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Magnesium in PDB 3p23: Crystal Structure of the Human Kinase and Rnase Domains in Complex with Adp

Enzymatic activity of Crystal Structure of the Human Kinase and Rnase Domains in Complex with Adp

All present enzymatic activity of Crystal Structure of the Human Kinase and Rnase Domains in Complex with Adp:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of the Human Kinase and Rnase Domains in Complex with Adp, PDB code: 3p23 was solved by M.M.U.Ali, L.H.Pearl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.73 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 109.850, 83.200, 116.080, 90.00, 94.79, 90.00
R / Rfree (%) 23.5 / 29.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Human Kinase and Rnase Domains in Complex with Adp (pdb code 3p23). 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 the Human Kinase and Rnase Domains in Complex with Adp, PDB code: 3p23:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3p23

Go back to Magnesium Binding Sites List in 3p23
Magnesium binding site 1 out of 4 in the Crystal Structure of the Human Kinase and Rnase Domains in Complex with Adp


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 the Human Kinase and Rnase Domains in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:45.9
occ:1.00
O2B A:ADP1002 2.6 34.7 1.0
OD2 A:ASP711 2.7 54.8 1.0
O A:HIS692 2.8 45.2 1.0
O5' A:ADP1002 3.2 20.7 1.0
OD1 A:ASN693 3.2 52.1 1.0
O1A A:ADP1002 3.3 54.8 1.0
C8 A:ADP1002 3.4 37.6 1.0
C3' A:ADP1002 3.6 39.4 1.0
CG A:ASP711 3.7 55.3 1.0
PB A:ADP1002 3.8 45.3 1.0
PA A:ADP1002 3.8 51.0 1.0
C A:HIS692 3.9 41.3 1.0
C2' A:ADP1002 3.9 36.8 1.0
OD1 A:ASP711 4.0 61.1 1.0
O3B A:ADP1002 4.0 25.2 1.0
N7 A:ADP1002 4.1 26.5 1.0
N9 A:ADP1002 4.2 39.5 1.0
C5' A:ADP1002 4.2 25.1 1.0
O3A A:ADP1002 4.3 0.6 1.0
C4' A:ADP1002 4.3 33.7 1.0
CG A:ASN693 4.4 53.4 1.0
C1' A:ADP1002 4.5 39.9 1.0
CA A:ASN693 4.5 43.2 1.0
O4' A:ADP1002 4.5 35.6 1.0
O3' A:ADP1002 4.5 43.5 1.0
O A:HOH19 4.6 30.1 1.0
N A:ASN693 4.6 31.6 1.0
CB A:HIS692 4.7 63.0 1.0
CA A:HIS692 4.8 54.6 1.0
CD2 A:LEU695 4.8 31.3 1.0
NZ A:LYS599 4.8 51.9 1.0
CB A:ASP711 4.9 46.0 1.0

Magnesium binding site 2 out of 4 in 3p23

Go back to Magnesium Binding Sites List in 3p23
Magnesium binding site 2 out of 4 in the Crystal Structure of the Human Kinase and Rnase Domains in Complex with Adp


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 the Human Kinase and Rnase Domains in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:48.9
occ:1.00
O2B B:ADP1002 2.6 50.6 1.0
OD2 B:ASP711 2.9 56.9 1.0
O1A B:ADP1002 2.9 49.2 1.0
O B:HIS692 3.2 42.5 1.0
O5' B:ADP1002 3.4 16.7 1.0
OD1 B:ASN693 3.4 56.7 1.0
C8 B:ADP1002 3.5 37.6 1.0
CG B:ASP711 3.7 57.2 1.0
PA B:ADP1002 3.7 42.4 1.0
O B:HOH33 3.8 42.6 1.0
N7 B:ADP1002 3.9 31.4 1.0
OD1 B:ASP711 3.9 61.9 1.0
C B:HIS692 4.0 45.3 1.0
PB B:ADP1002 4.0 43.1 1.0
C3' B:ADP1002 4.0 43.8 1.0
O3A B:ADP1002 4.4 0.9 1.0
N9 B:ADP1002 4.4 40.7 1.0
C2' B:ADP1002 4.4 42.3 1.0
CG B:ASN693 4.5 52.9 1.0
CA B:ASN693 4.5 44.8 1.0
C5' B:ADP1002 4.6 26.9 1.0
OG B:SER710 4.6 61.8 1.0
N B:ASN693 4.6 45.5 1.0
CB B:HIS692 4.7 65.2 1.0
O3B B:ADP1002 4.7 42.2 1.0
CD2 B:LEU695 4.8 27.5 1.0
C4' B:ADP1002 4.8 34.5 1.0
C1' B:ADP1002 4.9 41.5 1.0
CB B:ASP711 4.9 52.2 1.0
C5 B:ADP1002 5.0 30.0 1.0
O3' B:ADP1002 5.0 49.5 1.0
NZ B:LYS599 5.0 60.7 1.0
CA B:HIS692 5.0 52.0 1.0
O4' B:ADP1002 5.0 39.8 1.0

