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Magnesium in PDB 5h2r: Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 15B

Protein crystallography data

The structure of Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 15B, PDB code: 5h2r was solved by C.G.Noble, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.16 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.756, 97.756, 120.783, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 22.4

Other elements in 5h2r:

The structure of Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 15B also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 15B (pdb code 5h2r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 15B, PDB code: 5h2r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5h2r

Go back to Magnesium Binding Sites List in 5h2r
Magnesium binding site 1 out of 2 in the Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 15B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 15B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:13.1
occ:1.00
O A:HOH1204 2.0 8.4 1.0
O A:HOH1239 2.0 8.1 1.0
O A:HOH1102 2.0 10.7 1.0
OD1 A:ASP710 2.1 8.7 1.0
O A:HOH1112 2.1 7.8 1.0
O A:HOH1107 2.3 12.2 1.0
CG A:ASP710 3.1 8.5 1.0
OD2 A:ASP710 3.5 9.7 1.0
ZN A:ZN1001 3.9 15.1 1.0
NE2 A:HIS745 4.0 10.5 1.0
OE2 A:GLU742 4.0 13.8 1.0
O A:HOH1175 4.1 10.4 1.0
O A:HOH1219 4.1 13.3 1.0
O A:HOH1101 4.2 42.8 1.0
O A:HIS709 4.2 7.7 1.0
OG1 A:THR783 4.3 9.8 1.0
CD2 A:HIS745 4.3 11.2 1.0
CD2 A:HIS713 4.4 13.2 1.0
CD2 A:HIS709 4.4 8.8 1.0
OD2 A:ASP823 4.4 15.6 1.0
CB A:ASP710 4.4 6.7 1.0
NE2 A:HIS669 4.5 14.9 1.0
C23 A:LLN1003 4.5 15.2 1.0
C24 A:LLN1003 4.6 13.5 1.0
NE2 A:HIS713 4.7 12.9 1.0
CD2 A:HIS669 4.7 15.4 1.0
CB A:THR783 4.8 10.0 1.0
NE2 A:HIS709 4.8 8.4 1.0
CA A:ASP710 4.8 6.1 1.0
O A:THR783 4.9 12.9 1.0
CD A:GLU742 4.9 13.0 1.0

Magnesium binding site 2 out of 2 in 5h2r

Go back to Magnesium Binding Sites List in 5h2r
Magnesium binding site 2 out of 2 in the Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 15B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 15B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:16.5
occ:1.00
O B:HOH1228 1.9 11.8 1.0
OD1 B:ASP710 2.0 12.7 1.0
O B:HOH1101 2.1 11.8 1.0
O B:HOH1168 2.1 13.8 1.0
O B:HOH1103 2.2 7.8 1.0
O B:HOH1147 2.2 11.3 1.0
CG B:ASP710 3.1 11.3 1.0
OD2 B:ASP710 3.5 13.1 1.0
NE2 B:HIS745 3.9 13.2 1.0
OE2 B:GLU742 4.0 10.8 1.0
ZN B:ZN1001 4.0 16.5 1.0
O B:HIS709 4.1 14.9 1.0
O B:HOH1110 4.2 16.4 1.0
CD2 B:HIS745 4.2 13.5 1.0
OG1 B:THR783 4.2 14.2 1.0
CD2 B:HIS709 4.3 14.1 1.0
O B:HOH1247 4.3 10.2 1.0
CB B:ASP710 4.4 11.3 1.0
O B:HOH1111 4.4 25.0 1.0
CD2 B:HIS713 4.4 14.1 1.0
OD2 B:ASP823 4.5 12.7 1.0
NE2 B:HIS669 4.6 15.1 1.0
CA B:ASP710 4.7 10.5 1.0
NE2 B:HIS709 4.7 13.6 1.0
C24 B:LLN1003 4.7 11.6 1.0
CB B:THR783 4.7 17.2 1.0
C23 B:LLN1003 4.7 11.0 1.0
NE2 B:HIS713 4.8 13.5 1.0
CD2 B:HIS669 4.9 14.9 1.0
CD B:GLU742 4.9 12.2 1.0
C B:HIS709 4.9 14.8 1.0
O B:HOH1261 4.9 14.5 1.0

Reference:

P.S.Ng, C.G.Noble, F.S.B.Ng, S.H.Chew, C.C.Lim, V.Manoharan, K.F.Wan, P.Vachaspati, M.Kaiser, N.L.Ma, P.Gedeck, C.Kounde, S.P.S.Rao. Trypanosomal Phosphodiesterase B1 and B2 As A Potential Therapy For Human African Trypanosomiasis To Be Published.
Page generated: Mon Dec 14 20:25:57 2020

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