298N in Complex with Drosophila Hcf -Derived Thr-O-Glcnac Peptide, PDB code: 4zxl was solved by N.Selvan, D.M.F.Van Aalten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.90 / 2.60
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 118.560, 118.560, 148.441, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 22

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

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

Cadmium binding site 1 out of 15 in 4zxl

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Cadmium binding site 1 out of 15 in the Cpoga D298N in Complex with Drosophila Hcf -Derived Thr-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 Drosophila Hcf -Derived Thr-O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd701

b:61.7
occ:1.00
 OD2 A:ASP58 2.0 45.6 1.0
O A:HOH857 2.3 83.1 1.0
CG A:ASP58 2.9 49.6 1.0
OD1 A:ASP58 3.2 56.1 1.0
CB A:ASP58 4.3 45.6 1.0
NE2 A:GLN40 4.3 73.8 1.0
ND2 A:ASN39 4.7 95.5 1.0
OD1 A:ASN39 4.9 88.5 1.0

Cadmium binding site 2 out of 15 in 4zxl

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Cadmium binding site 2 out of 15 in the Cpoga D298N in Complex with Drosophila Hcf -Derived Thr-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 Drosophila Hcf -Derived Thr-O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd702

b:56.7
occ:1.00
 OE2 A:GLU51 2.0 57.3 1.0
OD1 A:ASP452 2.3 49.8 1.0
OD1 A:ASN450 2.3 36.4 1.0
O A:HOH838 2.4 36.2 1.0
CD A:GLU51 2.8 55.4 1.0
OE1 A:GLU51 3.0 58.9 1.0
CG A:ASP452 3.3 51.5 1.0
CG A:ASN450 3.4 34.5 1.0
OD2 A:ASP452 3.6 57.9 1.0
ND2 A:ASN450 4.0 33.8 1.0
CG A:GLU51 4.2 49.6 1.0
N A:ASN453 4.4 35.4 1.0
N A:ASP452 4.5 40.3 1.0
CB A:ASN450 4.6 34.4 1.0
CA A:ASN450 4.6 33.9 1.0
CB A:ASP452 4.6 44.9 1.0
CB A:ASN453 4.6 37.5 1.0
C A:ASN450 4.7 35.1 1.0
N A:MET451 4.8 34.4 1.0
CA A:ASP452 4.8 42.5 1.0
C A:ASP452 5.0 38.5 1.0
OG1 A:THR178 5.0 34.8 1.0

Cadmium binding site 3 out of 15 in 4zxl

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Cadmium binding site 3 out of 15 in the Cpoga D298N in Complex with Drosophila Hcf -Derived Thr-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 Drosophila Hcf -Derived Thr-O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd703

b:50.5
occ:1.00
 OE1 A:GLU170 2.2 28.0 1.0
OE2 A:GLU170 2.4 30.0 1.0
CD A:GLU170 2.6 19.9 1.0
OD1 A:ASP139 3.7 45.9 0.0
OD1 A:ASN138 3.9 37.3 0.0
N A:ASP58 4.1 45.6 1.0
CG A:GLU170 4.2 29.8 1.0
CA A:GLY57 4.5 42.9 1.0
N A:ASP139 4.6 43.8 1.0
CG A:ASP139 4.7 47.4 0.0
N A:GLY59 4.8 41.9 1.0
C A:GLY57 4.8 45.6 1.0
O A:GLY59 4.9 42.2 1.0
CB A:GLU170 4.9 30.8 1.0
CA A:ASP139 4.9 47.8 1.0
CB A:ASP58 5.0 45.6 1.0

Cadmium binding site 4 out of 15 in 4zxl

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Cadmium binding site 4 out of 15 in the Cpoga D298N in Complex with Drosophila Hcf -Derived Thr-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 Drosophila Hcf -Derived Thr-O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd704

b:58.3
occ:1.00
 O A:LEU68 2.1 44.1 1.0
OE2 A:GLU71 2.4 44.8 1.0
O A:HOH843 2.5 55.9 1.0
OE1 A:GLU71 2.5 42.1 1.0
CD A:GLU71 2.8 32.8 1.0
O A:HOH849 2.9 47.4 1.0
C A:LEU68 3.3 42.5 1.0
OE2 A:GLU72 3.9 69.6 1.0
CA A:VAL69 4.0 39.5 1.0
N A:VAL69 4.1 41.1 1.0
OE1 A:GLU72 4.3 63.5 1.0
CG A:GLU71 4.3 40.4 1.0
CA A:LEU68 4.4 41.8 1.0
CB A:LEU68 4.5 40.5 1.0
CD A:GLU72 4.5 65.3 1.0
N A:GLY70 4.6 38.4 1.0
C A:VAL69 4.8 39.3 1.0
N A:LEU68 4.9 37.9 1.0
CG A:LEU68 4.9 40.0 1.0

Cadmium binding site 5 out of 15 in 4zxl

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Cadmium binding site 5 out of 15 in the Cpoga D298N in Complex with Drosophila Hcf -Derived Thr-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 Drosophila Hcf -Derived Thr-O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd705

b:46.2
occ:1.00
 OE1 A:GLU108 2.1 47.9 1.0
O A:GLU73 2.2 38.0 1.0
O A:HOH803 2.3 31.6 1.0
OD1 A:ASP111 2.6 38.2 1.0
O A:HOH861 2.7 31.6 1.0
OD2 A:ASP111 2.9 44.3 1.0
CG A:ASP111 3.1 41.8 1.0
CD A:GLU108 3.3 45.1 1.0
C A:GLU73 3.4 41.3 1.0
CA A:ALA74 4.0 36.6 1.0
OE2 A:GLU108 4.1 39.0 1.0
C A:ALA74 4.2 37.4 1.0
N A:ALA74 4.2 36.5 1.0
CG A:GLU108 4.2 43.0 1.0
OD1 A:ASP110 4.3 46.4 1.0
CB A:GLU108 4.3 38.5 1.0
N A:ASP75 4.4 37.6 1.0
CA A:GLU73 4.5 51.9 1.0
O A:ALA74 4.5 41.9 1.0
CB A:ASP111 4.6 40.0 1.0
CB A:GLU73 4.8 59.1 1.0
N A:GLU108 4.9 31.2 1.0

