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Calcium in PDB 1clc: Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution

Enzymatic activity of Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution

All present enzymatic activity of Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution:
3.2.1.4;

Protein crystallography data

The structure of Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution, PDB code: 1clc was solved by P.M.Alzari, M.B.Lascombe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 98.900, 98.900, 191.400, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / n/a

Other elements in 1clc:

The structure of Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution (pdb code 1clc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution, PDB code: 1clc:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1clc

Go back to Calcium Binding Sites List in 1clc
Calcium binding site 1 out of 3 in the Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca650

b:29.7
occ:1.00
OD1 A:ASN239 2.3 33.6 1.0
OD2 A:ASP246 2.3 26.9 1.0
OD1 A:ASP243 2.3 27.7 1.0
O A:GLU236 2.3 30.6 1.0
O A:ILE241 2.4 32.5 1.0
O A:HOH741 2.4 36.2 1.0
CG A:ASN239 3.4 34.3 1.0
C A:GLU236 3.5 32.5 1.0
CG A:ASP246 3.5 28.6 1.0
CG A:ASP243 3.6 26.9 1.0
C A:ILE241 3.6 29.2 1.0
N A:ASP243 3.8 23.6 1.0
CA A:ASP243 3.9 24.8 1.0
ND2 A:ASN239 4.0 34.8 1.0
CA A:LYS237 4.1 39.7 1.0
C A:PRO242 4.1 26.9 1.0
OD1 A:ASP246 4.1 31.7 1.0
C A:LYS237 4.2 43.5 1.0
N A:ASN239 4.2 45.1 1.0
N A:ILE241 4.2 35.5 1.0
CB A:GLU236 4.2 29.8 1.0
N A:LYS237 4.2 36.6 1.0
O A:LYS237 4.2 48.0 1.0
O A:ASN239 4.3 41.8 1.0
CA A:ILE241 4.3 33.5 1.0
CB A:ASP243 4.4 24.8 1.0
O A:PRO242 4.4 28.0 1.0
OD2 A:ASP243 4.4 29.3 1.0
CA A:GLU236 4.5 31.2 1.0
C A:ASN239 4.5 40.9 1.0
CB A:ASN239 4.6 33.8 1.0
CB A:ILE241 4.6 34.3 1.0
N A:PRO242 4.6 26.6 1.0
O A:HOH819 4.6 47.9 1.0
CB A:ASP246 4.6 22.5 1.0
CA A:ASN239 4.6 37.6 1.0
N A:ASN238 4.7 44.7 1.0
CA A:PRO242 4.7 25.8 1.0

Calcium binding site 2 out of 3 in 1clc

Go back to Calcium Binding Sites List in 1clc
Calcium binding site 2 out of 3 in the Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca651

b:25.6
occ:1.00
O A:HOH677 2.3 23.6 1.0
OG1 A:THR356 2.4 23.6 1.0
OD1 A:ASP362 2.4 23.2 1.0
OD1 A:ASP361 2.5 29.9 1.0
O A:ASP401 2.5 27.6 1.0
OD2 A:ASP361 2.5 28.3 1.0
O A:HOH730 2.5 28.7 1.0
O A:SER358 2.5 33.7 1.0
CG A:ASP361 2.8 26.9 1.0
C A:ASP401 3.5 27.7 1.0
CG A:ASP362 3.5 21.2 1.0
CB A:THR356 3.5 22.9 1.0
C A:SER358 3.7 30.4 1.0
CG2 A:THR356 3.8 19.7 1.0
OD2 A:ASP362 3.9 24.1 1.0
OD1 A:ASP401 4.3 33.0 1.0
CA A:ASP401 4.3 25.1 1.0
CB A:ASP361 4.4 23.9 1.0
N A:ASN402 4.4 27.9 1.0
N A:SER358 4.4 32.0 1.0
CA A:ASP359 4.5 25.7 1.0
N A:ASP362 4.5 21.9 1.0
CA A:ASN402 4.5 26.7 1.0
N A:ASP359 4.5 29.6 1.0
CA A:SER358 4.6 30.0 1.0
CG A:ASP401 4.8 33.3 1.0
O A:TRP400 4.8 22.7 1.0
CB A:ASP362 4.8 22.5 1.0
CA A:THR356 4.8 27.3 1.0
N A:ASP361 4.9 29.5 1.0
CB A:SER358 4.9 28.4 1.0
N A:VAL403 5.0 26.7 1.0

Calcium binding site 3 out of 3 in 1clc

Go back to Calcium Binding Sites List in 1clc
Calcium binding site 3 out of 3 in the Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca652

b:33.0
occ:1.00
O A:ILE525 2.2 30.5 1.0
O A:SER520 2.3 28.2 1.0
O A:HOH856 2.3 35.5 1.0
O A:HOH668 2.4 29.2 1.0
OD1 A:ASP523 2.4 32.0 1.0
O A:HOH686 2.4 29.5 1.0
C A:SER520 3.4 28.8 1.0
C A:ILE525 3.4 29.2 1.0
CG A:ASP523 3.4 31.6 1.0
OD2 A:ASP523 3.8 34.3 1.0
CA A:SER520 4.0 26.9 1.0
N A:ILE525 4.0 33.9 1.0
CA A:ILE525 4.1 30.1 1.0
O A:GLU527 4.2 24.7 1.0
O A:ASP523 4.2 41.9 1.0
O A:HOH822 4.3 47.4 1.0
O A:TRP526 4.3 24.4 1.0
O A:HOH710 4.5 33.8 1.0
N A:TRP526 4.5 25.9 1.0
CB A:ILE525 4.5 30.7 1.0
C A:TRP526 4.5 23.5 1.0
O A:HOH968 4.5 63.6 1.0
N A:GLY521 4.5 31.7 1.0
O A:HOH865 4.5 56.6 1.0
C A:ASP523 4.6 35.0 1.0
O A:HOH1008 4.6 78.2 1.0
CB A:SER520 4.6 23.7 1.0
N A:ASP523 4.6 28.3 1.0
CA A:TRP526 4.7 23.4 1.0
CB A:ASP523 4.8 27.8 1.0
C A:GLU527 4.8 24.8 1.0
CA A:GLY521 4.8 28.9 1.0
O A:ARG519 4.9 26.9 1.0
CA A:ASP523 4.9 28.7 1.0
C A:GLY524 5.0 35.2 1.0
CA A:PRO528 5.0 23.4 1.0

Reference:

M.B.Lascombe, H.Souchon, M.Juy, P.M.Alzari. Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution To Be Published.
Page generated: Sat Dec 12 02:51:40 2020

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