Magnesium 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:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 6ac9

Go back to Magnesium Binding Sites List in 6ac9
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg402

b:56.5
occ:1.00
O A:HOH670 2.7 42.5 1.0
O2A A:ANP401 2.8 0.5 1.0
O A:HOH586 3.0 29.9 1.0
O3A A:ANP401 3.2 0.4 1.0
PA A:ANP401 3.4 0.3 1.0
CB A:ASP197 3.6 24.1 1.0
C8 A:ANP401 3.8 36.5 1.0
O5' A:ANP401 3.9 92.2 1.0
CG2 A:VAL196 3.9 25.6 1.0
CA A:ASP197 3.9 22.3 1.0
NZ A:LYS71 4.0 40.7 1.0
N A:ASP197 4.0 22.6 1.0
CG A:ASP197 4.1 35.4 1.0
O1B A:ANP401 4.2 0.2 1.0
OD2 A:ASP197 4.2 35.9 1.0
PB A:ANP401 4.3 0.7 1.0
N7 A:ANP401 4.3 33.7 1.0
C2' A:ANP401 4.5 60.7 1.0
CB A:VAL196 4.5 25.7 1.0
O A:HOH507 4.5 25.1 1.0
C A:VAL196 4.8 28.8 1.0
OD1 A:ASN182 4.8 22.4 1.0
O1A A:ANP401 4.9 0.8 1.0
N9 A:ANP401 4.9 39.9 1.0
OD1 A:ASP197 4.9 34.2 1.0
CE A:LYS71 5.0 47.5 1.0

Magnesium binding site 2 out of 4 in 6ac9

Go back to Magnesium Binding Sites List in 6ac9
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg406

b:51.7
occ:1.00
O1A B:ANP401 2.8 0.3 1.0
O B:HOH652 2.9 45.9 1.0
O B:HOH579 3.0 31.8 1.0
CB B:ASP197 3.5 26.1 1.0
CG2 B:VAL196 3.8 25.3 1.0
PA B:ANP401 3.8 0.8 1.0
C8 B:ANP401 3.8 51.9 1.0
CA B:ASP197 3.9 24.0 1.0
N B:ASP197 3.9 23.2 1.0
CG B:ASP197 4.0 35.8 1.0
O3A B:ANP401 4.0 0.3 1.0
NZ B:LYS71 4.1 46.9 1.0
OD1 B:ASP197 4.2 37.9 1.0
O5' B:ANP401 4.3 99.5 1.0
N7 B:ANP401 4.3 47.0 1.0
CB B:VAL196 4.3 25.5 1.0
O B:HOH504 4.4 30.0 1.0
O2G B:ANP401 4.4 0.8 1.0
C2' B:ANP401 4.5 72.6 1.0
OD1 B:ASN182 4.6 26.2 1.0
C B:VAL196 4.7 26.4 1.0
OD2 B:ASP197 4.7 36.5 1.0
N9 B:ANP401 4.8 57.2 1.0
O2' B:ANP401 5.0 71.4 1.0

Magnesium binding site 3 out of 4 in 6ac9

Go back to Magnesium Binding Sites List in 6ac9
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg405

b:53.4
occ:1.00
O1A C:ANP402 2.4 98.1 1.0
O C:HOH539 2.5 48.0 1.0
O C:HOH551 3.1 38.3 1.0
PA C:ANP402 3.4 98.6 1.0
NZ C:LYS71 3.4 54.1 1.0
CB C:ASP197 3.5 33.0 1.0
O5' C:ANP402 3.5 90.4 1.0
C8 C:ANP402 3.6 47.4 1.0
O1B C:ANP402 3.8 0.4 1.0
CA C:ASP197 3.9 30.3 1.0
O3A C:ANP402 4.0 1.0 1.0
N C:ASP197 4.0 31.1 1.0
CG C:ASP197 4.0 44.9 1.0
CG2 C:VAL196 4.0 33.0 1.0
N7 C:ANP402 4.2 45.3 1.0
CE C:LYS71 4.3 54.8 1.0
OD2 C:ASP197 4.4 53.1 1.0
PB C:ANP402 4.4 0.7 1.0
O C:HOH501 4.5 31.6 1.0
CB C:VAL196 4.5 32.7 1.0
OD1 C:ASP197 4.5 47.0 1.0
C2' C:ANP402 4.6 67.0 1.0
O2A C:ANP402 4.7 98.5 1.0
N9 C:ANP402 4.7 52.0 1.0
C C:VAL196 4.7 32.0 1.0
OD1 C:ASN182 4.9 31.6 1.0
C5' C:ANP402 4.9 82.0 1.0

Magnesium binding site 4 out of 4 in 6ac9

Go back to Magnesium Binding Sites List in 6ac9
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg401

b:54.4
occ:1.00
O1A D:ANP402 2.0 79.9 1.0
OD1 D:ASN182 2.1 30.4 1.0
O2B D:ANP402 2.1 86.5 1.0
O D:HOH588 2.2 56.4 1.0
OD1 D:ASP197 2.3 48.6 1.0
CG D:ASN182 3.2 30.8 1.0
CG D:ASP197 3.2 46.0 1.0
PA D:ANP402 3.2 79.8 1.0
PB D:ANP402 3.3 88.1 1.0
O3A D:ANP402 3.4 84.0 1.0
CB D:ASP197 3.5 31.0 1.0
ND2 D:ASN182 3.6 20.4 1.0
O1B D:ANP402 4.0 87.4 1.0
O2A D:ANP402 4.2 78.5 1.0
O5' D:ANP402 4.3 75.6 1.0
OD2 D:ASP197 4.4 56.0 1.0
C5' D:ANP402 4.4 70.0 1.0
CB D:ASN182 4.4 25.1 1.0
O D:SER181 4.5 31.3 1.0
N3B D:ANP402 4.6 95.7 1.0
CA D:ASN182 4.6 27.3 1.0
O D:HOH633 4.8 56.3 1.0
OG D:SER181 4.8 37.9 1.0
C D:SER181 4.8 33.4 1.0
N D:ASN182 4.9 28.6 1.0
CA D:ASP197 5.0 28.1 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: Mon Dec 14 22:19:56 2020

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