Cadmium in PDB 2yds: Cpoga D298N in Complex with TAB1-Derived O-Glcnac Peptide
Enzymatic activity of Cpoga D298N in Complex with TAB1-Derived O-Glcnac Peptide
All present enzymatic activity of Cpoga D298N in Complex with TAB1-Derived O-Glcnac Peptide:
3.2.1.169;
Protein crystallography data
The structure of Cpoga D298N in Complex with TAB1-Derived O-Glcnac Peptide, PDB code: 2yds
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 /
2.55
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
118.090,
118.090,
148.260,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.007 /
23.846
|
Cadmium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
19;
Binding sites:
The binding sites of Cadmium atom in the Cpoga D298N in Complex with TAB1-Derived O-Glcnac Peptide
(pdb code 2yds). 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 TAB1-Derived O-Glcnac Peptide, PDB code: 2yds:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Cadmium binding site 1 out
of 19 in 2yds
Go back to
Cadmium Binding Sites List in 2yds
Cadmium binding site 1 out
of 19 in the Cpoga D298N in Complex with TAB1-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 TAB1-Derived O-Glcnac Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1619
b:55.3
occ:1.00
|
OE2
|
A:GLU51
|
1.5
|
42.6
|
1.0
|
O
|
A:HOH2004
|
1.9
|
21.8
|
1.0
|
OD1
|
A:ASP452
|
2.3
|
40.7
|
1.0
|
OD1
|
A:ASN450
|
2.6
|
34.9
|
1.0
|
CD
|
A:GLU51
|
2.7
|
42.9
|
1.0
|
CG
|
A:ASP452
|
3.3
|
39.4
|
1.0
|
OE1
|
A:GLU51
|
3.4
|
45.5
|
1.0
|
CG
|
A:ASN450
|
3.5
|
33.3
|
1.0
|
OD2
|
A:ASP452
|
3.6
|
43.4
|
1.0
|
CG
|
A:GLU51
|
3.9
|
39.4
|
1.0
|
ND2
|
A:ASN450
|
4.0
|
32.7
|
1.0
|
O
|
A:HOH2034
|
4.0
|
43.2
|
1.0
|
N
|
A:ASP452
|
4.5
|
36.2
|
1.0
|
CA
|
A:ASN450
|
4.5
|
32.8
|
1.0
|
N
|
A:ASN453
|
4.5
|
35.8
|
1.0
|
CB
|
A:ASN450
|
4.6
|
32.8
|
1.0
|
O
|
A:HOH2005
|
4.6
|
31.1
|
1.0
|
C
|
A:ASN450
|
4.6
|
33.2
|
1.0
|
CB
|
A:ASP452
|
4.6
|
37.0
|
1.0
|
CB
|
A:ASN453
|
4.8
|
35.4
|
1.0
|
N
|
A:MET451
|
4.8
|
33.8
|
1.0
|
CA
|
A:ASP452
|
4.9
|
36.8
|
1.0
|
OG1
|
A:THR178
|
4.9
|
31.6
|
1.0
|
|
Cadmium binding site 2 out
of 19 in 2yds
Go back to
Cadmium Binding Sites List in 2yds
Cadmium binding site 2 out
of 19 in the Cpoga D298N in Complex with TAB1-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 TAB1-Derived O-Glcnac Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1620
b:0.8
occ:1.00
|
OE1
|
A:GLU54
|
3.1
|
57.2
|
1.0
|
OE2
|
A:GLU54
|
3.1
|
58.5
|
1.0
|
CD
|
A:GLU54
|
3.4
|
54.8
|
1.0
|
CG
|
A:GLU54
|
4.8
|
44.4
|
1.0
|
|
Cadmium binding site 3 out
of 19 in 2yds
Go back to
Cadmium Binding Sites List in 2yds
Cadmium binding site 3 out
of 19 in the Cpoga D298N in Complex with TAB1-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 TAB1-Derived O-Glcnac Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1621
b:54.6
occ:1.00
|
OD2
|
A:ASP58
|
2.1
|
39.5
|
1.0
|
O
|
A:HOH2001
|
2.2
|
48.6
|
1.0
|
CG
|
A:ASP58
|
