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Zinc in PDB 6bto: BMP1 Complexed with (2~{S})-2-[[(1~{R},3~{S},4~{S})-2-[(2~{R})-2-[2- (Oxidanylamino)-2-Oxidanylidene-Ethyl]Heptanoyl]-2- Azabicyclo[2.2.1]Heptan-3-Yl]Carbonylamino]-2-Phenyl-Ethanoic Acid

Enzymatic activity of BMP1 Complexed with (2~{S})-2-[[(1~{R},3~{S},4~{S})-2-[(2~{R})-2-[2- (Oxidanylamino)-2-Oxidanylidene-Ethyl]Heptanoyl]-2- Azabicyclo[2.2.1]Heptan-3-Yl]Carbonylamino]-2-Phenyl-Ethanoic Acid

All present enzymatic activity of BMP1 Complexed with (2~{S})-2-[[(1~{R},3~{S},4~{S})-2-[(2~{R})-2-[2- (Oxidanylamino)-2-Oxidanylidene-Ethyl]Heptanoyl]-2- Azabicyclo[2.2.1]Heptan-3-Yl]Carbonylamino]-2-Phenyl-Ethanoic Acid:
3.4.24.19;

Protein crystallography data

The structure of BMP1 Complexed with (2~{S})-2-[[(1~{R},3~{S},4~{S})-2-[(2~{R})-2-[2- (Oxidanylamino)-2-Oxidanylidene-Ethyl]Heptanoyl]-2- Azabicyclo[2.2.1]Heptan-3-Yl]Carbonylamino]-2-Phenyl-Ethanoic Acid, PDB code: 6bto was solved by R.Gampe, L.Shewchuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.45 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.291, 124.643, 43.776, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.5

Zinc Binding Sites:

The binding sites of Zinc atom in the BMP1 Complexed with (2~{S})-2-[[(1~{R},3~{S},4~{S})-2-[(2~{R})-2-[2- (Oxidanylamino)-2-Oxidanylidene-Ethyl]Heptanoyl]-2- Azabicyclo[2.2.1]Heptan-3-Yl]Carbonylamino]-2-Phenyl-Ethanoic Acid (pdb code 6bto). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the BMP1 Complexed with (2~{S})-2-[[(1~{R},3~{S},4~{S})-2-[(2~{R})-2-[2- (Oxidanylamino)-2-Oxidanylidene-Ethyl]Heptanoyl]-2- Azabicyclo[2.2.1]Heptan-3-Yl]Carbonylamino]-2-Phenyl-Ethanoic Acid, PDB code: 6bto:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6bto

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Zinc binding site 1 out of 3 in the BMP1 Complexed with (2~{S})-2-[[(1~{R},3~{S},4~{S})-2-[(2~{R})-2-[2- (Oxidanylamino)-2-Oxidanylidene-Ethyl]Heptanoyl]-2- Azabicyclo[2.2.1]Heptan-3-Yl]Carbonylamino]-2-Phenyl-Ethanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of BMP1 Complexed with (2~{S})-2-[[(1~{R},3~{S},4~{S})-2-[(2~{R})-2-[2- (Oxidanylamino)-2-Oxidanylidene-Ethyl]Heptanoyl]-2- Azabicyclo[2.2.1]Heptan-3-Yl]Carbonylamino]-2-Phenyl-Ethanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:11.9
occ:1.00
 NE2 A:HIS97 2.1 12.4 1.0
NE2 A:HIS93 2.2 10.7 1.0
NE2 A:HIS103 2.2 11.7 1.0
O23 A:E8P304 2.3 29.0 1.0
O A:HOH471 2.4 16.0 1.0
O26 A:E8P304 2.4 27.0 1.0
C22 A:E8P304 3.0 29.9 1.0
CE1 A:HIS97 3.1 12.8 1.0
CD2 A:HIS93 3.1 11.2 1.0
CE1 A:HIS103 3.1 11.7 1.0
CD2 A:HIS103 3.1 11.8 1.0
N24 A:E8P304 3.1 29.4 1.0
CE1 A:HIS93 3.2 10.7 1.0
CD2 A:HIS97 3.2 13.3 1.0
O A:HOH467 4.2 15.9 1.0
ND1 A:HIS97 4.2 14.0 1.0
ND1 A:HIS103 4.2 11.7 1.0
O A:HOH412 4.3 25.0 1.0
CG A:HIS103 4.3 11.7 1.0
ND1 A:HIS93 4.3 11.1 1.0
CG A:HIS93 4.3 11.5 1.0
CG A:HIS97 4.3 14.3 1.0
C33 A:E8P304 4.3 31.3 1.0
OE2 A:GLU94 4.4 12.8 1.0
C19 A:E8P304 4.5 30.6 1.0
O A:HOH442 4.6 17.3 1.0
CE A:MET150 4.9 13.2 1.0