Magnesium binding site 3 out of 4 in 3p23

Go back to Magnesium Binding Sites List in 3p23
Magnesium binding site 3 out of 4 in the Crystal Structure of the Human Kinase and Rnase Domains in Complex with Adp


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 the Human Kinase and Rnase Domains in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1001

b:52.4
occ:1.00
O2B C:ADP1002 2.5 50.5 1.0
O C:HIS692 2.8 47.0 1.0
OD2 C:ASP711 3.0 66.6 1.0
O C:HOH22 3.1 34.4 1.0
OD1 C:ASN693 3.2 57.0 1.0
O1A C:ADP1002 3.2 59.1 1.0
O5' C:ADP1002 3.3 22.2 1.0
C8 C:ADP1002 3.3 30.2 1.0
C3' C:ADP1002 3.8 47.5 1.0
C C:HIS692 3.8 40.9 1.0
PA C:ADP1002 3.9 50.6 1.0
CG C:ASP711 3.9 70.5 1.0
PB C:ADP1002 3.9 49.0 1.0
N7 C:ADP1002 4.0 23.7 1.0
C2' C:ADP1002 4.0 48.0 1.0
OD1 C:ASP711 4.1 73.0 1.0
N9 C:ADP1002 4.2 35.9 1.0
CG C:ASN693 4.3 45.1 1.0
C5' C:ADP1002 4.4 20.7 1.0
O3A C:ADP1002 4.4 0.7 1.0
O3B C:ADP1002 4.4 25.6 1.0
CA C:ASN693 4.5 46.6 1.0
C4' C:ADP1002 4.5 33.9 1.0
N C:ASN693 4.5 35.8 1.0
OG C:SER710 4.5 73.5 1.0
C1' C:ADP1002 4.5 45.3 1.0
O4' C:ADP1002 4.6 42.8 1.0
CB C:HIS692 4.7 67.9 1.0
CA C:HIS692 4.8 55.4 1.0
O3' C:ADP1002 4.8 52.6 1.0
CD2 C:LEU695 4.9 45.5 1.0
O C:HOH62 4.9 28.7 1.0
NZ C:LYS599 4.9 65.7 1.0

Magnesium binding site 4 out of 4 in 3p23

Go back to Magnesium Binding Sites List in 3p23
Magnesium binding site 4 out of 4 in the Crystal Structure of the Human Kinase and Rnase Domains in Complex with Adp


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 the Human Kinase and Rnase Domains in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1001

b:61.4
occ:1.00
O2B D:ADP1002 2.7 60.8 1.0
O1A D:ADP1002 2.8 60.7 1.0
OD2 D:ASP711 2.8 53.9 1.0
O5' D:ADP1002 3.1 27.2 1.0
OD1 D:ASN693 3.3 50.5 1.0
C8 D:ADP1002 3.4 27.6 1.0
O D:HOH43 3.5 44.1 1.0
PA D:ADP1002 3.5 52.6 1.0
O D:HIS692 3.7 28.9 1.0
CG D:ASP711 3.8 49.4 1.0
N7 D:ADP1002 3.8 29.8 1.0
C3' D:ADP1002 3.9 39.4 1.0
PB D:ADP1002 3.9 53.1 1.0
OD1 D:ASP711 4.1 54.0 1.0
C D:HIS692 4.2 35.2 1.0
O3A D:ADP1002 4.2 0.5 1.0
C5' D:ADP1002 4.3 34.6 1.0
CG D:ASN693 4.3 45.1 1.0
O3B D:ADP1002 4.4 39.7 1.0
CA D:ASN693 4.4 33.3 1.0
N9 D:ADP1002 4.4 25.1 1.0
N D:ASN693 4.5 33.1 1.0
NZ D:LYS599 4.5 57.9 1.0
C2' D:ADP1002 4.5 40.3 1.0
C4' D:ADP1002 4.6 37.7 1.0
CB D:HIS692 4.8 44.5 1.0
O3' D:ADP1002 4.8 45.6 1.0
O2A D:ADP1002 4.9 52.5 1.0
O4' D:ADP1002 4.9 41.2 1.0
OG D:SER710 4.9 46.5 1.0
CD2 D:LEU695 4.9 24.2 1.0
C1' D:ADP1002 4.9 33.9 1.0
CB D:ASN693 4.9 42.7 1.0
C5 D:ADP1002 5.0 27.8 1.0

Reference:

M.M.Ali, T.Bagratuni, E.L.Davenport, P.R.Nowak, M.C.Silva-Santisteban, A.Hardcastle, C.Mcandrews, M.G.Rowlands, G.J.Morgan, W.Aherne, I.Collins, F.E.Davies, L.H.Pearl. Structure of the IRE1 Autophosphorylation Complex and Implications For the Unfolded Protein Response. Embo J. V. 30 894 2011.
ISSN: ISSN 0261-4189
PubMed: 21317875
DOI: 10.1038/EMBOJ.2011.18
Page generated: Mon Dec 14 08:38:36 2020

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