Cadmium binding site 6 out of 15 in 4zxl

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Cadmium binding site 6 out of 15 in the Cpoga D298N in Complex with Drosophila Hcf -Derived Thr-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 Drosophila Hcf -Derived Thr-O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd706

b:43.0
occ:1.00
 OD1 A:ASP117 2.1 45.2 1.0
OE2 A:GLU145 2.4 46.8 1.0
O A:HOH867 2.7 41.6 1.0
O A:HOH840 2.9 48.6 1.0
CG A:ASP117 2.9 48.3 1.0
OE1 A:GLU145 3.1 39.9 1.0
CD A:GLU145 3.2 44.3 1.0
OD2 A:ASP117 3.2 51.6 1.0
OG1 A:THR124 4.2 34.7 1.0
CB A:ASP117 4.3 42.9 1.0
CD1 A:LEU120 4.6 36.5 1.0
CG A:GLU145 4.6 39.3 1.0
CA A:ASP117 4.7 40.4 1.0
CG2 A:VAL109 4.9 32.6 1.0

Cadmium binding site 7 out of 15 in 4zxl

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Cadmium binding site 7 out of 15 in the Cpoga D298N in Complex with Drosophila Hcf -Derived Thr-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 Drosophila Hcf -Derived Thr-O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd707

b:58.5
occ:1.00
 OD2 A:ASP139 2.2 47.6 0.0
CG A:ASP139 2.6 47.4 0.0
OD1 A:ASP139 2.7 45.9 0.0
ND2 A:ASN138 3.8 37.9 0.0
CB A:ASP139 4.0 44.4 1.0
CG A:ASN138 4.6 38.7 0.0
OD1 A:ASN138 4.7 37.3 0.0

Cadmium binding site 8 out of 15 in 4zxl

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Cadmium binding site 8 out of 15 in the Cpoga D298N in Complex with Drosophila Hcf -Derived Thr-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 Drosophila Hcf -Derived Thr-O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd708

b:71.0
occ:1.00
 OD1 A:ASP252 2.4 36.0 1.0
CG A:ASP252 3.2 38.3 1.0
OD2 A:ASP252 3.2 44.4 1.0
O A:HOH802 3.3 30.7 1.0
OD2 A:ASP150 3.5 38.5 1.0
O A:HOH822 3.5 28.2 1.0
O A:HOH868 3.9 32.0 1.0
OD1 A:ASP150 4.2 43.1 1.0
CG A:ASP150 4.2 38.1 1.0
NZ A:LYS326 4.3 59.9 1.0
O A:LYS250 4.5 33.1 1.0
CB A:ASP252 4.6 34.1 1.0
CE A:LYS326 4.9 50.4 1.0

Cadmium binding site 9 out of 15 in 4zxl

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Cadmium binding site 9 out of 15 in the Cpoga D298N in Complex with Drosophila Hcf -Derived Thr-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 Drosophila Hcf -Derived Thr-O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd709

b:63.1
occ:1.00
 OE1 A:GLU272 2.2 57.9 1.0
NE2 A:HIS276 2.5 46.8 1.0
CD A:GLU272 3.3 51.5 1.0
CD2 A:HIS276 3.4 50.0 1.0
CE1 A:HIS276 3.4 50.7 1.0
CG A:GLU272 3.8 53.8 1.0
OE2 A:GLU272 4.3 49.0 1.0
CD A:ARG228 4.5 37.6 1.0
ND1 A:HIS276 4.5 55.9 1.0
CG A:HIS276 4.5 51.0 1.0
NH2 A:ARG264 4.9 66.9 1.0

Cadmium binding site 10 out of 15 in 4zxl

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Cadmium binding site 10 out of 15 in the Cpoga D298N in Complex with Drosophila Hcf -Derived Thr-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 Drosophila Hcf -Derived Thr-O-Glcnac Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd710

b:47.9
occ:1.00
 O A:HOH807 2.2 23.6 1.0
OE1 A:GLU282 2.3 54.7 1.0
OD1 A:ASP286 2.4 37.1 1.0
OD2 A:ASP286 2.5 40.5 1.0
CG A:ASP286 2.8 37.5 1.0
CD A:GLU282 3.3 51.6 1.0
OE2 A:GLU282 3.7 51.1 1.0
CB A:ASP286 4.3 34.2 1.0
CG A:GLU282 4.6 52.8 1.0
NZ A:LYS322 4.7 38.1 1.0
O A:GLU282 4.8 40.4 1.0

Reference:

D.Mariappa, N.Selvan, V.S.Borodkin, J.Alonso, A.T.Ferenbach, C.Shepherd, I.H.Navratilova, D.M.Van Aalten. A Mutant O-Glcnacase As A Probe to Reveal Global Dynamics of Protein O-Glcnacylation During Drosophila Embryonic Development. Biochem.J. V. 470 255 2015.
ISSN: ESSN 1470-8728
PubMed: 26348912
DOI: 10.1042/BJ20150610
Page generated: Thu Jul 10 14:07:38 2025

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