Vanadium in PDB 1dkt: CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate
Protein crystallography data
The structure of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate, PDB code: 1dkt
was solved by
Y.Bourne,
A.S.Arvai,
J.A.Tainer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
6.00 /
2.90
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.000,
94.000,
131.600,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19.5 /
25.8
|
Vanadium Binding Sites:
The binding sites of Vanadium atom in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate
(pdb code 1dkt). This binding sites where shown within
5.0 Angstroms radius around Vanadium atom.
In total 7 binding sites of Vanadium where determined in the
CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate, PDB code: 1dkt:
Jump to Vanadium binding site number:
1;
2;
3;
4;
5;
6;
7;
Vanadium binding site 1 out
of 7 in 1dkt
Go back to
Vanadium Binding Sites List in 1dkt
Vanadium binding site 1 out
of 7 in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate
Mono view
Stereo pair view
|
A full contact list of Vanadium with other atoms in the V binding
site number 1 of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:V100
b:18.1
occ:1.00
|
V1
|
A:V7O100
|
0.0
|
18.1
|
1.0
|
O3
|
A:V7O100
|
1.5
|
24.9
|
1.0
|
O1
|
A:V7O100
|
1.6
|
37.9
|
1.0
|
O2
|
A:V7O100
|
1.7
|
18.5
|
1.0
|
O4
|
A:V7O100
|
1.7
|
18.1
|
1.0
|
V2
|
A:V7O100
|
3.0
|
22.1
|
1.0
|
V3
|
A:V7O100
|
3.2
|
17.8
|
1.0
|
OG
|
A:SER51
|
3.3
|
52.3
|
1.0
|
CB
|
A:SER51
|
3.4
|
44.9
|
1.0
|
NH1
|
A:ARG71
|
3.4
|
24.7
|
1.0
|
O
|
A:HOH561
|
3.8
|
75.1
|
1.0
|
O6
|
A:V7O100
|
3.8
|
25.3
|
1.0
|
O7
|
A:V7O100
|
3.9
|
23.4
|
1.0
|
O
|
A:HOH559
|
3.9
|
15.6
|
1.0
|
O
|
A:HOH581
|
4.1
|
58.3
|
1.0
|
O
|
A:HOH583
|
4.2
|
2.4
|
1.0
|
O5
|
A:V7O100
|
4.3
|
27.9
|
1.0
|
CZ
|
A:ARG71
|
4.4
|
30.4
|
1.0
|
O8
|
A:V7O100
|
4.4
|
5.3
|
1.0
|
O9
|
A:V7O100
|
4.5
|
10.7
|
1.0
|
NH2
|
A:ARG71
|
4.5
|
28.3
|
1.0
|
CA
|
A:SER51
|
4.6
|
40.5
|
1.0
|
|
Vanadium binding site 2 out
of 7 in 1dkt
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Vanadium Binding Sites List in 1dkt
Vanadium binding site 2 out
of 7 in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate
Mono view
Stereo pair view
|
A full contact list of Vanadium with other atoms in the V binding
site number 2 of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:V100
b:22.1
occ:1.00
|
V2
|
A:V7O100
|
0.0
|
22.1
|
1.0
|
O5
|
A:V7O100
|
1.6
|
27.9
|
1.0
|
O6
|
A:V7O100
|
1.6
|
25.3
|
1.0
|
O4
|
A:V7O100
|
1.9
|
18.1
|
1.0
|
NH2
|
A:ARG71
|
