Magnesium in PDB 4qpf: New Lower Bone Affinity Bisphosphonate Drug Design For Effective Use in Diseases Characterized By Abnormal Bone Resorption

Enzymatic activity of New Lower Bone Affinity Bisphosphonate Drug Design For Effective Use in Diseases Characterized By Abnormal Bone Resorption

All present enzymatic activity of New Lower Bone Affinity Bisphosphonate Drug Design For Effective Use in Diseases Characterized By Abnormal Bone Resorption:
2.5.1.1; 2.5.1.10;

Protein crystallography data

The structure of New Lower Bone Affinity Bisphosphonate Drug Design For Effective Use in Diseases Characterized By Abnormal Bone Resorption, PDB code: 4qpf was solved by F.H.Ebetino, M.Lundy, A.A.Kwaasi, J.E.Dunford, Z.Duan, J.Triffitt, A.Mazur, G.Jeans, B.L.Barnett, R.G.G.Russell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.45 / 1.59
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 112.226, 112.226, 65.979, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 20.6

Other elements in 4qpf:

The structure of New Lower Bone Affinity Bisphosphonate Drug Design For Effective Use in Diseases Characterized By Abnormal Bone Resorption also contains other interesting chemical elements:

Fluorine (F) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the New Lower Bone Affinity Bisphosphonate Drug Design For Effective Use in Diseases Characterized By Abnormal Bone Resorption (pdb code 4qpf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the New Lower Bone Affinity Bisphosphonate Drug Design For Effective Use in Diseases Characterized By Abnormal Bone Resorption, PDB code: 4qpf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4qpf

Go back to Magnesium Binding Sites List in 4qpf
Magnesium binding site 1 out of 3 in the New Lower Bone Affinity Bisphosphonate Drug Design For Effective Use in Diseases Characterized By Abnormal Bone Resorption


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of New Lower Bone Affinity Bisphosphonate Drug Design For Effective Use in Diseases Characterized By Abnormal Bone Resorption within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:13.8
occ:1.00
 O5 A:39L901 2.0 11.2 1.0
O A:HOH1009 2.1 12.5 1.0
O A:HOH1003 2.1 12.8 1.0
OD2 A:ASP103 2.1 13.4 1.0
O2 A:39L901 2.1 12.2 1.0
OD2 A:ASP107 2.2 11.4 1.0
CG A:ASP103 3.1 13.6 1.0
MG A:MG903 3.1 13.1 1.0
CG A:ASP107 3.3 12.1 1.0
P2 A:39L901 3.3 13.7 1.0
P1 A:39L901 3.4 12.5 1.0
OD1 A:ASP103 3.4 12.4 1.0
C9 A:39L901 3.7 13.5 1.0
CB A:ASP107 3.7 12.7 1.0
O1 A:39L901 3.8 14.7 1.0
O A:HOH1022 3.9 15.1 1.0
C8 A:39L901 4.0 13.3 1.0
O4 A:39L901 4.1 13.9 1.0
NH2 A:ARG112 4.2 14.5 1.0
O A:HOH1006 4.3 13.4 1.0
O A:HOH1002 4.3 14.1 1.0
CB A:ASP103 4.4 12.8 1.0
O A:ASP103 4.4 13.6 1.0
OD1 A:ASP107 4.4 13.6 1.0
OG A:SER109 4.4 14.5 1.0
O A:HOH1016 4.5 15.8 1.0
OD1 A:ASP104 4.5 14.8 1.0
O6 A:39L901 4.5 14.4 1.0
O3 A:39L901 4.6 12.9 1.0
C A:ASP103 4.7 12.1 1.0
O A:HOH1017 4.7 14.6 1.0
O A:HOH1041 4.9 14.5 1.0
MG A:MG904 4.9 14.2 1.0
O A:HOH1026 5.0 14.8 1.0

Magnesium binding site 2 out of 3 in 4qpf

Go back to Magnesium Binding Sites List in 4qpf
Magnesium binding site 2 out of 3 in the New Lower Bone Affinity Bisphosphonate Drug Design For Effective Use in Diseases Characterized By Abnormal Bone Resorption


