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Magnesium in PDB 5o26: Crystal Structure of WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+

Enzymatic activity of Crystal Structure of WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+

All present enzymatic activity of Crystal Structure of WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+, PDB code: 5o26 was solved by D.M.Pinkas, J.C.Bufton, J.A.Newman, J.Kopec, O.Borkowska, R.Chalk, N.A.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, A.Bullock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.66 / 2.38
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.163, 56.400, 71.236, 79.79, 80.73, 90.00
R / Rfree (%) 22.8 / 27.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+ (pdb code 5o26). 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 WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+, PDB code: 5o26:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5o26

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Magnesium binding site 1 out of 4 in the Crystal Structure of WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+


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 WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:11.7
occ:1.00
 OD1 A:ASN280 2.0 14.2 1.0
OD2 A:ASP294 2.1 12.5 1.0
O A:HOH615 2.1 13.1 1.0
O2G A:ANP501 2.2 19.3 1.0
O2A A:ANP501 2.2 18.2 1.0
O A:HOH645 2.4 12.2 1.0
CG A:ASP294 2.6 11.2 1.0
OD1 A:ASP294 3.0 10.4 1.0
CG A:ASN280 3.2 12.6 1.0
PG A:ANP501 3.5 16.4 1.0
PA A:ANP501 3.5 15.4 1.0
CB A:ASP294 3.7 10.8 1.0
O A:HOH621 3.8 17.4 1.0
O1A A:ANP501 3.9 19.6 1.0
ND2 A:ASN280 3.9 13.0 1.0
N3B A:ANP501 3.9 16.8 1.0
O A:ASP279 4.0 11.3 1.0
O3G A:ANP501 4.0 17.6 1.0
NZ A:LYS159 4.2 11.4 1.0
CB A:ASN280 4.4 11.8 1.0
O5' A:ANP501 4.4 18.4 1.0
CA A:ASN280 4.5 10.7 1.0
C8 A:ANP501 4.5 15.4 1.0
OD2 A:ASP279 4.5 15.7 1.0
C A:ASP279 4.5 13.3 1.0
O3A A:ANP501 4.6 18.6 1.0
O1G A:ANP501 4.7 16.5 1.0
N A:ASN280 4.7 11.4 1.0
N7 A:ANP501 4.8 18.0 1.0
CE A:LYS277 4.9 13.0 1.0
PB A:ANP501 4.9 21.4 1.0

Magnesium binding site 2 out of 4 in 5o26

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Magnesium binding site 2 out of 4 in the Crystal Structure of WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+


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 WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:21.6
occ:1.00
 O1A A:ANP501 2.1 19.6 1.0
O3G A:ANP501 2.2 17.6 1.0
O2B A:ANP501 2.6 25.3 1.0
PA A:ANP501 3.5 15.4 1.0
PB A:ANP501 3.7 21.4 1.0
PG A:ANP501 3.7 16.4 1.0
O3A A:ANP501 3.8 18.6 1.0
O A:HOH613 4.0 20.3 1.0
NZ A:LYS277 4.1 14.9 1.0
O A:HOH615 4.2 13.1 1.0
O2A A:ANP501 4.3 18.2 1.0
N3B A:ANP501 4.3 16.8 1.0
OD2 A:ASP279 4.4 15.7 1.0
O2G A:ANP501 4.5 19.3 1.0
CA A:GLY156 4.5 22.9 1.0
O3' A:ANP501 4.6 22.3 1.0
O5' A:ANP501 4.6 18.4 1.0
O1G A:ANP501 4.7 16.5 1.0
C5' A:ANP501 4.7 19.7 1.0
CE A:LYS277 4.9 13.0 1.0
O1B A:ANP501 4.9 22.7 1.0

Magnesium binding site 3 out of 4 in 5o26

Go back to Magnesium Binding Sites List in 5o26
Magnesium binding site 3 out of 4 in the Crystal Structure of WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+


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 WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:15.8
occ:1.00
 OD1 B:ASN280 2.0 14.7 1.0
OD2 B:ASP294 2.0 15.5 1.0
O B:HOH629 2.2 21.5 1.0
O1G B:ANP501 2.3 12.1 1.0
O B:HOH602 2.4 13.4 1.0
O1A B:ANP501 3.0 15.0 1.0
CG B:ASP294 3.1 15.4 1.0
CG B:ASN280 3.1 16.2 1.0
O B:ASP279 3.5 16.4 1.0
PG B:ANP501 3.6 10.3 1.0
O2A B:ANP501 3.6 13.0 1.0
OD1 B:ASP294 3.8 12.4 1.0
PA B:ANP501 3.8 13.8 1.0
OD2 B:ASP279 3.9 22.1 1.0
O3G B:ANP501 3.9 13.9 1.0
ND2 B:ASN280 3.9 10.9 1.0
C B:ASP279 4.0 16.8 1.0
CA B:ASN280 4.1 15.2 1.0
CB B:ASP294 4.1 10.4 1.0
N B:ASN280 4.2 15.9 1.0
CB B:ASN280 4.2 12.1 1.0
CE B:LYS277 4.3 13.1 1.0
N3B B:ANP501 4.3 18.2 1.0
O B:HOH645 4.5 15.3 1.0
CG B:ASP279 4.5 20.6 1.0
CB B:ASP279 4.6 13.4 1.0
O3A B:ANP501 4.7 14.9 1.0
O2G B:ANP501 4.8 14.2 1.0
NZ B:LYS159 4.9 12.3 1.0
CA B:ASP279 5.0 12.9 1.0

Magnesium binding site 4 out of 4 in 5o26

Go back to Magnesium Binding Sites List in 5o26
Magnesium binding site 4 out of 4 in the Crystal Structure of WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+


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 WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:17.5
occ:1.00
 O3G B:ANP501 2.1 13.9 1.0
O1B B:ANP501 2.1 11.9 1.0
O2A B:ANP501 2.2 13.0 1.0
O B:HOH602 3.3 13.4 1.0
PB B:ANP501 3.5 14.7 1.0
PA B:ANP501 3.5 13.8 1.0
NZ B:LYS277 3.6 10.1 1.0
PG B:ANP501 3.6 10.3 1.0
O3A B:ANP501 4.0 14.9 1.0
O B:HOH633 4.1 9.3 1.0
O5' B:ANP501 4.1 21.6 1.0
N3B B:ANP501 4.2 18.2 1.0
O2G B:ANP501 4.5 14.2 1.0
O1G B:ANP501 4.5 12.1 1.0
CA B:GLY156 4.5 20.6 1.0
CE B:LYS277 4.5 13.1 1.0
OD2 B:ASP279 4.5 22.1 1.0
O2B B:ANP501 4.6 18.7 1.0
N B:ALA157 4.7 18.4 1.0
O1A B:ANP501 4.7 15.0 1.0

Reference:

D.M.Pinkas, G.M.Daubner, J.C.Bufton, S.G.Bartual, C.E.Sanvitale, D.R.Alessi, A.Bullock. Crystal Structure of WNK3 Kinase Domain in A Diphosphorylated State and in Complex with Amp-Pnp/MG2+ To Be Published.
Page generated: Sun Sep 29 23:43:48 2024

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