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Calcium in PDB 1kfg: The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor

Enzymatic activity of The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor

All present enzymatic activity of The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor:
3.2.1.4;

Protein crystallography data

The structure of The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor, PDB code: 1kfg was solved by D.Mandelman, A.Belaich, J.-P.Belaich, H.Driguez, R.Haser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.42 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.040, 57.730, 86.630, 93.86, 100.83, 99.54
R / Rfree (%) 16.7 / 20.4

Other elements in 1kfg:

The structure of The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor (pdb code 1kfg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor, PDB code: 1kfg:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1kfg

Go back to Calcium Binding Sites List in 1kfg
Calcium binding site 1 out of 4 in the The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca9015

b:13.3
occ:1.00
 OE1 A:GLU503 2.3 15.3 1.0
O A:ASN578 2.3 15.3 1.0
OD1 A:ASN581 2.3 15.3 1.0
O A:ASP500 2.3 12.2 1.0
OD1 A:ASP582 2.4 13.6 1.0
O A:HOH9071 2.6 13.3 1.0
CD A:GLU503 3.0 14.9 1.0
OE2 A:GLU503 3.1 15.7 1.0
CG A:ASP582 3.3 13.2 1.0
CG A:ASN581 3.4 16.7 1.0
C A:ASN578 3.4 15.0 1.0
C A:ASP500 3.5 13.9 1.0
OD2 A:ASP582 3.7 14.2 1.0
ND2 A:ASN581 3.8 17.2 1.0
CA A:ASN578 4.2 15.3 1.0
N A:ASP500 4.2 12.5 1.0
N A:ASN578 4.2 15.4 1.0
CA A:ASP500 4.3 12.0 1.0
N A:PRO579 4.3 16.7 1.0
CB A:ASN578 4.4 13.7 1.0
CD2 A:LEU501 4.4 9.2 1.0
CB A:ASP500 4.4 13.7 1.0
N A:ASP582 4.5 15.7 1.0
CA A:PRO579 4.5 16.6 1.0
CG A:GLU503 4.5 14.6 1.0
N A:LEU501 4.5 13.0 1.0
CA A:LEU501 4.6 14.0 1.0
CB A:ASP582 4.6 13.0 1.0
C A:ASN581 4.6 15.5 1.0
CB A:ASN581 4.7 16.0 1.0
N A:ASN581 4.8 15.2 1.0
CA A:ASP582 4.9 13.9 1.0
C A:PRO579 4.9 18.2 1.0
CG A:ASN578 4.9 12.8 1.0
CA A:ASN581 4.9 15.9 1.0

Calcium binding site 2 out of 4 in 1kfg

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Calcium binding site 2 out of 4 in the The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca9017

b:11.7
occ:1.00
 OD1 A:ASP213 2.4 12.0 1.0
O A:HOH9023 2.4 8.9 1.0
OD2 A:ASP212 2.5 11.7 1.0
O A:SER209 2.5 11.5 1.0
O A:ASP259 2.5 10.6 1.0
O A:HOH9030 2.5 9.7 1.0
OG A:SER209 2.5 11.6 1.0
OD1 A:ASP212 2.6 9.8 1.0
CG A:ASP212 2.9 12.4 1.0
C A:SER209 3.3 12.2 1.0
CG A:ASP213 3.4 12.2 1.0
C A:ASP259 3.4 11.1 1.0
CB A:SER209 3.7 12.4 1.0
OD2 A:ASP213 3.7 14.0 1.0
CA A:SER209 3.9 11.6 1.0
N A:PHE210 4.1 10.6 1.0
N A:ASP260 4.1 12.5 1.0
OD2 A:ASP259 4.2 10.5 1.0
N A:SER209 4.2 11.0 1.0
CA A:ASP259 4.2 9.9 1.0
CA A:ASP260 4.3 12.7 1.0
CA A:PHE210 4.4 10.7 1.0
CB A:ASP212 4.4 10.9 1.0
N A:ASP213 4.6 11.8 1.0
OG A:SER207 4.6 8.2 1.0
CB A:ASP213 4.7 12.7 1.0
CB A:ALA151 4.7 10.9 1.0
N A:VAL261 4.8 10.3 1.0
O A:HOH9087 4.8 13.8 1.0
O A:TRP258 4.9 11.0 1.0
CG A:ASP259 4.9 9.2 1.0

