Zinc in PDB 6sdm: Nadh-Dependent Variant of Tbadh

Enzymatic activity of Nadh-Dependent Variant of Tbadh

All present enzymatic activity of Nadh-Dependent Variant of Tbadh:
1.1.1.80;

Protein crystallography data

The structure of Nadh-Dependent Variant of Tbadh, PDB code: 6sdm was solved by L.Selles Vidal, J.W.Murray, J.T.Heap, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.68 / 2.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.123, 123.946, 169.240, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 23.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Nadh-Dependent Variant of Tbadh (pdb code 6sdm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Nadh-Dependent Variant of Tbadh, PDB code: 6sdm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6sdm

Go back to Zinc Binding Sites List in 6sdm
Zinc binding site 1 out of 4 in the Nadh-Dependent Variant of Tbadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Nadh-Dependent Variant of Tbadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:0.4
occ:1.00
SG A:CYS37 2.4 0.4 1.0
CB A:CYS37 2.4 0.4 1.0
NE2 A:HIS59 2.7 73.1 1.0
OD2 A:ASP150 2.8 74.1 1.0
CE1 A:HIS59 2.9 82.9 1.0
OG A:SER39 3.2 0.5 1.0
CB A:SER39 3.4 0.9 1.0
CA A:CYS37 3.9 88.1 1.0
CD2 A:HIS59 4.0 72.1 1.0
CG A:ASP150 4.0 65.9 1.0
N A:SER39 4.0 88.7 1.0
ND1 A:HIS59 4.2 83.7 1.0
OE2 A:GLU60 4.3 58.2 1.0
CA A:SER39 4.3 98.8 1.0
C A:CYS37 4.4 81.5 1.0
N A:THR38 4.6 72.8 1.0
OD1 A:ASP150 4.7 61.2 1.0
CG A:HIS59 4.7 76.9 1.0
N A:CYS37 4.8 78.7 1.0
CE A:MET151 4.8 40.9 1.0
CD A:GLU60 4.9 56.0 1.0
O A:CYS37 5.0 95.9 1.0
CB A:ASP150 5.0 55.4 1.0

Zinc binding site 2 out of 4 in 6sdm

Go back to Zinc Binding Sites List in 6sdm
Zinc binding site 2 out of 4 in the Nadh-Dependent Variant of Tbadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Nadh-Dependent Variant of Tbadh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:0.2
occ:1.00
CD2 B:HIS59 1.9 0.1 1.0
NE2 B:HIS59 2.2 0.2 1.0
OD2 B:ASP150 2.8 69.8 1.0
CG B:HIS59 3.2 0.8 1.0
CE1 B:HIS59 3.5 0.3 1.0
CG B:ASP150 3.6 62.8 1.0
CG B:GLU60 3.7 46.9 1.0
CB B:ASP150 3.8 35.6 1.0
OE2 B:GLU60 3.9 45.5 1.0
ND1 B:HIS59 3.9 0.0 1.0
CD B:GLU60 4.0 61.4 1.0
CB B:CYS37 4.1 46.6 1.0
CB B:ALA85 4.2 35.1 1.0
CB B:HIS59 4.2 87.1 1.0
O B:HIS59 4.4 63.2 1.0
SG B:CYS37 4.4 93.4 1.0
C B:HIS59 4.4 54.1 1.0
CA B:HIS59 4.7 64.7 1.0
OD1 B:ASP150 4.8 69.3 1.0
OE1 B:GLU60 4.8 61.2 1.0
OG B:SER39 4.8 86.5 1.0
N B:GLU60 4.8 40.2 1.0
N B:HIS59 4.9 55.9 1.0

Zinc binding site 3 out of 4 in 6sdm

Go back to Zinc Binding Sites List in 6sdm
Zinc binding site 3 out of 4 in the Nadh-Dependent Variant of Tbadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Nadh-Dependent Variant of Tbadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:1.0
occ:1.00
CB C:CYS37 2.2 0.1 1.0
SG C:CYS37 2.5 0.5 1.0
OD2 C:ASP150 2.7 0.0 1.0
NE2 C:HIS59 3.0 0.7 1.0
OE1 C:GLU60 3.5 92.8 1.0
CE1 C:HIS59 3.6 0.8 1.0
CA C:CYS37 3.7 0.9 1.0
CG C:ASP150 3.9 88.5 1.0
OG C:SER39 4.0 0.0 1.0
CD2 C:HIS59 4.1 0.9 1.0
CD C:GLU60 4.1 94.6 1.0
CE C:MET151 4.3 68.9 1.0
N C:CYS37 4.3 0.3 1.0
CB C:SER39 4.3 0.6 1.0
C C:CYS37 4.4 0.4 1.0
OD1 C:ASP150 4.7 91.8 1.0
OE2 C:GLU60 4.7 93.6 1.0
ND1 C:HIS59 4.7 1.0 1.0
N C:SER39 4.7 0.3 1.0
CB C:ASP150 4.7 78.5 1.0
N C:THR38 4.8 0.3 1.0
CG C:GLU60 4.8 95.3 1.0
NZ C:LYS346 4.9 85.4 1.0
CG C:HIS59 5.0 0.9 1.0

Zinc binding site 4 out of 4 in 6sdm

Go back to Zinc Binding Sites List in 6sdm
Zinc binding site 4 out of 4 in the Nadh-Dependent Variant of Tbadh


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Nadh-Dependent Variant of Tbadh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:0.4
occ:1.00
OD2 D:ASP150 2.2 0.8 1.0
CE1 D:HIS59 2.5 68.1 1.0
NE2 D:HIS59 2.9 75.3 1.0
CB D:CYS37 3.1 88.1 1.0
SG D:CYS37 3.3 95.6 1.0
CG D:ASP150 3.3 81.9 1.0
OE2 D:GLU60 3.7 58.1 1.0
ND1 D:HIS59 3.7 57.5 1.0
OG D:SER39 3.9 0.8 1.0
CB D:ASP150 4.0 67.9 1.0
CD D:GLU60 4.1 64.7 1.0
CD2 D:HIS59 4.3 72.6 1.0
OD1 D:ASP150 4.3 93.9 1.0
CE D:MET151 4.3 53.0 1.0
CB D:SER39 4.4 95.2 1.0
CG D:GLU60 4.5 47.9 1.0
CA D:CYS37 4.6 81.3 1.0
CG D:HIS59 4.6 66.9 1.0
OE1 D:GLU60 4.6 82.0 1.0
NZ D:LYS346 4.9 64.8 1.0

Reference:

L.Selles Vidal, J.W.Murray, J.T.Heap. Nadh-Dependent Variant of Tbadh To Be Published.
Page generated: Wed Dec 16 12:47:00 2020

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