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of New Lower Bone Affinity Bisphosphonate Drug Design For Effective Use in Diseases Characterized By Abnormal Bone Resorption within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:13.1
occ:1.00
 OD1 A:ASP103 2.1 12.4 1.0
O2 A:39L901 2.1 12.2 1.0
O A:HOH1017 2.1 14.6 1.0
O A:HOH1026 2.1 14.8 1.0
O A:HOH1006 2.1 13.4 1.0
OD2 A:ASP107 2.1 11.4 1.0
CG A:ASP107 3.0 12.1 1.0
CG A:ASP103 3.0 13.6 1.0
MG A:MG902 3.1 13.8 1.0
OD1 A:ASP107 3.2 13.6 1.0
OD2 A:ASP103 3.3 13.4 1.0
P1 A:39L901 3.3 12.5 1.0
O3 A:39L901 3.4 12.9 1.0
OD1 A:ASP174 4.0 19.5 1.0
NE2 A:GLN171 4.1 16.6 1.0
OE1 A:GLN171 4.2 16.5 1.0
O A:HOH1003 4.2 12.8 1.0
NZ A:LYS266 4.3 11.5 0.5
NZ A:LYS266 4.3 14.3 0.5
O1 A:39L901 4.3 14.7 1.0
OD2 A:ASP174 4.3 20.5 1.0
CB A:ASP103 4.4 12.8 1.0
CG A:ASP174 4.4 18.4 1.0
O A:HOH1027 4.4 15.6 1.0
CB A:ASP107 4.5 12.7 1.0
C9 A:39L901 4.6 13.5 1.0
C8 A:39L901 4.6 13.3 1.0
CD A:GLN171 4.6 16.4 1.0
CE A:LYS266 4.7 15.1 0.5
O5 A:39L901 4.7 11.2 1.0
O A:HOH1009 4.8 12.5 1.0
C2 A:39L901 4.8 14.1 1.0
O A:ASP103 4.8 13.6 1.0
C3 A:39L901 4.8 15.1 1.0
NZ A:LYS200 5.0 15.6 1.0
N2 A:39L901 5.0 13.2 1.0

Magnesium binding site 3 out of 3 in 4qpf

Go back to Magnesium Binding Sites List in 4qpf
Magnesium binding site 3 out of 3 in the New Lower Bone Affinity Bisphosphonate Drug Design For Effective Use in Diseases Characterized By Abnormal Bone Resorption


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of New Lower Bone Affinity Bisphosphonate Drug Design For Effective Use in Diseases Characterized By Abnormal Bone Resorption within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg904

b:14.2
occ:1.00
 O4 A:39L901 2.0 13.9 1.0
O1 A:39L901 2.0 14.7 1.0
O A:HOH1007 2.1 13.4 1.0
OD2 A:ASP243 2.1 12.0 1.0
O A:HOH1035 2.1 15.1 1.0
O A:HOH1002 2.2 14.1 1.0
CG A:ASP243 3.1 15.8 1.0
P2 A:39L901 3.2 13.7 1.0
P1 A:39L901 3.4 12.5 1.0
OD1 A:ASP243 3.5 19.4 1.0
F A:39L901 3.5 13.9 1.0
C9 A:39L901 3.6 13.5 1.0
NZ A:LYS257 3.8 22.3 0.5
OD1 A:ASP247 3.9 20.6 1.0
O5 A:39L901 4.0 11.2 1.0
O A:HOH1064 4.0 26.4 1.0
O A:HOH1027 4.1 15.6 1.0
O A:HOH1003 4.1 12.8 1.0
O A:ASP243 4.2 16.1 1.0
NE2 A:GLN240 4.2 14.7 1.0
O2 A:39L901 4.3 12.2 1.0
OD1 A:ASP261 4.3 15.8 1.0
OD2 A:ASP261 4.4 16.1 1.0
O6 A:39L901 4.4 14.4 1.0
O3 A:39L901 4.4 12.9 1.0
CB A:ASP243 4.4 14.3 1.0
OD1 A:ASP244 4.5 14.9 1.0
C A:ASP243 4.5 14.2 1.0
CG A:ASP247 4.6 19.0 1.0
O A:HOH1022 4.7 15.1 1.0
CB A:ASP247 4.8 14.9 1.0
CG A:ASP261 4.8 16.7 1.0
MG A:MG902 4.9 13.8 1.0
N A:ASP244 4.9 13.9 1.0
NZ A:LYS257 5.0 22.9 0.5
CE A:LYS257 5.0 22.2 0.5

Reference:

F.H.Ebetino, M.Lundy, A.A.Kwaasi, J.E.Dunford, Z.Duan, J.Triffitt, A.Mazur, G.Jeans, B.L.Barnett, R.G.G.Russell. New Lower Bone Affinity Bisphosphonate Drug Design For Effective Use in Diseases Characterized By Abnormal Bone Resorption To Be Published.
Page generated: Mon Dec 14 19:24:05 2020

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