Zinc binding site 2 out of 3 in 6bto

Go back to Zinc Binding Sites List in 6bto
Zinc binding site 2 out of 3 in the BMP1 Complexed with (2~{S})-2-[[(1~{R},3~{S},4~{S})-2-[(2~{R})-2-[2- (Oxidanylamino)-2-Oxidanylidene-Ethyl]Heptanoyl]-2- Azabicyclo[2.2.1]Heptan-3-Yl]Carbonylamino]-2-Phenyl-Ethanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of BMP1 Complexed with (2~{S})-2-[[(1~{R},3~{S},4~{S})-2-[(2~{R})-2-[2- (Oxidanylamino)-2-Oxidanylidene-Ethyl]Heptanoyl]-2- Azabicyclo[2.2.1]Heptan-3-Yl]Carbonylamino]-2-Phenyl-Ethanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:78.6
occ:1.00
 OD2 A:ASP145 2.7 21.8 1.0
OD1 A:ASP189 3.1 20.1 1.0
C A:GLY188 3.3 26.3 1.0
N A:ASP189 3.3 25.1 1.0
CB A:ASP145 3.4 21.1 1.0
CG A:ASP145 3.5 21.8 1.0
O A:GLY188 3.5 26.8 1.0
CB A:SER148 3.6 15.8 1.0
OG A:SER148 3.7 15.5 1.0
CA A:ASP189 3.7 24.4 1.0
CA A:GLY188 3.9 27.3 1.0
CG A:ASP189 3.9 21.1 1.0
OG A:SER186 4.1 24.1 1.0
OE1 A:GLN192 4.2 26.9 1.0
OE1 A:GLU104 4.3 17.4 1.0
CB A:ASP189 4.4 23.0 1.0
CA A:SER148 4.5 16.4 1.0
CD A:GLU104 4.5 16.2 1.0
OE2 A:GLU104 4.6 16.4 1.0
OD1 A:ASP145 4.7 22.3 1.0
CB A:GLN192 4.8 30.1 1.0
OD2 A:ASP189 4.8 20.4 1.0
CD A:GLN192 4.8 28.1 1.0
CA A:ASP145 4.9 20.8 1.0
C A:ASP189 5.0 26.6 1.0

Zinc binding site 3 out of 3 in 6bto

Go back to Zinc Binding Sites List in 6bto
Zinc binding site 3 out of 3 in the BMP1 Complexed with (2~{S})-2-[[(1~{R},3~{S},4~{S})-2-[(2~{R})-2-[2- (Oxidanylamino)-2-Oxidanylidene-Ethyl]Heptanoyl]-2- Azabicyclo[2.2.1]Heptan-3-Yl]Carbonylamino]-2-Phenyl-Ethanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of BMP1 Complexed with (2~{S})-2-[[(1~{R},3~{S},4~{S})-2-[(2~{R})-2-[2- (Oxidanylamino)-2-Oxidanylidene-Ethyl]Heptanoyl]-2- Azabicyclo[2.2.1]Heptan-3-Yl]Carbonylamino]-2-Phenyl-Ethanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:8.3
occ:1.00
 O B:HOH532 1.9 17.8 1.0
NE2 B:HIS93 2.0 8.4 1.0
NE2 B:HIS103 2.0 7.9 1.0
NE2 B:HIS97 2.1 8.1 1.0
CD2 B:HIS103 3.0 7.9 1.0
CE1 B:HIS103 3.0 8.0 1.0
CE1 B:HIS93 3.0 8.5 1.0
CD2 B:HIS93 3.0 8.4 1.0
CD2 B:HIS97 3.0 8.0 1.0
CE1 B:HIS97 3.1 8.2 1.0
ND1 B:HIS103 4.1 8.2 1.0
O B:HOH445 4.1 23.5 1.0
CG B:HIS103 4.1 8.1 1.0
ND1 B:HIS93 4.1 8.6 1.0
OE2 B:GLU94 4.1 10.4 1.0
CG B:HIS93 4.2 8.6 1.0
ND1 B:HIS97 4.2 8.2 1.0
CG B:HIS97 4.2 8.1 1.0
CE B:MET150 4.4 7.5 1.0
O B:HOH409 4.5 12.0 1.0
O B:HOH503 4.6 32.4 1.0
O B:HOH518 4.7 26.5 1.0
OG B:SER67 4.9 18.5 1.0
CD B:GLU94 4.9 9.9 1.0

Reference:

L.S.Kallander, D.Washburn, M.A.Hilfiker, H.S.Eidam, B.G.Lawhorn, J.Prendergast, R.Fox, S.Dowdell, S.Manns, T.Hoang, S.Zhao, G.Ye, M.Hammond, D.A.Holt, T.Roethke, X.Hong, R.A.Reid, R.Gampe, H.Zhang, E.Diaz, A.R.Rendina, A.M.Quinn, B.Willette. Reverse Hydroxamate Inhibitors of Bone Morphogenetic Protein 1. Acs Med Chem Lett V. 9 736 2018.
ISSN: ISSN 1948-5875
PubMed: 30034610
DOI: 10.1021/ACSMEDCHEMLETT.8B00173
Page generated: Mon Oct 28 18:20:05 2024

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