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Calcium in PDB 1h5v: Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form

Enzymatic activity of Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form

All present enzymatic activity of Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form:
3.2.1.4;

Protein crystallography data

The structure of Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form, PDB code: 1h5v was solved by A.Varrot, G.Sulzenbacher, M.Schulein, H.Driguez, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 75.169, 75.169, 135.471, 90.00, 90.00, 90.00
R / Rfree (%) 12 / 13.8

Other elements in 1h5v:

The structure of Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form (pdb code 1h5v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form, PDB code: 1h5v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1h5v

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Calcium binding site 1 out of 10 in the Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:25.3
occ:1.00
 OE2 A:GLU124 2.1 32.7 1.0
O A:HOH2346 2.2 26.2 1.0
O A:HOH2287 2.3 32.8 1.0
OD2 A:ASP120 2.5 20.8 1.0
OD1 A:ASP120 2.6 15.4 1.0
CG A:ASP120 2.9 14.8 1.0
CD A:GLU124 3.4 29.5 1.0
CG A:GLU124 4.1 23.0 1.0
O A:HOH2342 4.3 16.8 1.0
OE1 A:GLU124 4.3 33.2 1.0
CB A:ASP120 4.4 12.4 1.0
ND2 A:ASN165 4.6 15.4 1.0
OD1 A:ASN165 4.7 18.1 1.0
O A:ASP120 5.0 13.2 1.0

Calcium binding site 2 out of 10 in 1h5v

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Calcium binding site 2 out of 10 in the Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca306

b:17.1
occ:1.00
 O A:GLY127 2.3 18.1 1.0
OD1 A:ASN168 2.3 16.5 1.0
O A:HOH2295 2.4 22.9 1.0
O A:HOH2027 2.4 20.5 1.0
OD1 A:ASN169 2.4 11.9 0.6
OD1 A:ASP166 2.4 14.4 1.0
ND2 A:ASN169 3.2 11.0 0.5
CG A:ASP166 3.2 12.7 1.0
CG A:ASN169 3.4 11.4 0.6
CG A:ASN168 3.5 15.2 1.0
C A:GLY127 3.5 15.3 1.0
CG A:ASN169 3.6 10.3 0.5
OD2 A:ASP166 3.6 12.4 1.0
OD1 A:ASN169 4.0 10.1 0.5
ND2 A:ASN169 4.0 13.2 0.6
ND2 A:ASN168 4.1 19.2 1.0
N A:ASN169 4.1 11.0 1.0
O A:HOH2298 4.2 33.5 1.0
CB A:ASP166 4.3 12.6 1.0
CA A:ASP128 4.4 14.5 1.0
CB A:ASN169 4.4 10.7 0.5
CB A:ASN169 4.4 10.8 0.6
OE1 A:GLN11 4.4 18.2 1.0
N A:ASP128 4.4 14.3 1.0
N A:ASN168 4.4 13.0 1.0
CA A:ASP166 4.4 12.9 1.0
CA A:GLY127 4.4 15.5 1.0
O A:HOH2299 4.6 32.1 1.0
C A:ASP128 4.6 14.1 1.0
CB A:ASN168 4.7 15.6 1.0
C A:ASP166 4.7 12.8 1.0
NE2 A:GLN11 4.7 16.1 1.0
O A:TYR129 4.8 12.9 1.0
CA A:ASN168 4.8 12.8 1.0
C A:ASN168 4.8 11.6 1.0
N A:PRO167 4.8 13.6 1.0
CD A:PRO167 4.8 15.6 1.0
CA A:ASN169 4.8 10.9 1.0
CD A:GLN11 4.9 14.9 1.0
N A:TYR129 4.9 12.2 1.0

Calcium binding site 3 out of 10 in 1h5v

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Calcium binding site 3 out of 10 in the Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca307

b:19.0
occ:1.00
 OE1 A:GLU157 2.3 18.5 1.0
O A:HOH2338 2.4 25.9 1.0
O A:HOH2337 3.1 29.4 1.0
CD A:GLU157 3.4 13.7 1.0
OE2 A:GLU157 4.0 17.9 1.0
NZ A:LYS112 4.3 13.1 1.0
O A:HOH2134 4.4 31.5 1.0
O A:HOH2332 4.5 17.6 1.0
CG A:GLU157 4.5 17.5 1.0
O A:HOH2148 4.6 40.5 1.0
CE A:LYS112 4.7 12.2 1.0

