Atomistry » Magnesium » PDB 3zx4-4a28 » 3zxt
Atomistry »
  Magnesium »
    PDB 3zx4-4a28 »
      3zxt »

Magnesium in PDB 3zxt: Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg

Enzymatic activity of Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg

All present enzymatic activity of Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg:
2.7.11.1;

Protein crystallography data

The structure of Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg, PDB code: 3zxt was solved by I.De Diego, F.Lehmann, M.Wilmanns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 106.83 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.407, 76.578, 106.892, 90.00, 92.01, 90.00
R / Rfree (%) 21.601 / 28.46

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg (pdb code 3zxt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg, PDB code: 3zxt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3zxt

Go back to Magnesium Binding Sites List in 3zxt
Magnesium binding site 1 out of 6 in the Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1278

b:42.2
occ:1.00
O1A A:ACP1277 2.0 49.2 1.0
ND2 A:ASN144 2.2 38.9 1.0
OD2 A:ASP161 2.3 42.1 1.0
O1B A:ACP1277 2.5 43.9 1.0
CG A:ASN144 3.1 38.1 1.0
OD1 A:ASN144 3.3 36.9 1.0
CG A:ASP161 3.3 41.4 1.0
PA A:ACP1277 3.5 52.4 1.0
CB A:ASP161 3.8 40.5 1.0
PB A:ACP1277 3.8 56.5 1.0
OE2 A:GLU143 3.9 58.6 1.0
C5' A:ACP1277 4.0 55.0 1.0
O3A A:ACP1277 4.2 52.8 1.0
O A:HOH2015 4.2 47.8 1.0
CD A:GLU143 4.3 55.4 1.0
O5' A:ACP1277 4.3 47.2 1.0
O2A A:ACP1277 4.3 54.5 1.0
OD1 A:ASP161 4.3 39.8 1.0
C4' A:ACP1277 4.4 46.5 1.0
MG A:MG1279 4.4 51.5 1.0
CG A:GLU143 4.5 49.9 1.0
CB A:ASN144 4.6 37.2 1.0
O A:GLU143 4.7 48.4 1.0
C3B A:ACP1277 4.7 53.8 1.0
OD2 A:ASP139 4.7 41.3 1.0
O3G A:ACP1277 4.9 56.7 1.0
CA A:ASN144 4.9 40.4 1.0
OE1 A:GLU143 5.0 60.2 1.0
C A:GLU143 5.0 45.7 1.0
C3' A:ACP1277 5.0 48.5 1.0

Magnesium binding site 2 out of 6 in 3zxt

Go back to Magnesium Binding Sites List in 3zxt
Magnesium binding site 2 out of 6 in the Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1279

b:51.5
occ:1.00
O2B A:ACP1277 2.4 52.4 1.0
O1B A:ACP1277 2.6 43.9 1.0
OD1 A:ASP161 2.7 39.8 1.0
O A:HOH2031 2.8 50.3 1.0
OD2 A:ASP161 2.9 42.1 1.0
PB A:ACP1277 3.0 56.5 1.0
O2G A:ACP1277 3.0 48.0 1.0
CG A:ASP161 3.2 41.4 1.0
OD2 A:ASP139 3.8 41.3 1.0
O3A A:ACP1277 3.9 52.8 1.0
PG A:ACP1277 4.2 63.4 1.0
C3B A:ACP1277 4.4 53.8 1.0
MG A:MG1278 4.4 42.2 1.0
O1A A:ACP1277 4.4 49.2 1.0
O A:PHE162 4.4 38.8 1.0
CB A:ASP161 4.7 40.5 1.0
NZ A:LYS42 4.8 47.1 1.0
PA A:ACP1277 4.9 52.4 1.0
O3G A:ACP1277 4.9 56.7 1.0

Magnesium binding site 3 out of 6 in 3zxt

Go back to Magnesium Binding Sites List in 3zxt
Magnesium binding site 3 out of 6 in the Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1277

b:44.7
occ:1.00
O1B B:ACP1279 2.1 41.9 1.0
ND2 B:ASN144 2.4 38.9 1.0
OD2 B:ASP161 2.4 40.4 1.0
O1A B:ACP1279 2.4 41.6 1.0
O2A B:ACP1279 3.0 46.2 1.0
PA B:ACP1279 3.2 43.6 1.0
CG B:ASP161 3.4 40.9 1.0
PB B:ACP1279 3.4 46.8 1.0
CG B:ASN144 3.5 39.0 1.0
O3' B:ACP1279 3.6 45.0 1.0
OE2 B:GLU143 3.6 48.3 1.0
O3A B:ACP1279 3.8 50.3 1.0
OD1 B:ASN144 3.9 39.8 1.0
CB B:ASP161 3.9 40.6 1.0
CG B:GLU143 4.2 45.4 1.0
O2B B:ACP1279 4.3 48.4 1.0
CD B:GLU143 4.3 47.9 1.0
OD1 B:ASP161 4.3 39.8 1.0
C3' B:ACP1279 4.3 45.7 1.0
O B:GLU143 4.5 43.3 1.0
O5' B:ACP1279 4.5 45.2 1.0
C3B B:ACP1279 4.6 48.6 1.0
C5' B:ACP1279 4.6 46.6 1.0
CB B:ASN144 4.7 39.3 1.0
C4' B:ACP1279 4.7 42.5 1.0
C B:GLU143 4.9 42.7 1.0
MG B:MG1278 4.9 58.4 1.0
CA B:ASN144 4.9 41.2 1.0
O1G B:ACP1279 5.0 59.5 1.0
N B:ASN144 5.0 42.9 1.0