3.0
|
28.3
|
1.0
|
O2
|
A:V7O100
|
3.0
|
18.5
|
1.0
|
V1
|
A:V7O100
|
3.0
|
18.1
|
1.0
|
V3
|
A:V7O100
|
3.1
|
17.8
|
1.0
|
O8
|
A:V7O100
|
3.3
|
5.3
|
1.0
|
CZ
|
A:ARG71
|
3.7
|
30.4
|
1.0
|
NH1
|
A:ARG71
|
3.7
|
24.7
|
1.0
|
O9
|
A:V7O100
|
3.8
|
10.7
|
1.0
|
O
|
A:HOH583
|
3.8
|
2.4
|
1.0
|
O1
|
A:V7O100
|
3.8
|
37.9
|
1.0
|
O
|
A:HOH560
|
3.9
|
21.0
|
1.0
|
O3
|
A:V7O100
|
4.2
|
24.9
|
1.0
|
O7
|
A:V7O100
|
4.7
|
23.4
|
1.0
|
O
|
A:HOH559
|
4.8
|
15.6
|
1.0
|
NE
|
A:ARG71
|
4.9
|
29.8
|
1.0
|
CE
|
A:LYS11
|
5.0
|
18.0
|
1.0
|
|
Vanadium binding site 3 out
of 7 in 1dkt
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Vanadium Binding Sites List in 1dkt
Vanadium binding site 3 out
of 7 in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate
Mono view
Stereo pair view
|
A full contact list of Vanadium with other atoms in the V binding
site number 3 of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:V100
b:17.8
occ:1.00
|
V3
|
A:V7O100
|
0.0
|
17.8
|
1.0
|
O8
|
A:V7O100
|
1.5
|
5.3
|
1.0
|
O7
|
A:V7O100
|
1.7
|
23.4
|
1.0
|
O9
|
A:V7O100
|
1.7
|
10.7
|
1.0
|
O4
|
A:V7O100
|
1.8
|
18.1
|
1.0
|
O
|
A:HOH559
|
3.1
|
15.6
|
1.0
|
V2
|
A:V7O100
|
3.1
|
22.1
|
1.0
|
V1
|
A:V7O100
|
3.2
|
18.1
|
1.0
|
O2
|
A:V7O100
|
3.3
|
18.5
|
1.0
|
V4
|
A:V7O100
|
3.3
|
21.2
|
1.0
|
NH1
|
A:ARG71
|
3.4
|
24.7
|
1.0
|
O3
|
A:V7O100
|
3.4
|
24.9
|
1.0
|
O5
|
A:V7O100
|
3.5
|
27.9
|
1.0
|
NH2
|
A:ARG71
|
3.7
|
28.3
|
1.0
|
CB
|
A:SER51
|
3.9
|
44.9
|
1.0
|
NE1
|
A:TRP54
|
3.9
|
12.4
|
1.0
|
O10
|
A:V7O100
|
4.0
|
27.2
|
1.0
|
CZ
|
A:ARG71
|
4.0
|
30.4
|
1.0
|
NH1
|
A:ARG20
|
4.1
|
28.6
|
1.0
|
O11
|
A:V7O100
|
4.2
|
7.1
|
1.0
|
O
|
A:HOH551
|
4.3
|
47.0
|
1.0
|
O6
|
A:V7O100
|
4.3
|
25.3
|
1.0
|
CE
|
A:LYS11
|
4.4
|
18.0
|
1.0
|
O
|
A:HOH560
|
4.5
|
21.0
|
1.0
|
NZ
|
A:LYS11
|
4.6
|
25.3
|
1.0
|
OG
|
A:SER51
|
4.7
|
52.3
|
1.0
|
N
|
A:SER51
|
4.7
|
36.1
|
1.0
|
O1
|
A:V7O100
|
4.7
|
37.9
|
1.0
|
CE2
|
A:TRP54
|
4.8
|
2.0
|
1.0
|
CZ2
|
A:TRP54
|
4.8
|
2.9
|
1.0
|
CA
|
A:SER51
|
4.9
|
40.5
|
1.0
|
O12
|
A:V7O100
|
4.9
|
4.7
|
1.0
|
CD1
|
A:TRP54
|
4.9
|
9.9
|
1.0
|
O
|
A:HOH583
|
4.9
|
2.4
|
1.0
|
|
Vanadium binding site 4 out
of 7 in 1dkt
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Vanadium Binding Sites List in 1dkt
Vanadium binding site 4 out
of 7 in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate
Mono view
Stereo pair view
|
A full contact list of Vanadium with other atoms in the V binding
site number 4 of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:V100
b:21.2
occ:1.00
|
V4
|
A:V7O100
|
0.0
|
21.2
|
1.0
|
O11
|
A:V7O100
|
1.5
|
7.1
|
1.0
|
O10
|
A:V7O100
|
1.5
|
27.2
|
1.0
|
O12
|
A:V7O100
|
1.8
|
4.7
|
1.0
|
O9
|
A:V7O100
|
1.8
|
10.7
|
1.0
|
O
|
A:HOH559
|
2.9
|
15.6
|
1.0
|
V5
|
A:V7O100
|
3.1
|
21.9
|
1.0
|
V3
|
A:V7O100
|
3.3
|
17.8
|
1.0
|
O
|
A:HOH551
|
3.3
|
47.0
|
1.0
|
O8
|
A:V7O100
|
3.4
|
5.3
|
1.0
|
O7
|
A:V7O100
|
3.6
|
23.4
|
1.0
|
O16
|
A:V7O100
|
3.8
|
20.0
|
1.0
|
O
|
A:HOH560
|
4.1
|
21.0
|
1.0
|
O13
|
A:V7O100
|
4.1
|
2.0
|
1.0
|
O
|
A:HOH552
|
4.2
|
43.1
|
1.0
|
O14
|
A:V7O100
|
4.2
|
17.7
|
1.0
|
NZ
|
A:LYS11
|
4.3
|
25.3
|
1.0
|
O15
|
A:V7O100
|
4.5
|
18.0
|
1.0
|
V6
|
A:V7O100
|
4.5
|
16.8
|
1.0
|
NH1
|
A:ARG20
|
4.5
|
28.6
|
1.0
|
NH2
|
A:ARG20
|
4.6
|
35.0
|
1.0
|
O4
|
A:V7O100
|
4.6
|
18.1
|
1.0
|
O
|
A:HOH547
|
4.7
|
31.9
|
1.0
|
NH2
|
B:ARG20
|
4.7
|
41.7
|
1.0
|
O
|
A:HOH558
|
4.9
|
45.1
|
1.0
|
CZ
|
A:ARG20
|
4.9
|
28.3
|
1.0
|
O5
|
A:V7O100
|
5.0
|
27.9
|
1.0
|
|
Vanadium binding site 5 out
of 7 in 1dkt
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Vanadium Binding Sites List in 1dkt
Vanadium binding site 5 out
of 7 in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate
Mono view
Stereo pair view
|
A full contact list of Vanadium with other atoms in the V binding
site number 5 of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:V100
b:21.9
occ:1.00
|
V5
|
A:V7O100
|
0.0
|
21.9
|
1.0
|
O13
|
A:V7O100
|
1.5
|
2.0
|
1.0
|
O12
|
A:V7O100
|
1.7
|
4.7
|
1.0
|
O14
|
A:V7O100
|
1.7
|
17.7
|
1.0
|
V4
|
A:V7O100
|
3.1
|
21.2
|
1.0
|
V6
|
A:V7O100
|
3.1
|
16.8
|
1.0
|
O15
|
A:V7O100
|
3.1
|
18.0
|
1.0
|
V7
|
A:V7O100
|
3.2
|
22.9
|
1.0
|
O
|
A:HOH559
|
3.2
|
15.6
|
1.0
|
O17
|
A:V7O100
|
3.3
|
22.1
|
1.0
|
O16
|
A:V7O100
|
3.5
|
20.0
|
1.0
|
O11
|
A:V7O100
|
3.6
|
7.1
|
1.0
|
NH2
|
B:ARG20
|
3.9
|
41.7
|
1.0
|
O19
|
A:V7O100
|
4.0
|
28.5
|
1.0
|
O
|
A:HOH560
|
4.1
|
21.0
|
1.0
|
O18
|
A:V7O100
|
4.1
|
18.6
|
1.0
|
O9
|
A:V7O100
|
4.2
|
10.7
|
1.0
|
O10
|
A:V7O100
|
4.2
|
27.2
|
1.0
|
NZ
|
B:LYS11
|
4.2
|
43.4
|
1.0
|
NH1
|
B:ARG71
|
4.4
|
24.6
|
1.0
|
NH2
|
B:ARG71
|
4.4
|
31.2
|
1.0
|
O
|
A:HOH556
|
4.4
|
43.2
|
1.0
|
NE1
|
B:TRP54
|
4.8
|
16.6
|
1.0
|
CE
|
B:LYS11
|
4.8
|
37.2
|
1.0
|
CZ
|
B:ARG71
|
4.8
|
29.8
|
1.0
|
O
|
A:HOH583
|
4.9
|
2.4
|
1.0
|
O
|
A:HOH558
|
4.9
|
45.1
|
1.0
|
|
Vanadium binding site 6 out
of 7 in 1dkt
Go back to
Vanadium Binding Sites List in 1dkt
Vanadium binding site 6 out
of 7 in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate
Mono view
Stereo pair view
|
A full contact list of Vanadium with other atoms in the V binding
