Atomistry » Nickel » PDB 5xkt-6c8z » 6bi4
Atomistry »
  Nickel »
    PDB 5xkt-6c8z »
      6bi4 »

Nickel in PDB 6bi4: 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad.

Enzymatic activity of 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad.

All present enzymatic activity of 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad.:
4.2.1.46;

Protein crystallography data

The structure of 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad., PDB code: 6bi4 was solved by A.S.Halavaty, M.Kuhn, L.Shuvalova, G.Minasov, W.F.Anderson, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.95 / 2.91
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 165.557, 165.557, 292.121, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.4

Nickel Binding Sites:

The binding sites of Nickel atom in the 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad. (pdb code 6bi4). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad., PDB code: 6bi4:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6bi4

Go back to Nickel Binding Sites List in 6bi4
Nickel binding site 1 out of 2 in the 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni401

b:1.0
occ:1.00
 OE1 C:GLU72 1.8 0.5 1.0
OE1 A:GLU72 2.2 0.8 1.0
NE2 A:HIS68 2.6 62.5 1.0
NE2 C:HIS68 2.6 67.8 1.0
OE2 A:GLU72 2.7 0.3 1.0
CD C:GLU72 2.7 0.9 1.0
CD A:GLU72 2.7 0.9 1.0
CD2 C:HIS68 2.9 59.4 1.0
OE2 C:GLU72 3.0 0.3 1.0
CD2 A:HIS68 3.2 60.2 1.0
CE1 A:HIS68 3.7 64.5 1.0
CE1 C:HIS68 3.9 71.8 1.0
CG C:GLU72 4.0 96.9 1.0
CG A:GLU72 4.2 98.5 1.0
CG C:HIS68 4.2 58.5 1.0
CB C:GLU72 4.3 81.0 1.0
CG A:HIS68 4.5 56.6 1.0
ND1 C:HIS68 4.6 71.5 1.0
CB A:GLU72 4.7 84.0 1.0
ND1 A:HIS68 4.7 63.5 1.0
O C:HIS68 4.9 50.8 1.0
CG2 C:VAL69 4.9 62.5 1.0

Nickel binding site 2 out of 2 in 6bi4

Go back to Nickel Binding Sites List in 6bi4
Nickel binding site 2 out of 2 in the 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni401

b:0.7
occ:1.00
 OE1 D:GLU72 2.0 95.8 1.0
OE1 B:GLU72 2.3 71.0 1.0
NE2 D:HIS68 2.4 61.7 1.0
NE2 B:HIS68 2.6 47.7 1.0
OE2 B:GLU72 2.8 98.5 1.0
CD2 D:HIS68 2.8 57.0 1.0
CD D:GLU72 2.8 99.8 1.0
CD B:GLU72 2.9 92.1 1.0
OE2 D:GLU72 3.1 0.3 1.0
CD2 B:HIS68 3.2 45.6 1.0
CE1 D:HIS68 3.7 72.6 1.0
CE1 B:HIS68 3.7 49.7 1.0
CG D:HIS68 4.1 57.7 1.0
CG D:GLU72 4.2 94.6 1.0
CG B:GLU72 4.3 79.3 1.0
CB D:GLU72 4.4 72.2 1.0
ND1 D:HIS68 4.5 74.2 1.0
CG B:HIS68 4.5 44.3 1.0
ND1 B:HIS68 4.7 48.3 1.0
CB B:GLU72 4.8 66.4 1.0
O D:HIS68 4.9 48.2 1.0
CG2 D:VAL69 4.9 47.2 1.0

Reference:

A.S.Halavaty, M.Kuhn, L.Shuvalova, G.Minasov, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.9 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6-Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex with Nad. To Be Published.
Page generated: Wed Dec 16 01:50:27 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