Atomistry » Vanadium » PDB 1b8j-1yv3 » 1dkt
Atomistry »
  Vanadium »
    PDB 1b8j-1yv3 »
      1dkt »

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

Go back to 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

Go back to 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

Go back to 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

Go back to 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: Wed Dec 16 02:30:04 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy