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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

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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

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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

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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

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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

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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

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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

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