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Calcium in PDB 1g87: The Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum

Enzymatic activity of The Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum

All present enzymatic activity of The Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum:
3.2.1.4;

Protein crystallography data

The structure of The Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum, PDB code: 1g87 was solved by D.Mandelman, A.Belaich, J.P.Belaich, N.Aghajari, H.Driguez, R.Haser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.17 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.850, 57.720, 86.270, 94.22, 100.87, 99.61
R / Rfree (%) 17.4 / 20

Other elements in 1g87:

The structure of The Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum (pdb code 1g87). 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 Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum, PDB code: 1g87:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1g87

Go back to Calcium Binding Sites List in 1g87
Calcium binding site 1 out of 4 in the The Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca615

b:10.8
occ:1.00
 OE1 A:GLU503 2.3 12.7 1.0
OD1 A:ASN581 2.3 12.5 1.0
O A:ASN578 2.3 13.6 1.0
O A:ASP500 2.4 12.4 1.0
OD1 A:ASP582 2.4 13.0 1.0
O A:HOH682 2.4 12.5 1.0
CD A:GLU503 3.0 14.0 1.0
OE2 A:GLU503 3.0 13.3 1.0
CG A:ASP582 3.4 12.5 1.0
C A:ASN578 3.4 13.8 1.0
CG A:ASN581 3.4 12.4 1.0
C A:ASP500 3.6 12.4 1.0
OD2 A:ASP582 3.7 13.2 1.0
ND2 A:ASN581 3.8 12.1 1.0
CA A:ASN578 4.2 13.5 1.0
N A:ASP500 4.2 12.1 1.0
N A:ASN578 4.2 13.5 1.0
N A:PRO579 4.3 14.7 1.0
CA A:ASP500 4.3 12.2 1.0
CB A:ASN578 4.3 13.6 1.0
CA A:PRO579 4.4 15.2 1.0
CB A:ASP500 4.4 12.7 1.0
CD2 A:LEU501 4.4 12.3 1.0
N A:ASP582 4.4 12.6 1.0
CG A:GLU503 4.5 13.4 1.0
N A:LEU501 4.5 12.2 1.0
CA A:LEU501 4.6 12.4 1.0
CB A:ASP582 4.6 12.4 1.0
C A:ASN581 4.7 12.8 1.0
N A:ASN581 4.7 13.7 1.0
CB A:ASN581 4.7 12.6 1.0
C A:PRO579 4.8 15.5 1.0
CG A:ASN578 4.8 13.2 1.0
CA A:ASP582 4.8 12.4 1.0
CA A:ASN581 4.9 13.2 1.0
OD1 A:ASP500 5.0 13.2 1.0

Calcium binding site 2 out of 4 in 1g87

Go back to Calcium Binding Sites List in 1g87
Calcium binding site 2 out of 4 in the The Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca616

b:10.6
occ:1.00
 OD2 A:ASP212 2.4 9.4 1.0
O A:HOH897 2.4 9.0 1.0
OD2 A:ASP213 2.4 10.2 1.0
O A:HOH896 2.5 8.2 1.0
O A:ASP259 2.5 9.9 1.0
O A:SER209 2.5 10.4 1.0
OG A:SER209 2.6 11.0 1.0
OD1 A:ASP212 2.6 9.1 1.0
CG A:ASP212 2.9 9.5 1.0
C A:SER209 3.3 10.7 1.0
C A:ASP259 3.4 10.4 1.0
CG A:ASP213 3.4 10.9 1.0
CB A:SER209 3.7 11.1 1.0
OD1 A:ASP213 3.8 11.2 1.0
CA A:SER209 3.9 10.6 1.0
N A:ASP260 4.1 10.3 1.0
N A:PHE210 4.2 10.7 1.0
CA A:ASP259 4.2 9.7 1.0
N A:SER209 4.2 11.1 1.0
CA A:ASP260 4.2 11.2 1.0
OD2 A:ASP259 4.3 9.7 1.0
CA A:PHE210 4.4 10.8 1.0
CB A:ASP212 4.4 9.8 1.0
N A:ASP213 4.5 10.3 1.0
CB A:ASP213 4.6 9.7 1.0
OG A:SER207 4.6 10.0 1.0
CB A:ALA151 4.7 10.6 1.0
N A:VAL261 4.7 10.1 1.0
O A:TRP258 4.8 9.8 1.0
O A:HOH707 4.9 15.2 1.0
CG A:ASP259 4.9 10.7 1.0
CG2 A:VAL261 5.0 9.6 1.0