Calcium binding site 3 out of 4 in 1kfg

Go back to Calcium Binding Sites List in 1kfg
Calcium binding site 3 out of 4 in the The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca9014

b:13.3
occ:1.00
 O B:ASN578 2.2 13.6 1.0
OE2 B:GLU503 2.3 14.3 1.0
O B:ASP500 2.3 13.0 1.0
OD1 B:ASN581 2.3 15.4 1.0
O B:HOH9101 2.4 14.7 1.0
OD1 B:ASP582 2.4 12.4 1.0
OE1 B:GLU503 2.9 13.6 1.0
CD B:GLU503 3.0 14.4 1.0
C B:ASN578 3.3 12.5 1.0
CG B:ASP582 3.4 14.7 1.0
CG B:ASN581 3.4 14.1 1.0
C B:ASP500 3.5 12.8 1.0
OD2 B:ASP582 3.8 14.0 1.0
ND2 B:ASN581 3.9 13.0 1.0
CA B:ASN578 4.1 11.9 1.0
N B:ASN578 4.2 12.8 1.0
N B:ASP500 4.2 14.6 1.0
CB B:ASN578 4.2 11.8 1.0
N B:PRO579 4.3 13.0 1.0
CA B:ASP500 4.3 15.1 1.0
CB B:ASP500 4.3 15.5 1.0
CA B:PRO579 4.4 12.1 1.0
CG B:GLU503 4.4 13.6 1.0
N B:LEU501 4.5 13.3 1.0
N B:ASP582 4.5 13.9 1.0
CA B:LEU501 4.6 12.7 1.0
C B:ASN581 4.6 13.5 1.0
N B:ASN581 4.6 13.0 1.0
CD2 B:LEU501 4.7 11.3 1.0
CB B:ASP582 4.7 12.5 1.0
CB B:ASN581 4.7 13.9 1.0
C B:PRO579 4.8 13.8 1.0
CG B:ASN578 4.8 12.6 1.0
CA B:ASN581 4.9 12.8 1.0
CA B:ASP582 4.9 14.0 1.0
OD1 B:ASP500 5.0 17.4 1.0

Calcium binding site 4 out of 4 in 1kfg

Go back to Calcium Binding Sites List in 1kfg
Calcium binding site 4 out of 4 in the The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The X-Ray Crystal Structure of CEL9G From Clostridium Cellulolyticum Complexed with A Thio-Oligosaccharide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca9016

b:13.6
occ:1.00
 OD1 B:ASP213 2.3 13.7 1.0
O B:SER209 2.4 14.3 1.0
O B:HOH9024 2.5 13.0 1.0
OD2 B:ASP212 2.5 12.6 1.0
O B:HOH9040 2.5 10.3 1.0
O B:ASP259 2.5 12.5 1.0
OD1 B:ASP212 2.6 14.6 1.0
OG B:SER209 2.6 13.4 1.0
CG B:ASP212 2.9 13.5 1.0
C B:SER209 3.2 15.8 1.0
CG B:ASP213 3.3 14.8 1.0
C B:ASP259 3.5 13.3 1.0
CB B:SER209 3.7 15.9 1.0
OD2 B:ASP213 3.7 14.8 1.0
CA B:SER209 3.9 16.0 1.0
N B:PHE210 4.1 14.2 1.0
N B:SER209 4.2 15.0 1.0
N B:ASP260 4.3 11.7 1.0
CA B:ASP259 4.3 11.8 1.0
OD1 B:ASP259 4.3 12.1 1.0
CA B:PHE210 4.4 13.1 1.0
CA B:ASP260 4.4 13.7 1.0
CB B:ASP212 4.4 11.5 1.0
N B:ASP213 4.5 11.5 1.0
OG B:SER207 4.6 13.8 1.0
CB B:ASP213 4.6 13.7 1.0
CB B:ALA151 4.8 11.2 1.0
N B:VAL261 4.8 11.5 1.0
O B:TRP258 4.9 12.1 1.0
CG B:ASP259 4.9 14.6 1.0
O B:HOH9095 5.0 17.9 1.0

Reference:

D.Mandelman, A.Belaich, J.-P.Belaich, N.Aghajari, H.Driguez, R.Haser. The X-Ray Crystal Structure of the Multidomain Endoglucanase CEL9G From Clostridium Cellulolyticum Complexed with Natural and Synthetic Cello-Olligosaccharides J.Bacteriol. V. 185 4127 2003.
ISSN: ISSN 0021-9193
PubMed: 12837787
DOI: 10.1128/JB.185.14.4127-4135.2003
Page generated: Thu Jul 11 11:21:15 2024

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