2.8
|
39.4
|
1.0
|
OD1
|
A:ASP58
|
2.8
|
41.3
|
1.0
|
ND2
|
A:ASN39
|
4.3
|
58.9
|
1.0
|
CB
|
A:ASP58
|
4.3
|
37.6
|
1.0
|
OD1
|
A:ASN39
|
4.4
|
58.1
|
1.0
|
NE2
|
A:GLN40
|
4.6
|
51.9
|
1.0
|
CG
|
A:ASN39
|
4.8
|
54.9
|
1.0
|
O
|
A:HOH2007
|
4.9
|
18.8
|
1.0
|
|
Cadmium binding site 4 out
of 19 in 2yds
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Cadmium Binding Sites List in 2yds
Cadmium binding site 4 out
of 19 in the Cpoga D298N in Complex with TAB1-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 TAB1-Derived O-Glcnac Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1622
b:57.8
occ:1.00
|
OE1
|
A:GLU71
|
2.4
|
47.8
|
1.0
|
O
|
A:LEU68
|
2.4
|
37.6
|
1.0
|
O
|
A:HOH2009
|
2.5
|
33.3
|
1.0
|
OE2
|
A:GLU71
|
2.7
|
47.4
|
1.0
|
CD
|
A:GLU71
|
2.9
|
48.0
|
1.0
|
C
|
A:LEU68
|
3.5
|
36.6
|
1.0
|
OE2
|
A:GLU72
|
3.6
|
53.5
|
1.0
|
CA
|
A:VAL69
|
4.0
|
35.5
|
1.0
|
OE1
|
A:GLU72
|
4.1
|
53.4
|
1.0
|
N
|
A:VAL69
|
4.2
|
36.2
|
1.0
|
CD
|
A:GLU72
|
4.2
|
52.6
|
1.0
|
O
|
A:HOH2016
|
4.2
|
31.2
|
1.0
|
CG
|
A:GLU71
|
4.5
|
43.3
|
1.0
|
N
|
A:GLY70
|
4.6
|
36.1
|
1.0
|
CA
|
A:LEU68
|
4.7
|
36.8
|
1.0
|
C
|
A:VAL69
|
4.7
|
36.0
|
1.0
|
CB
|
A:LEU68
|
4.8
|
36.8
|
1.0
|
|
Cadmium binding site 5 out
of 19 in 2yds
Go back to
Cadmium Binding Sites List in 2yds
Cadmium binding site 5 out
of 19 in the Cpoga D298N in Complex with TAB1-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 TAB1-Derived O-Glcnac Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1623
b:46.9
occ:1.00
|
O
|
A:HOH2019
|
2.0
|
35.5
|
1.0
|
O
|
A:GLU73
|
2.3
|
38.5
|
1.0
|
OE1
|
A:GLU108
|
2.4
|
42.6
|
1.0
|
OD1
|
A:ASP111
|
2.6
|
42.9
|
1.0
|
OD2
|
A:ASP111
|
2.8
|
41.0
|
1.0
|
CG
|
A:ASP111
|
3.0
|
39.9
|
1.0
|
C
|
A:GLU73
|
3.4
|
39.0
|
1.0
|
CD
|
A:GLU108
|
3.6
|
39.0
|
1.0
|
OD1
|
A:ASP110
|
4.1
|
44.3
|
1.0
|
CA
|
A:ALA74
|
4.1
|
37.6
|
1.0
|
N
|
A:ALA74
|
4.2
|
38.2
|
1.0
|
C
|
A:ALA74
|
4.3
|
37.5
|
1.0
|
OE2
|
A:GLU108
|
4.3
|
35.5
|
1.0
|
O
|
A:HOH2010
|
4.4
|
47.1
|
1.0
|
N
|
A:ASP75
|
4.4
|
37.2
|
1.0
|
CA
|
A:GLU73
|
4.5
|
40.3
|
1.0
|
CG
|
A:GLU108
|
4.5
|
35.0
|
1.0
|
CB
|
A:ASP111
|
4.5
|
38.3
|
1.0
|
CB
|
A:GLU108
|
4.5
|
32.7
|
1.0
|
CB
|
A:GLU73
|
4.6
|
41.5
|
1.0
|
O
|
A:ALA74
|
4.8
|
37.4
|
1.0
|
N
|
A:GLU108
|
4.9
|
31.9
|
1.0
|
|
Cadmium binding site 6 out
of 19 in 2yds
Go back to
Cadmium Binding Sites List in 2yds
Cadmium binding site 6 out
of 19 in the Cpoga D298N in Complex with TAB1-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 TAB1-Derived O-Glcnac Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1624
b:40.1
occ:1.00
|
O
|
A:HOH2021
|
1.9
|
13.5
|
1.0
|
OD2
|
A:ASP112
|
2.2
|
47.8
|
1.0
|
O
|
A:HOH2020
|
2.6
|
29.6
|
1.0
|
CG
|
A:ASP112
|
3.4
|
43.9
|
1.0
|
OD1
|
A:ASP112
|
3.9
|
46.5
|
1.0
|
CB
|
A:ASP112
|
4.7
|
41.0
|
1.0
|
|
Cadmium binding site 7 out
of 19 in 2yds
Go back to
Cadmium Binding Sites List in 2yds
Cadmium binding site 7 out
