Zinc 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:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 15B, PDB code: 5h2r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5h2r

Go back to Zinc Binding Sites List in 5h2r
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:15.1
occ:1.00
OD2 A:ASP710 2.1 9.7 1.0
NE2 A:HIS709 2.1 8.4 1.0
NE2 A:HIS673 2.2 9.5 1.0
OD1 A:ASP823 2.2 12.1 1.0
O A:HOH1175 2.2 10.4 1.0
O A:HOH1102 2.3 10.7 1.0
CD2 A:HIS709 3.0 8.8 1.0
CG A:ASP823 3.1 12.3 1.0
CD2 A:HIS673 3.1 10.1 1.0
CG A:ASP710 3.1 8.5 1.0
CE1 A:HIS709 3.2 8.6 1.0
CE1 A:HIS673 3.2 8.4 1.0
OD2 A:ASP823 3.3 15.6 1.0
OD1 A:ASP710 3.6 8.7 1.0
MG A:MG1002 3.9 13.1 1.0
CD2 A:HIS669 4.1 15.4 1.0
O A:HOH1239 4.1 8.1 1.0
CG A:HIS709 4.2 8.3 1.0
O A:HOH1162 4.2 12.3 1.0
NE2 A:HIS669 4.2 14.9 1.0
ND1 A:HIS709 4.3 8.9 1.0
CG A:HIS673 4.3 8.7 1.0
ND1 A:HIS673 4.3 8.8 1.0
CB A:ASP710 4.4 6.7 1.0
CB A:ASP823 4.5 10.3 1.0
CG2 A:VAL677 4.9 12.1 1.0
O A:HOH1107 4.9 12.2 1.0
CA A:ASP823 4.9 9.3 1.0
C24 A:LLN1003 5.0 13.5 1.0

Zinc binding site 2 out of 2 in 5h2r

Go back to Zinc Binding Sites List in 5h2r
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:16.5
occ:1.00
OD1 B:ASP823 2.1 10.2 1.0
NE2 B:HIS709 2.1 13.6 1.0
NE2 B:HIS673 2.2 11.0 1.0
OD2 B:ASP710 2.2 13.1 1.0
O B:HOH1110 2.3 16.4 1.0
O B:HOH1101 2.5 11.8 1.0
CD2 B:HIS709 3.0 14.1 1.0
CG B:ASP823 3.1 11.6 1.0
CD2 B:HIS673 3.1 12.1 1.0
CE1 B:HIS709 3.2 13.9 1.0
CG B:ASP710 3.2 11.3 1.0
CE1 B:HIS673 3.2 11.2 1.0
OD2 B:ASP823 3.3 12.7 1.0
OD1 B:ASP710 3.7 12.7 1.0
MG B:MG1002 4.0 16.5 1.0
O B:HOH1113 4.1 12.3 1.0
O B:HOH1228 4.1 11.8 1.0
NE2 B:HIS669 4.1 15.1 1.0
CD2 B:HIS669 4.1 14.9 1.0
CG B:HIS709 4.2 13.6 1.0
CG B:HIS673 4.2 10.9 1.0
ND1 B:HIS709 4.3 15.1 1.0
ND1 B:HIS673 4.3 11.9 1.0
CB B:ASP710 4.4 11.3 1.0
CB B:ASP823 4.5 9.0 1.0
CG2 B:VAL677 4.7 13.3 1.0
CA B:ASP823 4.9 8.1 1.0
O B:HOH1103 4.9 7.8 1.0
C24 B:LLN1003 4.9 11.6 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: Wed Dec 16 06:20:00 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy