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Zinc in PDB 6fdw: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-356

Protein crystallography data

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-356, PDB code: 6fdw was solved by A.K.Singh, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.91 / 1.96
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.690, 119.260, 67.970, 90.00, 108.38, 90.00
R / Rfree (%) 19 / 23.7

Other elements in 6fdw:

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-356 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 Pde-B1 Catalytic Domain with Inhibitor Npd-356 (pdb code 6fdw). 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 Pde-B1 Catalytic Domain with Inhibitor Npd-356, PDB code: 6fdw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6fdw

Go back to Zinc Binding Sites List in 6fdw
Zinc binding site 1 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-356


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 Pde-B1 Catalytic Domain with Inhibitor Npd-356 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:41.5
occ:1.00
O A:HOH1105 1.9 38.9 1.0
OD2 A:ASP710 1.9 33.5 1.0
NE2 A:HIS673 2.1 37.3 1.0
NE2 A:HIS709 2.2 34.0 1.0
O A:HOH1165 2.2 41.0 1.0
OD1 A:ASP822 2.3 38.0 1.0
CD2 A:HIS709 3.0 32.2 1.0
CD2 A:HIS673 3.1 37.3 1.0
CE1 A:HIS673 3.1 37.7 1.0
CG A:ASP710 3.1 35.1 1.0
CG A:ASP822 3.2 38.1 1.0
CE1 A:HIS709 3.2 33.9 1.0
OD2 A:ASP822 3.4 42.2 1.0
OD1 A:ASP710 3.7 34.3 1.0
MG A:MG1003 3.9 32.2 1.0
O A:HOH1193 4.1 40.6 1.0
CD2 A:HIS669 4.1 40.8 1.0
O A:HOH1166 4.1 44.7 1.0
ND1 A:HIS673 4.2 34.7 1.0
CG A:HIS673 4.2 40.3 1.0
CG A:HIS709 4.2 36.0 1.0
CB A:ASP710 4.3 35.3 1.0
ND1 A:HIS709 4.3 31.8 1.0
NE2 A:HIS669 4.4 40.5 1.0
CB A:ASP822 4.6 38.3 1.0
O A:HOH1107 4.6 29.6 1.0
C21 A:D621001 4.9 50.3 1.0
CG2 A:VAL677 5.0 35.6 1.0
CA A:ASP822 5.0 36.4 1.0

Zinc binding site 2 out of 2 in 6fdw

Go back to Zinc Binding Sites List in 6fdw
Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-356


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 Pde-B1 Catalytic Domain with Inhibitor Npd-356 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:36.7
occ:1.00
NE2 B:HIS673 2.1 32.8 1.0
OD2 B:ASP710 2.1 33.9 1.0
O B:HOH1158 2.1 30.2 1.0
OD1 B:ASP822 2.2 32.1 1.0
NE2 B:HIS709 2.2 30.1 1.0
O B:HOH1109 2.3 34.5 1.0
CG B:ASP822 3.0 33.5 1.0
CD2 B:HIS673 3.1 35.7 1.0
CE1 B:HIS673 3.1 37.1 1.0
CD2 B:HIS709 3.1 27.8 1.0
CG B:ASP710 3.2 37.7 1.0
CE1 B:HIS709 3.2 32.7 1.0
OD2 B:ASP822 3.3 35.0 1.0
OD1 B:ASP710 3.7 32.2 1.0
MG B:MG1003 3.8 22.1 1.0
O B:HOH1182 4.0 33.1 1.0
CD2 B:HIS669 4.1 35.6 1.0
ND1 B:HIS673 4.2 31.4 1.0
CG B:HIS673 4.2 37.0 1.0
CG B:HIS709 4.3 29.3 1.0
NE2 B:HIS669 4.3 32.1 1.0
ND1 B:HIS709 4.3 30.1 1.0
O B:HOH1132 4.4 40.1 1.0
CB B:ASP710 4.4 33.1 1.0
CB B:ASP822 4.4 33.0 1.0
O B:HOH1107 4.7 29.8 1.0
CA B:ASP822 4.9 34.3 1.0
CG2 B:VAL677 5.0 30.2 1.0
C21 B:D621001 5.0 49.0 1.0

Reference:

I.G.Salado, C.Moreno, G.Sakaine, A.K.Singh, A.R.Blaazer, M.Siderius, A.Matheeussen, S.Gul, L.Maes, R.Leurs, D.G.Brown, K.Augustyns. TBRPDEB1 Structure with Inhibitor Npd-356 To Be Published.
Page generated: Wed Dec 16 11:47:19 2020

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