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Cobalt in PDB 4c4d: Covalent Glycosyl-Enzyme Intermediate of Hypocrea Jecorina CEL7A E217Q Mutant Trapped Using Dnp-2-Deoxy-2-Fluoro-Cellotrioside

Enzymatic activity of Covalent Glycosyl-Enzyme Intermediate of Hypocrea Jecorina CEL7A E217Q Mutant Trapped Using Dnp-2-Deoxy-2-Fluoro-Cellotrioside

All present enzymatic activity of Covalent Glycosyl-Enzyme Intermediate of Hypocrea Jecorina CEL7A E217Q Mutant Trapped Using Dnp-2-Deoxy-2-Fluoro-Cellotrioside:
3.2.1.91;

Protein crystallography data

The structure of Covalent Glycosyl-Enzyme Intermediate of Hypocrea Jecorina CEL7A E217Q Mutant Trapped Using Dnp-2-Deoxy-2-Fluoro-Cellotrioside, PDB code: 4c4d was solved by M.Haddad-Momeni, L.Mackenzie, M.Sandgren, S.G.Withers, J.Stahlberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.57 / 1.32
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 82.930, 83.290, 110.760, 90.00, 90.00, 90.00
R / Rfree (%) 16.675 / 18.673

Other elements in 4c4d:

The structure of Covalent Glycosyl-Enzyme Intermediate of Hypocrea Jecorina CEL7A E217Q Mutant Trapped Using Dnp-2-Deoxy-2-Fluoro-Cellotrioside also contains other interesting chemical elements:

Fluorine (F) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Covalent Glycosyl-Enzyme Intermediate of Hypocrea Jecorina CEL7A E217Q Mutant Trapped Using Dnp-2-Deoxy-2-Fluoro-Cellotrioside (pdb code 4c4d). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Covalent Glycosyl-Enzyme Intermediate of Hypocrea Jecorina CEL7A E217Q Mutant Trapped Using Dnp-2-Deoxy-2-Fluoro-Cellotrioside, PDB code: 4c4d:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 4c4d

Go back to Cobalt Binding Sites List in 4c4d
Cobalt binding site 1 out of 3 in the Covalent Glycosyl-Enzyme Intermediate of Hypocrea Jecorina CEL7A E217Q Mutant Trapped Using Dnp-2-Deoxy-2-Fluoro-Cellotrioside


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Covalent Glycosyl-Enzyme Intermediate of Hypocrea Jecorina CEL7A E217Q Mutant Trapped Using Dnp-2-Deoxy-2-Fluoro-Cellotrioside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co435

b:5.7
occ:0.50
 OE2 A:GLU325 2.1 6.8 1.0
OE2 A:GLU295 2.1 6.9 1.0
OE1 A:GLU295 2.2 6.8 1.0
CD A:GLU295 2.5 6.9 1.0
CD A:GLU325 3.1 6.7 1.0
OE1 A:GLU325 3.4 6.9 1.0
O A:HOH2512 3.9 10.9 1.0
CG A:GLU295 4.0 7.1 1.0
ND2 A:ASN301 4.0 7.4 1.0
O A:HOH2483 4.3 9.3 1.0
CG A:GLU325 4.4 6.8 1.0
OG A:SER297 4.7 8.0 1.0
CB A:ALA299 4.8 7.1 1.0
CB A:GLU295 4.9 7.4 1.0
O A:HOH2511 4.9 8.5 1.0

Cobalt binding site 2 out of 3 in 4c4d

Go back to Cobalt Binding Sites List in 4c4d
Cobalt binding site 2 out of 3 in the Covalent Glycosyl-Enzyme Intermediate of Hypocrea Jecorina CEL7A E217Q Mutant Trapped Using Dnp-2-Deoxy-2-Fluoro-Cellotrioside


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Covalent Glycosyl-Enzyme Intermediate of Hypocrea Jecorina CEL7A E217Q Mutant Trapped Using Dnp-2-Deoxy-2-Fluoro-Cellotrioside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co436

b:17.6
occ:0.75
 O A:HOH2377 1.9 31.6 1.0
OE2 A:GLU239 2.0 18.9 1.0
NE2 A:HIS206 2.1 12.6 1.0
O A:HOH2400 2.1 24.1 1.0
O A:HOH2375 2.2 24.5 1.0
O A:HOH2376 2.4 24.2 1.0
CD A:GLU239 2.9 17.6 1.0
CE1 A:HIS206 3.1 12.7 1.0
CD2 A:HIS206 3.1 12.2 1.0
OE1 A:GLU239 3.2 19.7 1.0
ND1 A:HIS206 4.2 12.2 1.0
CG A:HIS206 4.3 11.5 1.0
O A:HOH2349 4.3 19.9 1.0
CG A:GLU239 4.3 16.5 1.0
O A:HOH2164 4.7 18.8 1.0

Cobalt binding site 3 out of 3 in 4c4d

Go back to Cobalt Binding Sites List in 4c4d
Cobalt binding site 3 out of 3 in the Covalent Glycosyl-Enzyme Intermediate of Hypocrea Jecorina CEL7A E217Q Mutant Trapped Using Dnp-2-Deoxy-2-Fluoro-Cellotrioside


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Covalent Glycosyl-Enzyme Intermediate of Hypocrea Jecorina CEL7A E217Q Mutant Trapped Using Dnp-2-Deoxy-2-Fluoro-Cellotrioside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co437

b:13.7
occ:0.50
 OD2 A:ASP249 1.9 17.0 0.5
O A:HOH2413 1.9 24.9 0.5
O A:HOH2402 2.0 29.0 1.0
O A:HOH2414 2.1 18.2 0.5
O A:HOH2415 2.2 18.4 0.5
CG A:ASP249 2.9 16.7 0.5
OD1 A:ASP249 3.1 16.6 0.5
CB A:ASP249 4.3 17.0 1.0
OD2 A:ASP241 4.3 18.8 1.0
O A:HOH2411 4.3 29.5 1.0
OD1 A:ASN250 4.9 19.7 0.2
CG A:ASP241 5.0 17.1 1.0

Reference:

B.C.Knott, M.Haddad Momeni, M.F.Crowley, L.F.Mackenzie, A.W.Gotz, M.Sandgren, S.G.Withers, J.Stahlberg, G.T.Beckham. The Mechanism of Cellulose Hydrolysis By A Two-Step, Retaining Cellobiohydrolase Elucidated By Structural and Transition Path Sampling Studies. J.Am.Chem.Soc. V. 136 321 2014.
ISSN: ISSN 0002-7863
PubMed: 24341799
DOI: 10.1021/JA410291U
Page generated: Sun Jul 13 19:39:30 2025

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