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Calcium in PDB 5oxg: Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854

Enzymatic activity of Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854

All present enzymatic activity of Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854:
2.7.11.30;

Protein crystallography data

The structure of Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854, PDB code: 5oxg was solved by E.P.Williams, F.J.Sorrell, J.Kopec, R.P.Nowak, K.Kupinska, F.Von Delft, N.Burgess-Brown, C.H.Arrowsmith, A.M.Edwards, C.Bountra, A.N.Bullock, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.65 / 2.13
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 85.860, 102.201, 177.300, 90.00, 93.96, 90.00
R / Rfree (%) 20.6 / 23.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854 (pdb code 5oxg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854, PDB code: 5oxg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5oxg

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Calcium binding site 1 out of 6 in the Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:96.1
occ:1.00
 OD2 A:ASP269 3.2 59.2 1.0
CG2 A:THR203 3.4 0.4 1.0
OD1 A:ASP269 3.4 57.5 1.0
CG2 A:THR271 3.5 61.6 1.0
O A:MET270 3.5 45.7 1.0
CG A:ASP269 3.6 52.4 1.0
CB A:THR203 4.3 0.7 1.0
C A:MET270 4.4 49.0 1.0
N A:MET270 4.7 45.0 1.0
CB A:ASP269 4.9 47.0 1.0
CB A:THR271 4.9 57.7 1.0
OG1 A:THR203 4.9 99.9 1.0

Calcium binding site 2 out of 6 in 5oxg

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Calcium binding site 2 out of 6 in the Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:67.8
occ:1.00
 O A:GLU413 2.8 37.1 1.0
O A:LYS428 3.0 45.6 1.0
N A:LYS428 3.3 48.0 1.0
CD1 A:TYR427 3.3 46.5 1.0
CA A:GLU413 3.4 36.1 1.0
NE A:ARG416 3.5 53.4 1.0
C A:GLU413 3.5 38.1 1.0
CD A:ARG416 3.5 51.8 1.0
CE1 A:TYR427 3.6 46.1 1.0
CB A:ARG416 3.7 48.4 1.0
CA A:TYR427 3.8 47.9 1.0
C A:LYS428 3.9 44.7 1.0
CG A:TYR427 4.0 46.9 1.0
CB A:GLU413 4.0 38.0 1.0
C A:TYR427 4.0 47.8 1.0
CA A:LYS428 4.1 48.2 1.0
CG A:ARG416 4.2 50.9 1.0
O A:ASP426 4.2 51.3 1.0
CG A:ARG417 4.4 44.0 1.0
CB A:TYR427 4.4 47.3 1.0
CZ A:TYR427 4.5 44.6 1.0
CG A:GLU413 4.5 38.1 1.0
O A:TRP412 4.6 41.5 1.0
CD A:ARG417 4.6 44.5 1.0
N A:GLU413 4.6 37.0 1.0
CZ3 A:TRP412 4.7 43.3 1.0
CZ A:ARG416 4.7 54.4 1.0
CD2 A:TYR427 4.8 43.6 1.0
N A:TYR427 4.8 46.5 1.0
CB A:LYS428 4.8 50.4 1.0
N A:VAL414 4.8 39.3 1.0
C A:ASP426 4.9 49.9 1.0
CE3 A:TRP412 4.9 41.6 1.0
CE2 A:TYR427 5.0 44.2 1.0

Calcium binding site 3 out of 6 in 5oxg

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Calcium binding site 3 out of 6 in the Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:0.4
occ:1.00
 O B:GLU413 2.6 37.8 1.0
CD1 B:TYR427 3.3 38.8 1.0
C B:GLU413 3.4 36.2 1.0
O B:LYS428 3.4 47.2 1.0
N B:LYS428 3.5 44.5 1.0
CA B:GLU413 3.5 35.5 1.0
NE B:ARG416 3.6 46.4 1.0
CB B:ARG416 3.6 40.5 1.0
CD B:ARG416 3.6 44.0 1.0
CA B:TYR427 3.7 41.3 1.0
CE1 B:TYR427 3.8 38.7 1.0
CG B:ARG417 3.9 38.3 1.0
CG B:TYR427 4.0 40.2 1.0
CB B:GLU413 4.1 34.9 1.0
O B:ASP426 4.1 48.1 1.0
C B:TYR427 4.1 44.5 1.0
CD B:ARG417 4.2 37.0 1.0
CG B:ARG416 4.2 42.8 1.0
C B:LYS428 4.3 45.9 1.0
CB B:TYR427 4.4 39.7 1.0
CA B:LYS428 4.5 47.0 1.0
O B:TRP412 4.5 38.9 1.0
N B:TYR427 4.6 43.8 1.0
N B:VAL414 4.7 33.7 1.0
CG B:GLU413 4.7 36.2 1.0
CZ B:TYR427 4.7 39.2 1.0
N B:GLU413 4.7 36.5 1.0
C B:ASP426 4.8 47.2 1.0
CA B:ARG416 4.8 40.4 1.0
CZ B:ARG416 4.8 51.2 1.0
N B:ARG417 4.9 38.0 1.0
CD2 B:TYR427 4.9 39.2 1.0

Calcium binding site 4 out of 6 in 5oxg

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Calcium binding site 4 out of 6 in the Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:73.2
occ:1.00
 CB C:ALA205 3.9 47.7 1.0
CG2 C:THR271 3.9 45.0 1.0
CB C:GLN278 4.2 50.6 1.0
CB C:ASP269 4.2 42.4 1.0
CD2 C:TRP280 4.3 45.1 1.0
CG C:TRP280 4.3 40.5 1.0
CD1 C:TRP280 4.5 40.5 1.0
CE2 C:TRP280 4.5 44.6 1.0
O C:ASP269 4.5 40.6 1.0
O C:GLN278 4.5 43.1 1.0
O C:HOH613 4.5 46.4 1.0
NE1 C:TRP280 4.6 42.1 1.0
C C:ASP269 4.6 40.0 1.0
N C:THR271 4.6 42.8 1.0
CB C:THR271 4.7 44.3 1.0
CE3 C:TRP280 4.7 47.4 1.0
CB C:TRP280 4.8 40.1 1.0
CA C:MET270 4.8 42.1 1.0
C C:MET270 4.8 42.3 1.0
N C:MET270 4.9 39.1 1.0
CD C:GLN278 4.9 64.2 1.0
C C:GLN278 4.9 44.0 1.0
OE1 C:GLN278 4.9 65.3 1.0

Calcium binding site 5 out of 6 in 5oxg

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Calcium binding site 5 out of 6 in the Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:0.9
occ:1.00
 O C:GLU413 2.9 44.1 1.0
O C:LYS428 2.9 43.2 1.0
N C:LYS428 3.2 50.7 1.0
CD1 C:TYR427 3.3 44.0 1.0
CA C:GLU413 3.4 40.9 1.0
NE C:ARG416 3.5 52.3 1.0
C C:GLU413 3.6 39.1 1.0
CD C:ARG416 3.6 48.0 1.0
CE1 C:TYR427 3.6 44.4 1.0
CA C:TYR427 3.8 47.5 1.0
CB C:ARG416 3.8 43.1 1.0
C C:LYS428 3.9 46.7 1.0
CB C:GLU413 4.0 42.4 1.0
CG C:TYR427 4.0 45.0 1.0
C C:TYR427 4.0 49.7 1.0
CA C:LYS428 4.1 51.0 1.0
CG C:ARG416 4.2 47.3 1.0
O C:ASP426 4.2 47.8 1.0
CG C:GLU413 4.4 41.3 1.0
CZ C:TYR427 4.4 45.2 1.0
CB C:TYR427 4.4 45.9 1.0
CG C:ARG417 4.4 46.8 1.0
O C:TRP412 4.6 43.0 1.0
CD C:ARG417 4.6 47.2 1.0
N C:GLU413 4.6 42.4 1.0
CZ3 C:TRP412 4.7 39.0 1.0
CD2 C:TYR427 4.7 44.5 1.0
CZ C:ARG416 4.8 53.6 1.0
N C:TYR427 4.8 48.9 1.0
CB C:LYS428 4.8 53.5 1.0
N C:VAL414 4.9 40.9 1.0
CE3 C:TRP412 4.9 36.6 1.0
CE2 C:TYR427 4.9 47.0 1.0
C C:ASP426 4.9 51.3 1.0

Calcium binding site 6 out of 6 in 5oxg

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Calcium binding site 6 out of 6 in the Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the ACVR1 (ALK2) Kinase in Complex with Ldn- 212854 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca503

b:0.1
occ:1.00
 O D:GLU413 2.6 30.4 1.0
CD1 D:TYR427 3.3 37.2 1.0
O D:LYS428 3.4 36.1 1.0
C D:GLU413 3.4 28.6 1.0
N D:LYS428 3.5 41.1 1.0
CA D:GLU413 3.5 30.3 1.0
NE D:ARG416 3.6 39.5 1.0
CD D:ARG416 3.6 38.5 1.0
CB D:ARG416 3.6 34.8 1.0
CE1 D:TYR427 3.7 38.9 1.0
CA D:TYR427 3.7 41.0 1.0
CG D:ARG417 4.0 35.7 1.0
CB D:GLU413 4.0 30.8 1.0
CG D:TYR427 4.0 38.3 1.0
C D:TYR427 4.1 41.7 1.0
O D:ASP426 4.2 43.8 1.0
CG D:ARG416 4.2 37.1 1.0
C D:LYS428 4.3 39.8 1.0
CD D:ARG417 4.3 37.3 1.0
CB D:TYR427 4.4 40.5 1.0
CA D:LYS428 4.4 42.8 1.0
O D:TRP412 4.5 32.8 1.0
CG D:GLU413 4.6 31.2 1.0
CZ D:TYR427 4.7 40.4 1.0
N D:GLU413 4.7 30.9 1.0
N D:TYR427 4.7 39.8 1.0
N D:VAL414 4.7 30.1 1.0
C D:ASP426 4.8 45.9 1.0
CA D:ARG416 4.8 34.1 1.0
CZ D:ARG416 4.8 41.5 1.0
CD2 D:TYR427 4.9 37.8 1.0
N D:ARG417 5.0 36.4 1.0

Reference:

E.Williams, A.N.Bullock. Structural Basis For the Potent and Selective Binding of Ldn-212854 to the Bmp Receptor Kinase ALK2. Bone V. 109 251 2018.
ISSN: ISSN 1873-2763
PubMed: 28918311
DOI: 10.1016/J.BONE.2017.09.004
Page generated: Mon Jul 15 09:55:00 2024

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