Atomistry » Magnesium » PDB 5gxv-5hdb » 5h2q
Atomistry »
  Magnesium »
    PDB 5gxv-5hdb »
      5h2q »

Magnesium in PDB 5h2q: Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 13E

Protein crystallography data

The structure of Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 13E, PDB code: 5h2q 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) 84.19 / 1.66
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.210, 97.210, 120.440, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 20

Other elements in 5h2q:

The structure of Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 13E 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 13E (pdb code 5h2q). 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 13E, PDB code: 5h2q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5h2q

Go back to Magnesium Binding Sites List in 5h2q
Magnesium binding site 1 out of 2 in the Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 13E


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 13E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:15.5
occ:1.00
O A:HOH1291 2.1 14.9 1.0
OD1 A:ASP710 2.1 12.7 1.0
O A:HOH1101 2.1 13.3 1.0
O A:HOH1122 2.1 16.0 1.0
O A:HOH1116 2.2 15.7 1.0
O A:HOH1106 2.2 13.0 1.0
CG A:ASP710 3.1 13.4 1.0
OD2 A:ASP710 3.5 12.7 1.0
ZN A:ZN1001 3.9 17.1 1.0
NE2 A:HIS745 4.0 12.5 1.0
OE2 A:GLU742 4.0 17.1 1.0
O A:HOH1199 4.1 15.7 1.0
O A:HIS709 4.2 14.3 1.0
OG1 A:THR783 4.2 13.2 1.0
O A:HOH1303 4.3 17.0 1.0
CD2 A:HIS709 4.3 11.8 1.0
CD2 A:HIS745 4.3 13.5 1.0
OD2 A:ASP823 4.4 16.7 1.0
CB A:ASP710 4.4 9.9 1.0
CD2 A:HIS713 4.5 16.1 1.0
O A:HOH1104 4.5 28.7 1.0
C19 A:LLI1003 4.5 16.5 1.0
NE2 A:HIS669 4.6 15.8 1.0
C18 A:LLI1003 4.6 20.0 1.0
CB A:THR783 4.7 15.4 1.0
NE2 A:HIS709 4.7 11.6 1.0
NE2 A:HIS713 4.8 15.8 1.0
CA A:ASP710 4.8 9.7 1.0
CD2 A:HIS669 4.8 16.3 1.0
O A:THR783 4.8 16.9 1.0
CD A:GLU742 4.9 18.0 1.0
O A:HOH1175 4.9 20.7 1.0
CG A:GLU742 5.0 14.6 1.0

Magnesium binding site 2 out of 2 in 5h2q

Go back to Magnesium Binding Sites List in 5h2q
Magnesium binding site 2 out of 2 in the Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 13E


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 13E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:15.5
occ:1.00
OD1 B:ASP710 2.0 14.7 1.0
O B:HOH1106 2.1 14.3 1.0
O B:HOH1102 2.1 15.8 1.0
O B:HOH1267 2.1 16.2 1.0
O B:HOH1155 2.1 14.2 1.0
O B:HOH1137 2.1 13.8 1.0
CG B:ASP710 3.1 17.3 1.0
OD2 B:ASP710 3.5 15.7 1.0
NE2 B:HIS745 4.0 17.2 1.0
ZN B:ZN1001 4.0 18.8 1.0
OE2 B:GLU742 4.1 17.0 1.0
O B:HIS709 4.1 15.7 1.0
OG1 B:THR783 4.1 14.4 1.0
O B:HOH1108 4.2 15.3 1.0
CD2 B:HIS709 4.3 17.1 1.0
CD2 B:HIS745 4.3 17.4 1.0
O B:HOH1250 4.3 13.8 1.0
CB B:ASP710 4.4 13.3 1.0
O B:HOH1113 4.4 26.4 1.0
OD2 B:ASP823 4.4 16.9 1.0
CD2 B:HIS713 4.6 16.5 1.0
NE2 B:HIS669 4.6 17.7 1.0
C19 B:LLI1003 4.6 16.2 1.0
NE2 B:HIS709 4.7 16.6 1.0
C18 B:LLI1003 4.7 15.1 1.0
CB B:THR783 4.7 19.1 1.0
CA B:ASP710 4.8 13.4 1.0
CD2 B:HIS669 4.9 17.8 1.0
NE2 B:HIS713 4.9 15.5 1.0
O B:HOH1245 4.9 17.0 1.0
CD B:GLU742 4.9 20.6 1.0
O B:THR783 4.9 14.0 1.0
CG B:GLU742 4.9 17.6 1.0
C B:HIS709 5.0 18.0 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 20:25:56 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy