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Cobalt in PDB 1uc4: Structure of Diol Dehydratase Complexed with (S)-1,2- Propanediol

Enzymatic activity of Structure of Diol Dehydratase Complexed with (S)-1,2- Propanediol

All present enzymatic activity of Structure of Diol Dehydratase Complexed with (S)-1,2- Propanediol:
4.2.1.28;

Protein crystallography data

The structure of Structure of Diol Dehydratase Complexed with (S)-1,2- Propanediol, PDB code: 1uc4 was solved by N.Shibata, Y.Nakanishi, M.Fukuoka, M.Yamanishi, N.Yasuoka, T.Toraya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.92 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.830, 121.950, 208.240, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23

Other elements in 1uc4:

The structure of Structure of Diol Dehydratase Complexed with (S)-1,2- Propanediol also contains other interesting chemical elements:

Potassium (K) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of Diol Dehydratase Complexed with (S)-1,2- Propanediol (pdb code 1uc4). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Structure of Diol Dehydratase Complexed with (S)-1,2- Propanediol, PDB code: 1uc4:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 1uc4

Go back to Cobalt Binding Sites List in 1uc4
Cobalt binding site 1 out of 2 in the Structure of Diol Dehydratase Complexed with (S)-1,2- Propanediol


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Diol Dehydratase Complexed with (S)-1,2- Propanediol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co2601

b:17.0
occ:1.00
CO B:CNC2601 0.0 17.0 1.0
N24 B:CNC2601 1.9 16.5 1.0
N21 B:CNC2601 1.9 17.2 1.0
N22 B:CNC2601 1.9 17.3 1.0
N23 B:CNC2601 1.9 16.8 1.0
N3B B:CNC2601 2.3 15.3 1.0
C9 B:CNC2601 2.9 18.1 1.0
C19 B:CNC2601 2.9 15.9 1.0
C4 B:CNC2601 2.9 16.4 1.0
C1 B:CNC2601 2.9 16.7 1.0
C11 B:CNC2601 2.9 16.7 1.0
C16 B:CNC2601 3.0 14.6 1.0
C14 B:CNC2601 3.0 15.9 1.0
C6 B:CNC2601 3.0 17.4 1.0
C2B B:CNC2601 3.2 15.6 1.0
C10 B:CNC2601 3.2 16.0 1.0
C5 B:CNC2601 3.4 16.0 1.0
C9B B:CNC2601 3.4 16.2 1.0
C15 B:CNC2601 3.4 14.9 1.0
C20 B:CNC2601 3.6 16.7 1.0
C4B B:CNC2601 4.0 17.6 1.0
C2 B:CNC2601 4.1 17.6 1.0
C18 B:CNC2601 4.2 16.9 1.0
C3 B:CNC2601 4.2 17.6 1.0
C8 B:CNC2601 4.2 17.9 1.0
C17 B:CNC2601 4.3 16.0 1.0
C13 B:CNC2601 4.3 17.3 1.0
C12 B:CNC2601 4.3 17.4 1.0
C7 B:CNC2601 4.3 19.9 1.0
N1B B:CNC2601 4.5 17.1 1.0
C8B B:CNC2601 4.6 16.1 1.0
C26 B:CNC2601 4.6 18.3 1.0
C49 B:CNC2601 4.7 18.2 1.0
C41 B:CNC2601 4.8 22.2 1.0
C35 B:CNC2601 4.9 15.6 1.0
C46 B:CNC2601 5.0 17.5 1.0
C53 B:CNC2601 5.0 14.4 1.0
C48 B:CNC2601 5.0 17.3 1.0

Cobalt binding site 2 out of 2 in 1uc4

Go back to Cobalt Binding Sites List in 1uc4
Cobalt binding site 2 out of 2 in the Structure of Diol Dehydratase Complexed with (S)-1,2- Propanediol


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Diol Dehydratase Complexed with (S)-1,2- Propanediol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Co3601

b:23.4
occ:1.00
CO E:CNC3601 0.0 23.4 1.0
N24 E:CNC3601 1.9 25.5 1.0
N21 E:CNC3601 1.9 29.1 1.0
N22 E:CNC3601 1.9 26.9 1.0
N23 E:CNC3601 1.9 25.1 1.0
N3B E:CNC3601 2.3 26.5 1.0
C9 E:CNC3601 2.9 26.7 1.0
C19 E:CNC3601 2.9 26.1 1.0
C4 E:CNC3601 2.9 29.8 1.0
C1 E:CNC3601 2.9 28.4 1.0
C11 E:CNC3601 3.0 25.8 1.0
C16 E:CNC3601 3.0 25.0 1.0
C14 E:CNC3601 3.0 25.8 1.0
C6 E:CNC3601 3.0 28.2 1.0
C10 E:CNC3601 3.3 25.8 1.0
C2B E:CNC3601 3.3 25.6 1.0
C5 E:CNC3601 3.4 29.5 1.0
C15 E:CNC3601 3.4 24.5 1.0
C9B E:CNC3601 3.5 27.9 1.0
C20 E:CNC3601 3.6 28.2 1.0
O28 E:CNC3601 4.0 40.2 1.0
C4B E:CNC3601 4.0 29.5 1.0
C18 E:CNC3601 4.2 25.5 1.0
C2 E:CNC3601 4.2 30.7 1.0
C3 E:CNC3601 4.2 31.2 1.0
C8 E:CNC3601 4.3 26.9 1.0
C17 E:CNC3601 4.3 23.2 1.0
C12 E:CNC3601 4.3 26.9 1.0
C13 E:CNC3601 4.3 25.4 1.0
C7 E:CNC3601 4.4 27.9 1.0
N1B E:CNC3601 4.5 27.0 1.0
C27 E:CNC3601 4.5 38.3 1.0
C8B E:CNC3601 4.6 28.5 1.0
C26 E:CNC3601 4.7 33.2 1.0
C49 E:CNC3601 4.8 27.1 1.0
C41 E:CNC3601 4.9 27.4 1.0
C35 E:CNC3601 4.9 30.8 1.0
C53 E:CNC3601 5.0 23.1 1.0

Reference:

N.Shibata, Y.Nakanishi, M.Fukuoka, M.Yamanishi, N.Yasuoka, T.Toraya. Structural Rationalization For the Lack of Stereospecificity in Coenzyme B12-Dependent Diol Dehydratase J.Biol.Chem. V. 278 22717 2003.
ISSN: ISSN 0021-9258
PubMed: 12684496
DOI: 10.1074/JBC.M301513200
Page generated: Tue Jul 30 14:39:56 2024

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