Magnesium binding site 4 out of 6 in 3zxt

Go back to Magnesium Binding Sites List in 3zxt
Magnesium binding site 4 out of 6 in the Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1278

b:58.4
occ:1.00
O2B B:ACP1279 2.0 48.4 1.0
OD1 B:ASP161 2.5 39.8 1.0
OD2 B:ASP161 3.0 40.4 1.0
CG B:ASP161 3.1 40.9 1.0
PB B:ACP1279 3.5 46.8 1.0
O1B B:ACP1279 3.6 41.9 1.0
O3G B:ACP1279 3.7 52.5 1.0
OD2 B:ASP139 3.9 45.2 1.0
CA B:GLY163 4.3 36.0 1.0
O3A B:ACP1279 4.3 50.3 1.0
N B:GLY163 4.4 37.0 1.0
CB B:ASP161 4.6 40.6 1.0
C B:GLY163 4.6 36.8 1.0
N B:LEU164 4.7 37.2 1.0
CG B:LEU164 4.7 38.4 1.0
PG B:ACP1279 4.8 55.7 1.0
C3B B:ACP1279 4.8 48.6 1.0
MG B:MG1277 4.9 44.7 1.0
O B:ASP161 4.9 36.3 1.0
CG B:ASP139 4.9 44.4 1.0
O B:HOH2009 5.0 30.9 1.0

Magnesium binding site 5 out of 6 in 3zxt

Go back to Magnesium Binding Sites List in 3zxt
Magnesium binding site 5 out of 6 in the Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1277

b:41.0
occ:0.50
O1A C:ACP1278 2.4 42.8 0.5
ND2 C:ASN144 2.4 58.6 1.0
OD2 C:ASP161 2.6 65.3 1.0
O3' C:ACP1278 2.7 43.9 0.5
O1B C:ACP1278 2.9 43.7 0.5
CG C:ASN144 3.6 58.0 1.0
C3' C:ACP1278 3.6 44.3 0.5
CG C:ASP161 3.8 61.7 1.0
PA C:ACP1278 3.9 47.3 0.5
OD1 C:ASN144 3.9 59.0 1.0
CG C:GLU143 4.0 68.6 1.0
CD C:GLU143 4.0 74.5 1.0
OE1 C:GLU143 4.1 79.0 1.0
PB C:ACP1278 4.1 50.9 0.5
CB C:ASP161 4.2 57.4 1.0
C5' C:ACP1278 4.2 44.1 0.5
C4' C:ACP1278 4.4 45.2 0.5
O3A C:ACP1278 4.4 47.1 0.5
O C:GLU143 4.5 63.3 1.0
O2B C:ACP1278 4.6 48.7 0.5
O5' C:ACP1278 4.6 44.7 0.5
OE2 C:GLU143 4.6 76.9 1.0
OD1 C:ASP161 4.8 61.2 1.0
CB C:ASN144 4.8 55.9 1.0
C C:GLU143 4.8 61.0 1.0
C2' C:ACP1278 4.9 45.4 0.5
CD1 C:ILE160 4.9 53.4 1.0
CA C:ASN144 5.0 57.3 1.0
O2A C:ACP1278 5.0 49.8 0.5
CE C:LYS141 5.0 56.2 1.0

Magnesium binding site 6 out of 6 in 3zxt

Go back to Magnesium Binding Sites List in 3zxt
Magnesium binding site 6 out of 6 in the Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Dimeric Structure of Dapk-1 Catalytic Domain in Complex with Amppcp-Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1278

b:58.4
occ:0.50
O1A D:ACP1277 2.0 67.8 0.7
O1B D:ACP1277 2.4 73.9 0.7
OD2 D:ASP161 2.7 62.2 1.0
O3' D:ACP1277 3.2 69.7 0.7
ND2 D:ASN144 3.2 58.0 1.0
OE1 D:GLU143 3.3 78.7 1.0
PA D:ACP1277 3.5 69.1 0.7
C5' D:ACP1277 3.5 63.9 0.7
O D:HOH2035 3.6 74.0 1.0
CG D:ASP161 3.6 61.4 1.0
C3' D:ACP1277 3.7 61.4 0.7
PB D:ACP1277 3.7 80.5 0.7
O5' D:ACP1277 4.0 61.9 0.7
CD D:GLU143 4.0 79.2 1.0
O3A D:ACP1277 4.1 69.0 0.7
C4' D:ACP1277 4.2 60.5 0.7
CB D:ASP161 4.2 57.7 1.0
CG D:ASN144 4.2 57.0 1.0
O1G D:ACP1277 4.3 67.6 0.7
OD1 D:ASN144 4.3 57.7 1.0
OD1 D:ASP161 4.5 62.9 1.0
OE2 D:GLU143 4.5 83.0 1.0
O2B D:ACP1277 4.5 68.5 0.7
O2A D:ACP1277 4.6 72.4 0.7
CG D:GLU143 4.9 75.0 1.0

Reference:

I.De Diego, J.Kuper, F.Lehmann, M.Wilmanns. A Journey Through the Dap Kinase Architecture To Be Published.
Page generated: Thu Aug 15 14:08:57 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy