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Nickel in PDB 6sf1: Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1).

Enzymatic activity of Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1).

All present enzymatic activity of Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1).:
2.7.11.30;

Protein crystallography data

The structure of Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1)., PDB code: 6sf1 was solved by R.M.Salmon, J.Guo, M.Yu, W.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.93 / 2.80
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 57.570, 57.570, 304.062, 90.00, 90.00, 120.00
R / Rfree (%) 24.4 / 27.9

Nickel Binding Sites:

The binding sites of Nickel atom in the Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1). (pdb code 6sf1). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1)., PDB code: 6sf1:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in 6sf1

Go back to Nickel Binding Sites List in 6sf1
Nickel binding site 1 out of 5 in the Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1).


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:100.0
occ:1.00
 OE2 A:GLU58 3.2 0.8 1.0
CD2 B:LEU378 3.2 52.6 1.0
N B:TYR358 3.5 54.0 1.0
OD1 B:ASN357 3.5 87.9 1.0
CG A:GLU58 3.7 92.1 1.0
CD A:GLU58 3.8 0.4 1.0
CA B:ASN357 3.9 66.4 1.0
CD B:LYS386 3.9 61.8 1.0
CB B:ASN357 4.0 65.6 1.0
CG B:ASN357 4.1 74.3 1.0
NZ B:LYS386 4.2 67.3 1.0
CG B:LEU378 4.2 51.8 1.0
C B:ASN357 4.2 52.3 1.0
ND1 B:HIS377 4.3 84.0 1.0
CB B:TYR358 4.4 60.5 1.0
CA B:TYR358 4.5 56.1 1.0
CE1 B:HIS377 4.6 88.3 1.0
CE B:LYS386 4.7 57.6 1.0
CD1 B:LEU378 4.9 50.9 1.0
O B:TYR358 4.9 74.4 1.0
OE1 A:GLU58 5.0 0.7 1.0

Nickel binding site 2 out of 5 in 6sf1

Go back to Nickel Binding Sites List in 6sf1
Nickel binding site 2 out of 5 in the Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1).


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni202

b:0.1
occ:1.00
 CD A:ARG78 3.9 50.2 1.0
N A:GLU75 4.0 64.1 1.0
CA A:GLU75 4.0 54.0 1.0
OE1 A:GLU75 4.1 82.7 1.0
CB A:GLU75 4.2 54.6 1.0
CG A:ARG74 4.2 66.8 1.0
NH1 A:ARG78 4.2 54.8 1.0
CB A:ARG74 4.4 53.8 1.0
C A:ARG74 4.4 64.9 1.0
CG A:ARG78 4.8 48.5 1.0
O A:ARG74 4.8 72.7 1.0
NE A:ARG78 4.9 51.8 1.0
CA A:ARG74 4.9 51.4 1.0

Nickel binding site 3 out of 5 in 6sf1

Go back to Nickel Binding Sites List in 6sf1
Nickel binding site 3 out of 5 in the Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1).


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni501

b:97.1
occ:1.00
 O B:HOH603 2.9 52.7 1.0
N B:ARG325 3.7 67.3 1.0
CA B:LYS324 4.0 65.6 1.0
CB B:ARG325 4.3 60.4 1.0
C B:LYS324 4.3 71.6 1.0
CB B:LYS324 4.4 69.1 1.0
CB B:CYS421 4.6 52.3 1.0
CA B:ARG325 4.6 60.3 1.0
CD2 B:LEU364 4.7 70.1 1.0
ND1 B:HIS363 4.8 57.0 1.0
SG B:CYS421 4.9 78.6 1.0
N B:CYS421 4.9 44.9 1.0
CE1 B:HIS363 4.9 63.1 1.0

Nickel binding site 4 out of 5 in 6sf1

Go back to Nickel Binding Sites List in 6sf1
Nickel binding site 4 out of 5 in the Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1).


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:93.2
occ:1.00
 N B:LYS368 3.4 50.3 1.0
CA B:THR367 3.7 51.0 1.0
CB B:THR367 3.8 49.6 1.0
CG B:LYS368 3.9 59.7 1.0
NZ B:LYS368 3.9 1.0 1.0
C B:THR367 4.0 51.4 1.0
CG2 B:THR367 4.2 45.1 1.0
CB B:LYS368 4.2 45.9 1.0
CA B:LYS368 4.4 47.6 1.0
CD B:LYS368 4.5 84.8 1.0
NE2 A:HIS73 4.5 73.3 1.0
CE B:LYS368 4.8 98.6 1.0
O B:HOH602 4.9 48.0 1.0
N B:THR367 4.9 50.3 1.0
O B:PRO366 5.0 64.3 1.0

Nickel binding site 5 out of 5 in 6sf1

Go back to Nickel Binding Sites List in 6sf1
Nickel binding site 5 out of 5 in the Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1).


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Bone Morphogenetic Protein 10 (BMP10) Complexed with Extracellular Domain of Activin Receptor-Like Kinase 1 (ALK1). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni503

b:0.4
occ:1.00
 OE1 B:GLU334 3.5 0.5 1.0
N B:ASP331 3.6 61.7 1.0
O B:TYR329 4.1 63.5 1.0
CB B:ASP331 4.2 62.1 1.0
O B:ASP331 4.2 80.8 1.0
CA B:ILE330 4.3 62.3 1.0
CB B:GLU334 4.3 67.7 1.0
CA B:ASP331 4.4 57.2 1.0
C B:ILE330 4.4 65.6 1.0
CG2 B:ILE335 4.6 47.8 1.0
CD B:GLU334 4.7 0.3 1.0
C B:ASP331 4.7 66.4 1.0
CG2 B:ILE330 4.9 74.1 1.0

Reference:

R.M.Salmon, J.Guo, J.H.Wood, Z.Tong, J.S.Beech, A.Lawera, M.Yu, D.J.Grainger, J.Reckless, N.W.Morrell, W.Li. Molecular Basis of ALK1-Mediated Signalling By BMP9/BMP10 and Their Prodomain-Bound Forms Nat Commun V. 11 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-020-15425-3
Page generated: Thu Oct 10 08:52:56 2024

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