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Magnesium in PDB 6unr: Kinase Domain of ALK2-K492A/K493A with Amppnp

Enzymatic activity of Kinase Domain of ALK2-K492A/K493A with Amppnp

All present enzymatic activity of Kinase Domain of ALK2-K492A/K493A with Amppnp:
2.7.11.30;

Protein crystallography data

The structure of Kinase Domain of ALK2-K492A/K493A with Amppnp, PDB code: 6unr was solved by C.Agnew, N.Jura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.14 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 59.122, 87.124, 138.916, 90, 90, 90
R / Rfree (%) 24.4 / 30.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Kinase Domain of ALK2-K492A/K493A with Amppnp (pdb code 6unr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Kinase Domain of ALK2-K492A/K493A with Amppnp, PDB code: 6unr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6unr

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Magnesium binding site 1 out of 8 in the Kinase Domain of ALK2-K492A/K493A with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kinase Domain of ALK2-K492A/K493A with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:65.7
occ:1.00
 MG A:MG509 2.6 67.5 1.0
OD1 A:ASN341 3.4 46.7 1.0
O2A A:ANP501 3.5 122.6 1.0
C8 A:ANP501 3.7 61.0 1.0
O A:LYS340 3.7 41.3 1.0
N7 A:ANP501 4.0 56.2 1.0
O A:HOH610 4.4 46.6 1.0
CA A:ASN341 4.4 44.9 1.0
CB A:ALA353 4.4 39.3 1.0
O3A A:ANP501 4.4 138.2 1.0
CG A:ASN341 4.5 49.4 1.0
PA A:ANP501 4.5 130.1 1.0
C2' A:ANP501 4.6 78.5 1.0
C A:LYS340 4.7 49.4 1.0
CB A:ASP354 4.7 37.4 1.0
N9 A:ANP501 4.7 68.5 1.0
CB A:ASN341 5.0 44.5 1.0
O2' A:ANP501 5.0 75.2 1.0

Magnesium binding site 2 out of 8 in 6unr

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Magnesium binding site 2 out of 8 in the Kinase Domain of ALK2-K492A/K493A with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kinase Domain of ALK2-K492A/K493A with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:76.1
occ:1.00
 O A:VAL435 2.5 79.4 1.0
NH1 A:ARG380 3.2 50.5 1.0
C A:PRO436 3.4 88.5 1.0
O A:TYR432 3.5 82.5 1.0
NH2 A:ARG380 3.5 53.0 1.0
N A:ASN437 3.6 93.0 1.0
O A:PRO436 3.6 92.8 1.0
C A:VAL435 3.6 77.9 1.0
CA A:TYR432 3.6 69.5 1.0
CZ A:ARG380 3.8 56.5 1.0
C A:TYR432 3.9 69.5 1.0
CA A:PRO436 4.0 82.2 1.0
CG2 A:VAL435 4.1 76.3 1.0
CA A:ASN437 4.1 94.3 1.0
O A:PHE431 4.2 65.8 1.0
N A:PRO436 4.2 79.6 1.0
CB A:TYR432 4.4 66.7 1.0
N A:TYR432 4.5 63.7 1.0
CA A:VAL435 4.7 76.8 1.0
C A:PHE431 4.7 67.2 1.0
N A:VAL435 4.8 72.2 1.0
CB A:ASN437 4.9 96.1 1.0
CB A:VAL435 5.0 77.4 1.0

Magnesium binding site 3 out of 8 in 6unr

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Magnesium binding site 3 out of 8 in the Kinase Domain of ALK2-K492A/K493A with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Kinase Domain of ALK2-K492A/K493A with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:112.3
occ:1.00
 OE1 A:GLU250 3.2 58.0 1.0
CE2 A:PHE246 3.7 65.8 1.0
NH1 A:ARG247 3.8 43.5 1.0
CD2 A:PHE246 3.9 64.0 1.0
OD1 A:ASN372 4.0 83.1 1.0
CD A:GLU250 4.1 62.0 1.0
CA A:GLY371 4.2 69.3 1.0
OE2 A:GLU250 4.3 64.4 1.0
N A:ASN372 4.6 67.8 1.0
CD A:ARG247 4.6 50.1 1.0
CG A:ASN372 4.7 82.2 1.0
CZ A:ARG247 4.8 44.7 1.0
C A:GLY371 4.9 72.2 1.0
CZ A:PHE246 4.9 63.4 1.0

Magnesium binding site 4 out of 8 in 6unr

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Magnesium binding site 4 out of 8 in the Kinase Domain of ALK2-K492A/K493A with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Kinase Domain of ALK2-K492A/K493A with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:84.3
occ:1.00
 O A:VAL255 2.4 78.7 1.0
O A:GLY328 2.6 81.4 1.0
C A:VAL255 3.1 75.2 1.0
CA A:VAL255 3.3 68.3 1.0
C A:GLY328 3.5 75.5 1.0
O A:THR254 3.6 82.4 1.0
CA A:LYS329 3.6 60.2 1.0
N A:LYS329 4.0 68.4 1.0
CG1 A:VAL255 4.0 70.2 1.0
CB A:LYS329 4.2 60.9 1.0
CB A:VAL255 4.3 62.9 1.0
N A:MET256 4.3 80.8 1.0
N A:VAL255 4.4 72.5 1.0
CD A:PRO330 4.4 54.0 1.0
C A:THR254 4.4 73.8 1.0
CB A:MET256 4.7 103.0 1.0
CA A:GLY328 4.8 80.0 1.0
C A:LYS329 4.8 59.3 1.0
N A:GLY328 4.9 95.2 1.0
CA A:MET256 4.9 95.7 1.0