Calcium binding site 3 out of 4 in 1g87

Go back to Calcium Binding Sites List in 1g87
Calcium binding site 3 out of 4 in the The Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca615

b:12.5
occ:1.00
 O B:ASN578 2.3 13.7 1.0
O B:ASP500 2.3 12.0 1.0
OE2 B:GLU503 2.3 12.2 1.0
OD1 B:ASN581 2.3 13.9 1.0
OD1 B:ASP582 2.4 11.1 1.0
O B:HOH939 2.4 13.1 1.0
OE1 B:GLU503 2.9 12.3 1.0
CD B:GLU503 3.0 12.7 1.0
CG B:ASP582 3.4 11.1 1.0
C B:ASN578 3.4 12.4 1.0
CG B:ASN581 3.4 14.3 1.0
C B:ASP500 3.5 12.2 1.0
OD2 B:ASP582 3.7 10.3 1.0
ND2 B:ASN581 3.9 13.8 1.0
N B:ASP500 4.2 12.5 1.0
CA B:ASN578 4.2 12.7 1.0
CA B:ASP500 4.3 12.7 1.0
N B:ASN578 4.3 12.6 1.0
CB B:ASN578 4.3 12.8 1.0
CB B:ASP500 4.3 13.4 1.0
N B:PRO579 4.3 13.2 1.0
CA B:PRO579 4.4 12.8 1.0
CG B:GLU503 4.5 11.8 1.0
N B:ASP582 4.5 12.4 1.0
N B:LEU501 4.5 12.2 1.0
CA B:LEU501 4.6 11.8 1.0
CD2 B:LEU501 4.6 12.2 1.0
C B:ASN581 4.7 12.8 1.0
CB B:ASP582 4.7 11.6 1.0
N B:ASN581 4.7 13.9 1.0
CB B:ASN581 4.7 14.1 1.0
C B:PRO579 4.8 13.6 1.0
OD1 B:ASP500 4.8 14.1 1.0
CA B:ASP582 4.9 12.1 1.0
CG B:ASN578 4.9 12.9 1.0
CA B:ASN581 4.9 13.5 1.0

Calcium binding site 4 out of 4 in 1g87

Go back to Calcium Binding Sites List in 1g87
Calcium binding site 4 out of 4 in the The Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of Endoglucanase 9G From Clostridium Cellulolyticum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca616

b:11.8
occ:1.00
 OD1 B:ASP213 2.4 13.1 1.0
O B:HOH929 2.4 9.7 1.0
OD2 B:ASP212 2.4 12.1 1.0
O B:HOH928 2.4 13.3 1.0
O B:SER209 2.5 12.6 1.0
O B:ASP259 2.5 12.2 1.0
OG B:SER209 2.5 12.7 1.0
OD1 B:ASP212 2.6 12.1 1.0
CG B:ASP212 2.9 11.5 1.0
C B:SER209 3.2 13.1 1.0
CG B:ASP213 3.3 12.8 1.0
C B:ASP259 3.4 12.3 1.0
CB B:SER209 3.6 13.3 1.0
OD2 B:ASP213 3.7 13.2 1.0
CA B:SER209 3.9 13.6 1.0
N B:PHE210 4.1 12.4 1.0
N B:ASP260 4.2 11.8 1.0
N B:SER209 4.2 13.8 1.0
CA B:ASP259 4.2 11.6 1.0
CA B:ASP260 4.3 12.4 1.0
OD1 B:ASP259 4.3 12.1 1.0
CA B:PHE210 4.4 12.1 1.0
CB B:ASP212 4.4 11.4 1.0
N B:ASP213 4.5 11.2 1.0
OG B:SER207 4.6 12.8 1.0
CB B:ASP213 4.6 11.3 1.0
CB B:ALA151 4.8 10.6 1.0
O B:TRP258 4.8 10.0 1.0
N B:VAL261 4.8 10.7 1.0
O B:HOH779 4.8 21.6 1.0
CG B:ASP259 4.9 13.1 1.0

Reference:

D.Mandelman, A.Belaich, J.P.Belaich, N.Aghajari, H.Driguez, R.Haser. X-Ray Crystal Structure of the Multidomain Endoglucanase CEL9G From Clostridium Cellulolyticum Complexed with Natural and Synthetic Cello-Oligosaccharides 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 08:33:13 2024

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