Calcium binding site 4 out of 10 in 1h5v

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Calcium binding site 4 out of 10 in the Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca308

b:19.5
occ:0.70
 O A:HOH2458 2.2 32.3 1.0
O A:HOH2446 2.3 28.3 1.0
OE1 A:GLN28 2.4 15.3 1.0
OD1 A:ASN256 2.4 17.5 1.0
O A:HOH2085 2.5 20.4 0.3
O A:HOH2090 2.9 32.5 1.0
CD A:GLN28 3.5 12.8 1.0
CG A:ASN256 3.7 13.7 1.0
CB A:GLN28 4.0 11.0 1.0
O A:HOH2075 4.2 17.0 0.5
O A:HOH2074 4.3 22.9 1.0
NE2 A:GLN28 4.3 12.5 1.0
CG A:GLN28 4.4 11.7 1.0
ND2 A:ASN256 4.4 13.8 1.0
CB A:ASN256 4.7 13.1 1.0
O A:ASP253 4.7 13.1 1.0
OD1 A:ASP253 4.8 14.4 1.0
CA A:ASN256 4.9 13.0 1.0
O A:HOH2087 4.9 30.4 1.0
O A:HOH2105 4.9 17.5 0.5

Calcium binding site 5 out of 10 in 1h5v

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Calcium binding site 5 out of 10 in the Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca309

b:24.2
occ:1.00
 O A:HOH2409 2.4 16.6 0.5
O A:HOH2412 2.4 19.0 0.5
O A:HOH2410 2.4 30.0 1.0
NA A:NA316 3.4 30.4 1.0
OD1 A:ASP219 4.1 24.4 1.0
CA A:ASP219 4.2 15.5 1.0
O A:LEU218 4.4 14.8 1.0
O A:ASP219 4.5 17.2 1.0
O A:HOH2204 4.6 28.3 1.0
O A:HOH2041 4.7 30.5 1.0
O A:HOH2203 4.7 22.7 0.5
O A:HOH2024 4.7 23.1 0.5
C A:ASP219 4.8 15.8 1.0
CG A:ASP219 4.9 20.5 1.0
CB A:ASP219 5.0 17.7 1.0
N A:ASP219 5.0 13.7 1.0

Calcium binding site 6 out of 10 in 1h5v

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Calcium binding site 6 out of 10 in the Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca310

b:22.9
occ:1.00
 O A:ILE14 2.3 12.5 1.0
O A:HOH2173 2.3 31.4 1.0
O A:HOH2034 2.4 22.9 1.0
O A:HOH2383 2.4 21.1 1.0
O A:HOH2033 2.4 27.2 1.0
O A:HOH2036 2.4 30.7 1.0
O A:HOH2032 2.4 25.1 1.0
C A:ILE14 3.5 10.9 1.0
CA A:SER15 4.0 12.1 1.0
N A:SER15 4.1 11.7 1.0
O A:HOH2172 4.3 33.7 1.0
O A:HOH2038 4.3 18.1 1.0
O A:HOH2380 4.4 17.5 1.0
CB A:SER15 4.4 13.8 1.0
O A:HOH2021 4.5 37.6 1.0
N A:ILE14 4.5 10.2 1.0
OG A:SER13 4.6 16.2 1.0
CA A:ILE14 4.6 10.0 1.0
O A:HOH2035 4.6 15.5 1.0
CB A:SER13 4.8 11.7 1.0
OD1 A:ASN194 4.8 14.7 1.0
O A:HOH2382 4.8 31.3 1.0
OG A:SER15 5.0 18.6 1.0