Magnesium binding site 5 out of 8 in 6unr

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Magnesium binding site 5 out of 8 in the Kinase Domain of ALK2-K492A/K493A with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Kinase Domain of ALK2-K492A/K493A with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:63.5
occ:1.00
 OD1 A:ASP354 2.6 53.3 1.0
OE1 A:GLU248 2.9 75.0 1.0
CG A:ASP354 3.4 50.2 1.0
NH2 A:ARG375 3.4 57.1 1.0
CE2 A:PHE237 3.5 48.3 1.0
NZ A:LYS235 3.6 73.4 1.0
CD A:GLU248 3.7 73.5 1.0
OD2 A:ASP354 3.7 54.4 1.0
CB A:SER244 3.7 45.8 1.0
CA A:GLY356 3.8 38.6 1.0
CZ A:PHE237 3.8 47.7 1.0
CG A:GLU248 3.9 58.1 1.0
N A:GLY356 4.0 40.5 1.0
CE A:LYS235 4.3 62.0 1.0
OG A:SER244 4.4 48.6 1.0
CZ A:ARG375 4.4 58.6 1.0
CB A:ASP354 4.5 37.4 1.0
O A:SER244 4.5 46.7 1.0
NH1 A:ARG375 4.5 53.9 1.0
CA A:ASP354 4.6 42.6 1.0
C A:SER244 4.6 49.9 1.0
CA A:SER244 4.7 42.9 1.0
CD2 A:PHE237 4.7 46.0 1.0
OD2 A:ASP241 4.8 87.5 1.0
OE2 A:GLU248 4.8 79.0 1.0
O A:HOH610 4.8 46.6 1.0
CD A:LYS235 4.9 51.1 1.0
C A:ASP354 4.9 49.4 1.0
N A:LEU355 5.0 52.7 1.0

Magnesium binding site 6 out of 8 in 6unr

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Magnesium binding site 6 out of 8 in the Kinase Domain of ALK2-K492A/K493A with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Kinase Domain of ALK2-K492A/K493A with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:70.9
occ:1.00
 N A:ASP354 2.5 45.5 1.0
OE2 A:GLU248 2.7 79.0 1.0
O A:HOH610 3.0 46.6 1.0
OH A:TYR252 3.1 51.3 1.0
CA A:ASP354 3.3 42.6 1.0
CD2 A:LEU263 3.5 53.8 1.0
C A:ALA353 3.5 44.0 1.0
CA A:ALA353 3.6 40.1 1.0
CD A:GLU248 3.7 73.5 1.0
CB A:ALA353 3.7 39.3 1.0
OE1 A:GLU248 3.9 75.0 1.0
CE2 A:TYR252 3.9 43.3 1.0
CZ A:TYR252 3.9 55.3 1.0
N A:LEU355 4.0 52.7 1.0
C A:ASP354 4.1 49.4 1.0
CB A:LEU263 4.3 48.6 1.0
CG A:LEU263 4.4 57.2 1.0
CD2 A:LEU281 4.4 42.6 1.0
CB A:ASP354 4.6 37.4 1.0
O A:ALA353 4.6 44.3 1.0
CG2 A:THR283 4.9 46.9 1.0
N A:ALA353 5.0 44.2 1.0

Magnesium binding site 7 out of 8 in 6unr

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Magnesium binding site 7 out of 8 in the Kinase Domain of ALK2-K492A/K493A with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Kinase Domain of ALK2-K492A/K493A with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg508

b:62.1
occ:1.00
 O A:LYS216 3.0 84.3 1.0
O2B A:ANP501 3.2 125.5 1.0
C A:LYS216 3.4 98.7 1.0
N A:LYS216 3.9 81.0 1.0
N A:GLY217 4.0 121.3 1.0
NZ A:LYS340 4.0 77.9 1.0
CA A:GLY217 4.0 120.6 1.0
CA A:LYS216 4.2 79.6 1.0
O1B A:ANP501 4.3 128.8 1.0
PB A:ANP501 4.3 132.1 1.0
O5' A:ANP501 4.4 121.9 1.0
C5' A:ANP501 4.6 106.0 1.0
CB A:LYS216 4.8 70.0 1.0
C A:GLY215 4.9 79.7 1.0
CA A:GLY215 5.0 74.1 1.0

Magnesium binding site 8 out of 8 in 6unr

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Magnesium binding site 8 out of 8 in the Kinase Domain of ALK2-K492A/K493A with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Kinase Domain of ALK2-K492A/K493A with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg509

b:67.5
occ:1.00
 MG A:MG502 2.6 65.7 1.0
OD1 A:ASN341 2.6 46.7 1.0
OD2 A:ASP354 3.3 54.4 1.0
O3A A:ANP501 3.3 138.2 1.0
O2A A:ANP501 3.3 122.6 1.0
O1G A:ANP501 3.4 130.5 1.0
NZ A:LYS235 3.6 73.4 1.0
CG A:ASN341 3.8 49.4 1.0
CB A:ASP354 3.9 37.4 1.0
CG A:ASP354 3.9 50.2 1.0
PA A:ANP501 4.0 130.1 1.0
N3B A:ANP501 4.2 132.3 1.0
PB A:ANP501 4.3 132.1 1.0
ND2 A:ASN341 4.4 53.0 1.0
PG A:ANP501 4.4 129.0 1.0
O A:HOH610 4.6 46.6 1.0
O A:LYS340 4.7 41.3 1.0
CE A:LYS235 4.9 62.0 1.0
O1B A:ANP501 4.9 128.8 1.0
O1A A:ANP501 5.0 131.5 1.0
CB A:ASN341 5.0 44.5 1.0

Reference:

C.Agnew, N.Jura. Kinase Domain of ALK2-K492A/K493A with Amppnp To Be Published.
Page generated: Tue Oct 1 21:08:43 2024

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