site number 6 of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:V100
b:16.8
occ:1.00
|
V6
|
A:V7O100
|
0.0
|
16.8
|
1.0
|
O15
|
A:V7O100
|
1.5
|
18.0
|
1.0
|
O16
|
A:V7O100
|
1.5
|
20.0
|
1.0
|
O14
|
A:V7O100
|
1.8
|
17.7
|
1.0
|
V7
|
A:V7O100
|
2.8
|
22.9
|
1.0
|
O18
|
A:V7O100
|
2.9
|
18.6
|
1.0
|
OG
|
B:SER51
|
3.0
|
33.0
|
1.0
|
O
|
A:HOH560
|
3.0
|
21.0
|
1.0
|
V5
|
A:V7O100
|
3.1
|
21.9
|
1.0
|
CB
|
B:SER51
|
3.1
|
39.8
|
1.0
|
O12
|
A:V7O100
|
3.4
|
4.7
|
1.0
|
N
|
B:SER51
|
3.6
|
40.3
|
1.0
|
O17
|
A:V7O100
|
3.8
|
22.1
|
1.0
|
NE1
|
B:TRP54
|
3.9
|
16.6
|
1.0
|
O13
|
A:V7O100
|
3.9
|
2.0
|
1.0
|
NH1
|
B:ARG71
|
4.0
|
24.6
|
1.0
|
CA
|
B:SER51
|
4.0
|
42.3
|
1.0
|
O11
|
A:V7O100
|
4.1
|
7.1
|
1.0
|
CD1
|
B:TRP54
|
4.3
|
16.3
|
1.0
|
O19
|
A:V7O100
|
4.3
|
28.5
|
1.0
|
V4
|
A:V7O100
|
4.5
|
21.2
|
1.0
|
NH2
|
B:ARG20
|
4.7
|
41.7
|
1.0
|
C
|
B:GLN50
|
4.7
|
38.1
|
1.0
|
O
|
A:HOH582
|
4.8
|
51.8
|
1.0
|
O
|
A:HOH583
|
4.9
|
2.4
|
1.0
|
|
Vanadium binding site 7 out
of 7 in 1dkt
Go back to
Vanadium Binding Sites List in 1dkt
Vanadium binding site 7 out
of 7 in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate
Mono view
Stereo pair view
|
A full contact list of Vanadium with other atoms in the V binding
site number 7 of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:V100
b:22.9
occ:1.00
|
V7
|
A:V7O100
|
0.0
|
22.9
|
1.0
|
O18
|
A:V7O100
|
1.5
|
18.6
|
1.0
|
O19
|
A:V7O100
|
1.5
|
28.5
|
1.0
|
O17
|
A:V7O100
|
1.7
|
22.1
|
1.0
|
O14
|
A:V7O100
|
1.7
|
17.7
|
1.0
|
V6
|
A:V7O100
|
2.8
|
16.8
|
1.0
|
NH1
|
B:ARG71
|
2.9
|
24.6
|
1.0
|
V5
|
A:V7O100
|
3.2
|
21.9
|
1.0
|
OG
|
B:SER51
|
3.4
|
33.0
|
1.0
|
O15
|
A:V7O100
|
3.8
|
18.0
|
1.0
|
O
|
A:HOH556
|
3.8
|
43.2
|
1.0
|
O13
|
A:V7O100
|
3.8
|
2.0
|
1.0
|
CZ
|
B:ARG71
|
3.8
|
29.8
|
1.0
|
NH2
|
B:ARG71
|
3.9
|
31.2
|
1.0
|
O
|
B:HOH555
|
3.9
|
38.7
|
1.0
|
O
|
A:HOH560
|
3.9
|
21.0
|
1.0
|
CB
|
B:SER51
|
3.9
|
39.8
|
1.0
|
O
|
A:HOH583
|
4.0
|
2.4
|
1.0
|
O16
|
A:V7O100
|
4.2
|
20.0
|
1.0
|
O
|
A:HOH557
|
4.3
|
36.6
|
1.0
|
O
|
A:HOH582
|
4.5
|
51.8
|
1.0
|
O12
|
A:V7O100
|
4.6
|
4.7
|
1.0
|
NE1
|
B:TRP54
|
4.8
|
16.6
|
1.0
|
O
|
A:HOH581
|
4.8
|
58.3
|
1.0
|
O
|
A:HOH559
|
4.9
|
15.6
|
1.0
|
|
Reference:
A.S.Arvai,
Y.Bourne,
M.J.Hickey,
J.A.Tainer.
Crystal Structure of the Human Cell Cycle Protein CKSHS1: Single Domain Fold with Similarity to Kinase N-Lobe Domain. J.Mol.Biol. V. 249 835 1995.
ISSN: ISSN 0022-2836
PubMed: 7791211
DOI: 10.1006/JMBI.1995.0341
Page generated: Fri Oct 11 11:22:30 2024
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