Calcium binding site 7 out of 10 in 1h5v

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Calcium binding site 7 out of 10 in the Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca311

b:21.9
occ:1.00
 O A:HOH2442 2.4 16.5 0.5
O A:HOH2449 2.5 20.6 0.5
O A:HOH2447 2.5 19.0 0.5
O A:HOH2514 2.6 24.6 1.0
O A:HOH2445 3.5 20.6 0.5
O A:HOH2226 4.2 19.8 0.5
OD1 A:ASP250 4.2 15.4 1.0
OD2 A:ASP253 4.2 20.4 1.0
O A:HOH2512 4.3 21.5 0.5
OE2 A:GLU302 4.5 20.5 1.0
O A:HOH2515 4.6 26.2 0.5
NE2 A:GLN246 4.7 13.8 1.0

Calcium binding site 8 out of 10 in 1h5v

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Calcium binding site 8 out of 10 in the Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca312

b:27.9
occ:1.00
 O A:HOH2044 1.9 18.5 0.5
O A:HOH2046 2.4 22.9 1.0
O A:HOH2456 2.4 20.1 0.5
O A:HOH2024 2.5 23.1 0.5
O A:HOH2045 2.5 17.0 0.5
O A:HOH2203 2.6 22.7 0.5
O A:HOH2453 3.2 36.0 1.0
OE2 A:GLU18 3.2 31.4 0.5
O A:HOH2234 3.3 33.8 1.0
O A:HOH2455 3.3 17.9 0.5
CD A:GLU18 3.4 28.6 0.5
OE1 A:GLU18 3.7 31.1 0.5
CB A:GLU18 3.9 20.1 1.0
CG A:GLU18 4.1 23.3 0.5
O A:HOH2457 4.3 16.8 1.0
O A:GLY17 4.7 16.6 1.0
O A:HOH2408 4.7 15.9 1.0
O A:ARG255 4.8 12.8 1.0
O A:ASN16 4.9 13.2 1.0
O A:HOH2204 5.0 28.3 1.0

Calcium binding site 9 out of 10 in 1h5v

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Calcium binding site 9 out of 10 in the Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca313

b:33.9
occ:1.00
 OD2 A:ASP75 2.3 19.9 1.0
O A:HOH2106 2.5 34.8 1.0
O A:HOH2202 2.7 29.1 1.0
CG A:ASP75 3.5 14.3 1.0
O A:HOH2179 3.6 38.9 1.0
O A:HOH2206 4.0 27.3 1.0
CB A:ASP75 4.1 14.3 1.0
O A:HOH2200 4.5 15.4 1.0
OD1 A:ASP75 4.5 15.4 1.0
OG A:SER77 4.9 16.3 1.0

Calcium binding site 10 out of 10 in 1h5v

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Calcium binding site 10 out of 10 in the Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Thiopentasaccharide Complex of the Endoglucanase CEL5A From Bacillus Agaradharens at 1.1 A Resolution in the Tetragonal Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca314

b:38.9
occ:1.00
 O A:HOH2189 2.0 20.0 1.0
O A:HOH2190 2.2 18.4 1.0
O A:HOH2081 2.3 35.9 1.0
O A:HOH2082 2.4 31.7 1.0
O A:ILE73 2.5 16.5 1.0
O A:HOH2186 2.6 22.3 1.0
C A:ILE73 3.6 13.2 1.0
NA A:NA315 4.1 26.1 1.0
CA A:ILE73 4.2 11.9 1.0
O A:HOH2188 4.5 34.8 1.0
O A:TYR72 4.5 11.6 1.0
CG2 A:ILE73 4.6 13.9 1.0
N A:ASP74 4.7 13.7 1.0
CD A:PRO76 4.9 15.0 1.0
CA A:ASP74 5.0 15.6 1.0
CG A:PRO76 5.0 16.2 1.0

Reference:

A.Varrot, M.Schulein, S.Fruchard, H.Driguez, G.J.Davies. Atomic Resolution Structure of Endoglucanase CEL5A in Complex with Methyl 4,4II,4III,4IV-Tetrathio-Alpha-Cellopentoside Highlights the Alternative Binding Modes Targeted By Substrate Mimics Acta Crystallogr.,Sect.D V. 57 1739 2001.
ISSN: ISSN 0907-4449
PubMed: 11679762
DOI: 10.1107/S0907444901013993
Page generated: Thu Jul 11 09:55:53 2024

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