of 19 in the Cpoga D298N in Complex with TAB1-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 TAB1-Derived O-Glcnac Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1625
b:46.4
occ:1.00
|
OD1
|
A:ASP117
|
2.1
|
39.5
|
1.0
|
OE2
|
A:GLU145
|
2.5
|
42.4
|
1.0
|
CG
|
A:ASP117
|
2.8
|
40.4
|
1.0
|
OD2
|
A:ASP117
|
2.8
|
42.8
|
1.0
|
CD
|
A:GLU145
|
3.3
|
37.8
|
1.0
|
OE1
|
A:GLU145
|
3.4
|
38.6
|
1.0
|
OG1
|
A:THR124
|
3.7
|
40.1
|
1.0
|
CB
|
A:ASP117
|
4.3
|
38.7
|
1.0
|
CB
|
A:THR124
|
4.8
|
38.7
|
1.0
|
CG
|
A:GLU145
|
4.8
|
33.6
|
1.0
|
CD1
|
A:LEU120
|
4.8
|
36.2
|
1.0
|
CA
|
A:ASP117
|
4.9
|
38.4
|
1.0
|
CA
|
A:VAL109
|
4.9
|
35.0
|
1.0
|
|
Cadmium binding site 8 out
of 19 in 2yds
Go back to
Cadmium Binding Sites List in 2yds
Cadmium binding site 8 out
of 19 in the Cpoga D298N in Complex with TAB1-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 TAB1-Derived O-Glcnac Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1626
b:52.9
occ:1.00
|
OD1
|
A:ASP139
|
2.5
|
36.9
|
0.0
|
OD2
|
A:ASP139
|
2.5
|
37.0
|
0.0
|
CG
|
A:ASP139
|
2.8
|
37.1
|
0.0
|
ND2
|
A:ASN138
|
3.2
|
35.2
|
0.0
|
CB
|
A:ASP139
|
4.2
|
37.3
|
1.0
|
CG
|
A:ASN138
|
4.5
|
35.3
|
0.0
|
O
|
A:HOH2026
|
4.6
|
19.3
|
1.0
|
O
|
A:HOH2027
|
4.9
|
27.3
|
1.0
|
OD1
|
A:ASN138
|
4.9
|
35.1
|
0.0
|
|
Cadmium binding site 9 out
of 19 in 2yds
Go back to
Cadmium Binding Sites List in 2yds
Cadmium binding site 9 out
of 19 in the Cpoga D298N in Complex with TAB1-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 TAB1-Derived O-Glcnac Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1627
b:67.8
occ:1.00
|
OD1
|
A:ASP252
|
2.6
|
39.8
|
1.0
|
CG
|
A:ASP252
|
3.4
|
35.0
|
1.0
|
OD2
|
A:ASP252
|
3.4
|
38.6
|
1.0
|
OD2
|
A:ASP150
|
3.8
|
40.5
|
1.0
|
OD1
|
A:ASP150
|
3.9
|
39.0
|
1.0
|
CG
|
A:ASP150
|
4.2
|
37.2
|
1.0
|
NZ
|
A:LYS326
|
4.2
|
49.0
|
1.0
|
O
|
A:LYS250
|
4.6
|
31.1
|
1.0
|
CB
|
A:ASP252
|
4.8
|
31.5
|
1.0
|
|
Cadmium binding site 10 out
of 19 in 2yds
Go back to
Cadmium Binding Sites List in 2yds
Cadmium binding site 10 out
of 19 in the Cpoga D298N in Complex with TAB1-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 TAB1-Derived O-Glcnac Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1628
b:36.1
occ:1.00
|
O
|
A:HOH2033
|
2.0
|
27.8
|
1.0
|
O
|
A:HOH2026
|
2.1
|
19.3
|
1.0
|
O
|
A:HOH2027
|
2.3
|
27.3
|
1.0
|
OE1
|
A:GLU170
|
2.3
|
33.3
|
1.0
|
OE2
|
A:GLU170
|
2.5
|
31.3
|
1.0
|
CD
|
A:GLU170
|
2.8
|
32.5
|
1.0
|
O
|
A:HOH2007
|
3.1
|
18.8
|
1.0
|
N
|
A:ASP58
|
4.2
|
36.1
|
1.0
|
OD1
|
A:ASP139
|
4.2
|
36.9
|
0.0
|
CG
|
A:GLU170
|
4.3
|
30.7
|
1.0
|
OD1
|
A:ASN138
|
4.3
|
35.1
|
0.0
|
CA
|
A:GLY57
|
4.5
|
34.2
|
1.0
|
N
|
A:ASP139
|
4.7
|
36.7
|
1.0
|
O
|
A:GLY59
|
4.7
|
37.4
|
1.0
|
N
|
A:GLY59
|
4.8
|
37.3
|
1.0
|
C
|
A:GLY57
|
4.8
|
35.2
|
1.0
|
CG
|
A:ASN138
|
4.9
|
35.3
|
0.0
|
|
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 Jul 19 15:29:30 2024
|