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Chlorine in PDB 6ac9: Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp

Enzymatic activity of Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp

All present enzymatic activity of Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp, PDB code: 6ac9 was solved by Y.S.Ngow, R.Sreekanth, H.S.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.596, 96.846, 192.520, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.3

Other elements in 6ac9:

The structure of Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp (pdb code 6ac9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp, PDB code: 6ac9:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6ac9

Go back to Chlorine Binding Sites List in 6ac9
Chlorine binding site 1 out of 4 in the Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:69.0
occ:1.00
 NH2 A:ARG148 3.0 50.3 1.0
NE2 A:HIS258 3.4 40.0 1.0
O A:HOH546 3.6 54.2 1.0
NH1 A:ARG148 3.6 39.2 1.0
CZ A:ARG148 3.8 49.7 1.0
CE1 A:HIS258 3.9 39.8 1.0
CD2 A:HIS258 4.5 40.0 1.0

Chlorine binding site 2 out of 4 in 6ac9

Go back to Chlorine Binding Sites List in 6ac9
Chlorine binding site 2 out of 4 in the Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:79.1
occ:1.00
 NH2 B:ARG148 3.3 43.3 1.0
NE2 B:HIS258 3.5 41.3 1.0
CE1 B:HIS258 3.7 40.9 1.0
NH1 B:ARG148 3.8 47.8 1.0
CZ B:ARG148 4.0 58.5 1.0
CD2 B:HIS258 4.7 41.4 1.0
ND1 B:HIS258 5.0 41.3 1.0

Chlorine binding site 3 out of 4 in 6ac9

Go back to Chlorine Binding Sites List in 6ac9
Chlorine binding site 3 out of 4 in the Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:67.7
occ:1.00
 NE2 C:HIS258 3.3 42.0 1.0
NH2 C:ARG148 3.6 40.3 1.0
CE1 C:HIS258 3.7 42.0 1.0
NH1 C:ARG148 3.9 31.8 1.0
CZ C:ARG148 4.2 47.5 1.0
CD2 C:HIS258 4.5 41.9 1.0

Chlorine binding site 4 out of 4 in 6ac9

Go back to Chlorine Binding Sites List in 6ac9
Chlorine binding site 4 out of 4 in the Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Vaccinia-Related Kinase 1 (VRK1) in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl405

b:61.9
occ:1.00
 NE2 D:HIS258 3.4 37.0 1.0
NH2 D:ARG148 3.5 29.7 1.0
NH1 D:ARG148 3.7 26.9 1.0
O D:HOH558 3.8 47.4 1.0
CZ D:ARG148 4.1 41.4 1.0
CE1 D:HIS258 4.1 36.9 1.0
CD2 D:HIS258 4.5 36.9 1.0
O D:HOH508 4.5 42.8 1.0

Reference:

Y.S.Ngow, S.Rajan, H.Ye, H.S.Yoon. Crystal Structure of Human Vaccinia-Related Kinase 1 in Complex with Amp-Pnp, A Non-Hydrolyzable Atp Analog. Protein Sci. V. 28 524 2019.
ISSN: ESSN 1469-896X
PubMed: 30461091
DOI: 10.1002/PRO.3552
Page generated: Fri Jul 26 21:59:53 2024

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