Calcium in PDB 8hcj: Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans

Enzymatic activity of Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans

All present enzymatic activity of Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans:
3.2.1.37;

Protein crystallography data

The structure of Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans, PDB code: 8hcj was solved by P.Vishwakarma, E.Sachdeva, A.Goyal, A.S.Ethayathulla, U.Das, P.Kaur, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 134.29 / 2.57
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 73.34, 89.662, 138.437, 102.73, 93.99, 98.24
R / Rfree (%) 16.3 / 20.9

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans (pdb code 8hcj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans, PDB code: 8hcj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 8hcj

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Calcium binding site 1 out of 16 in the Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:33.8
occ:1.00
 O D:HOH623 2.4 33.3 1.0
O D:HOH656 2.4 26.2 1.0
O D:HOH692 2.4 36.0 1.0
O D:HOH673 2.4 27.1 1.0
O D:HOH614 2.5 24.1 1.0
O D:HOH659 2.5 19.2 1.0
NE2 D:HIS263 2.7 23.4 1.0
CD2 D:HIS263 3.6 21.4 1.0
CE1 D:HIS263 3.7 28.7 1.0
O D:PRO150 3.8 22.1 1.0
O D:PRO212 4.1 25.2 1.0
CE3 D:TRP213 4.2 28.6 1.0
CB D:ALA94 4.3 23.4 1.0
O D:ALA95 4.4 20.0 1.0
O D:PRO264 4.6 15.7 1.0
CZ3 D:TRP213 4.6 33.8 1.0
CG D:HIS263 4.8 22.4 1.0
C D:PRO150 4.8 26.5 1.0
ND1 D:HIS263 4.8 27.8 1.0
O D:ALA94 4.9 25.0 1.0
C D:ALA94 4.9 27.3 1.0
C D:ALA95 4.9 21.4 1.0
O D:ASP149 5.0 38.8 1.0
O D:GLY211 5.0 20.9 1.0

Calcium binding site 2 out of 16 in 8hcj

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Calcium binding site 2 out of 16 in the Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:23.9
occ:1.00
 OD1 D:ASP447 2.2 22.4 1.0
OE1 D:GLN328 2.2 27.4 1.0
O D:VAL348 2.2 19.4 1.0
OE2 D:GLU330 2.6 27.7 1.0
OE1 D:GLU330 2.7 23.3 1.0
O D:ASP447 2.7 19.8 1.0
O D:HOH620 2.8 17.5 1.0
CD D:GLU330 3.0 29.7 1.0
CG D:ASP447 3.3 22.9 1.0
CD D:GLN328 3.3 22.9 1.0
C D:VAL348 3.5 23.1 1.0
C D:ASP447 3.5 20.7 1.0
CA D:ASP447 3.9 18.4 1.0
NE2 D:GLN328 4.0 25.9 1.0
OD2 D:ASP447 4.1 25.8 1.0
CB D:ASP447 4.2 19.4 1.0
O D:VAL346 4.3 22.2 1.0
CB D:GLN328 4.4 24.4 1.0
CG D:GLN328 4.4 23.5 1.0
N D:VAL348 4.4 22.7 1.0
N D:PHE349 4.4 22.7 1.0
CA D:PHE349 4.4 19.4 1.0
CA D:VAL348 4.4 18.9 1.0
O D:HOH702 4.4 23.2 1.0
CG D:GLU330 4.5 26.0 1.0
O D:HOH721 4.5 27.3 1.0
N D:TYR448 4.6 20.6 1.0
N D:ALA329 4.7 19.0 1.0
CA D:GLN328 4.8 20.9 1.0
CB D:VAL348 4.8 19.5 1.0
CB D:PHE349 4.8 19.3 1.0
CB D:TYR448 4.9 22.4 1.0
O D:HOH662 5.0 20.6 1.0

Calcium binding site 3 out of 16 in 8hcj

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Calcium binding site 3 out of 16 in the Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca501

b:42.6
occ:1.00
 O E:HOH671 2.1 39.0 1.0
O E:HOH693 2.2 42.9 1.0
O E:HOH629 2.3 51.5 1.0
O E:HOH730 2.4 38.2 1.0
O E:HOH608 2.6 25.7 1.0
NE2 E:HIS263 2.7 30.3 1.0
O E:HOH604 2.8 25.8 1.0
CD2 E:HIS263 3.5 21.3 1.0
CE1 E:HIS263 3.8 28.3 1.0
O E:PRO150 4.0 24.4 1.0
O E:PRO212 4.2 21.3 1.0
CE3 E:TRP213 4.2 16.1 1.0
CB E:ALA94 4.3 18.9 1.0
O E:ALA95 4.5 24.7 1.0
O E:PRO264 4.5 17.5 1.0
CZ3 E:TRP213 4.6 16.0 1.0
CG E:HIS263 4.7 19.6 1.0
O E:ALA94 4.8 30.3 1.0
C E:ALA94 4.8 23.7 1.0
ND1 E:HIS263 4.9 24.5 1.0
C E:PRO150 5.0 26.4 1.0
C E:ALA95 5.0 23.1 1.0
O E:GLY211 5.0 26.0 1.0

Calcium binding site 4 out of 16 in 8hcj

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Calcium binding site 4 out of 16 in the Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca502

b:25.1
occ:1.00
 OD1 E:ASP447 2.1 26.2 1.0
OE1 E:GLN328 2.3 26.6 1.0
O E:VAL348 2.4 14.5 1.0
OE2 E:GLU330 2.5 27.3 1.0
O E:ASP447 2.6 21.8 1.0
O E:HOH625 2.7 18.6 1.0
OE1 E:GLU330 2.8 18.2 1.0
CD E:GLU330 3.0 23.9 1.0
CG E:ASP447 3.3 24.6 1.0
CD E:GLN328 3.4 22.6 1.0
C E:ASP447 3.4 21.3 1.0
C E:VAL348 3.6 16.4 1.0
CA E:ASP447 3.8 18.1 1.0
OD2 E:ASP447 4.1 31.0 1.0
CB E:ASP447 4.1 20.1 1.0
NE2 E:GLN328 4.2 21.0 1.0
CB E:GLN328 4.2 18.9 1.0
O E:HOH781 4.3 31.3 1.0
CG E:GLN328 4.3 19.7 1.0
O E:VAL346 4.4 20.9 1.0
CA E:PHE349 4.5 16.4 1.0
N E:PHE349 4.5 16.4 1.0
N E:VAL348 4.5 21.7 1.0
N E:TYR448 4.5 18.8 1.0
CG E:GLU330 4.5 22.0 1.0
CA E:VAL348 4.5 17.6 1.0
N E:ALA329 4.6 17.2 1.0
CA E:GLN328 4.6 19.1 1.0
O E:HOH754 4.7 17.0 1.0
CB E:TYR448 4.8 17.2 1.0
CB E:PHE349 4.9 16.8 1.0
CB E:VAL348 4.9 16.7 1.0
CA E:TYR448 5.0 18.1 1.0
O E:HOH645 5.0 14.0 1.0

Calcium binding site 5 out of 16 in 8hcj

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Calcium binding site 5 out of 16 in the Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca501

b:43.8
occ:1.00
 O H:HOH685 2.4 24.2 1.0
O H:HOH711 2.4 28.7 1.0
O H:HOH637 2.6 31.7 1.0
O H:HOH633 2.6 26.6 1.0
NE2 H:HIS263 2.7 30.5 1.0
O H:HOH609 2.8 21.0 1.0
O H:HOH642 2.8 30.0 1.0
CD2 H:HIS263 3.6 28.5 1.0
CE1 H:HIS263 3.6 26.3 1.0
O H:PRO150 3.9 30.2 1.0
O H:PRO212 4.1 24.6 1.0
CE3 H:TRP213 4.2 20.7 1.0
CB H:ALA94 4.4 18.0 1.0
O H:PRO264 4.5 24.4 1.0
O H:ALA95 4.6 20.9 1.0
CZ3 H:TRP213 4.6 22.1 1.0
ND1 H:HIS263 4.7 26.1 1.0
CG H:HIS263 4.8 27.4 1.0
O H:GLY211 4.8 31.0 1.0
C H:PRO150 4.9 26.6 1.0
C H:GLY211 4.9 22.5 1.0
O H:ALA94 5.0 32.7 1.0

Calcium binding site 6 out of 16 in 8hcj

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Calcium binding site 6 out of 16 in the Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca502

b:24.9
occ:1.00
 OD1 H:ASP447 2.1 26.6 1.0
OE1 H:GLN328 2.3 20.2 1.0
O H:VAL348 2.3 26.0 1.0
O H:HOH698 2.3 17.7 1.0
OE2 H:GLU330 2.4 22.1 1.0
O H:ASP447 2.6 27.6 1.0
OE1 H:GLU330 2.7 16.2 1.0
CD H:GLU330 2.9 19.3 1.0
CG H:ASP447 3.3 25.6 1.0
CD H:GLN328 3.4 20.1 1.0
C H:ASP447 3.5 22.4 1.0
C H:VAL348 3.5 22.6 1.0
CA H:ASP447 3.8 19.0 1.0
CB H:ASP447 4.1 20.7 1.0
OD2 H:ASP447 4.2 28.5 1.0
CB H:GLN328 4.2 20.1 1.0
NE2 H:GLN328 4.2 18.0 1.0
CG H:GLN328 4.3 17.9 1.0
CA H:PHE349 4.3 19.2 1.0
N H:PHE349 4.3 20.9 1.0
CG H:GLU330 4.4 18.6 1.0
O H:HOH674 4.4 28.0 1.0
CA H:VAL348 4.5 20.2 1.0
N H:VAL348 4.5 21.3 1.0
O H:VAL346 4.5 24.1 1.0
N H:ALA329 4.5 19.3 1.0
N H:TYR448 4.6 21.5 1.0
O H:HOH755 4.6 17.5 1.0
CA H:GLN328 4.7 23.2 1.0
CB H:PHE349 4.7 16.4 1.0
O H:HOH648 4.8 19.2 1.0
CB H:VAL348 4.9 17.3 1.0
CB H:TYR448 4.9 22.0 1.0

Calcium binding site 7 out of 16 in 8hcj

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Calcium binding site 7 out of 16 in the Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:38.4
occ:1.00
 O A:HOH609 2.4 27.5 1.0
O A:HOH659 2.5 24.8 1.0
O A:HOH686 2.5 29.7 1.0
O A:HOH650 2.6 48.3 1.0
O A:HOH672 2.7 31.6 1.0
NE2 A:HIS263 2.7 32.6 1.0
O A:HOH607 2.9 39.5 1.0
CD2 A:HIS263 3.4 29.8 1.0
CE1 A:HIS263 3.9 32.9 1.0
O A:PRO150 4.0 36.1 1.0
O A:PRO212 4.1 31.0 1.0
CB A:ALA94 4.3 18.4 1.0
CE3 A:TRP213 4.4 23.9 1.0
O A:PRO264 4.6 26.3 1.0
O A:ALA95 4.6 32.1 1.0
CG A:HIS263 4.7 31.4 1.0
O A:GLY211 4.8 33.2 1.0
CZ3 A:TRP213 4.8 21.0 1.0
ND1 A:HIS263 4.9 36.5 1.0
C A:GLY211 4.9 34.5 1.0
O A:ALA94 4.9 33.1 1.0
C A:ALA94 4.9 26.2 1.0
C A:PRO150 4.9 33.9 1.0
CA A:GLY211 5.0 31.0 1.0
O A:ASP149 5.0 33.9 1.0

Calcium binding site 8 out of 16 in 8hcj

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Calcium binding site 8 out of 16 in the Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:28.9
occ:1.00
 OD1 A:ASP447 2.1 24.6 1.0
OE1 A:GLN328 2.2 22.6 1.0
O A:VAL348 2.3 25.6 1.0
OE1 A:GLU330 2.5 25.8 1.0
OE2 A:GLU330 2.6 26.5 1.0
O A:HOH641 2.7 19.1 1.0
O A:ASP447 2.7 23.3 1.0
CD A:GLU330 2.9 30.0 1.0
CD A:GLN328 3.2 21.4 1.0
CG A:ASP447 3.4 29.6 1.0
C A:VAL348 3.5 28.0 1.0
C A:ASP447 3.5 20.0 1.0
CA A:ASP447 3.9 18.1 1.0
NE2 A:GLN328 4.0 24.1 1.0
CB A:ASP447 4.2 21.6 1.0
OD2 A:ASP447 4.3 24.1 1.0
CG A:GLN328 4.3 20.5 1.0
CB A:GLN328 4.3 25.0 1.0
CA A:PHE349 4.4 21.9 1.0
N A:PHE349 4.4 24.7 1.0
O A:VAL346 4.4 19.6 1.0
O A:HOH741 4.4 22.4 1.0
CG A:GLU330 4.4 23.5 1.0
CA A:VAL348 4.5 24.0 1.0
N A:VAL348 4.5 23.1 1.0
N A:TYR448 4.6 23.2 1.0
N A:ALA329 4.6 23.9 1.0
CA A:GLN328 4.7 25.2 1.0
O A:HOH684 4.7 25.6 1.0
CB A:PHE349 4.8 20.4 1.0
CB A:VAL348 4.9 23.5 1.0
CB A:TYR448 4.9 21.3 1.0

Calcium binding site 9 out of 16 in 8hcj

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Calcium binding site 9 out of 16 in the Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:48.3
occ:1.00
 O B:HOH710 2.2 34.0 1.0
O B:HOH606 2.3 35.1 1.0
O B:HOH609 2.4 34.6 1.0
O B:HOH686 2.5 29.9 1.0
NE2 B:HIS263 2.5 42.2 1.0
O B:HOH673 2.8 47.0 1.0
O B:HOH613 2.8 28.0 1.0
CD2 B:HIS263 3.2 39.6 1.0
CE1 B:HIS263 3.7 35.5 1.0
CE3 B:TRP213 4.1 28.7 1.0
O B:PRO264 4.3 26.9 1.0
CB B:ALA94 4.3 31.1 1.0
O B:PRO150 4.3 29.6 1.0
O B:PRO212 4.3 33.5 1.0
O B:ALA95 4.4 28.4 1.0
CG B:HIS263 4.4 36.0 1.0
CZ3 B:TRP213 4.5 31.2 1.0
ND1 B:HIS263 4.7 36.7 1.0
O B:PRO34 4.7 27.1 1.0
C B:ALA94 4.9 31.3 1.0
O B:GLY211 5.0 31.7 1.0

Calcium binding site 10 out of 16 in 8hcj

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Calcium binding site 10 out of 16 in the Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:22.2
occ:1.00
 OE1 B:GLN328 2.2 27.0 1.0
OD1 B:ASP447 2.2 22.3 1.0
O B:VAL348 2.3 20.0 1.0
OE2 B:GLU330 2.5 24.1 1.0
O B:HOH678 2.5 20.2 1.0
OE1 B:GLU330 2.6 21.2 1.0
O B:ASP447 2.6 16.6 1.0
CD B:GLU330 2.9 20.8 1.0
CD B:GLN328 3.3 22.5 1.0
CG B:ASP447 3.4 21.8 1.0
C B:ASP447 3.5 17.8 1.0
C B:VAL348 3.5 24.2 1.0
CA B:ASP447 3.9 16.6 1.0
NE2 B:GLN328 4.2 21.5 1.0
CB B:GLN328 4.2 19.4 1.0
CB B:ASP447 4.2 19.9 1.0
CG B:GLN328 4.2 22.6 1.0
OD2 B:ASP447 4.3 26.2 1.0
O B:HOH736 4.3 46.5 1.0
CA B:PHE349 4.3 19.6 1.0
N B:PHE349 4.4 21.5 1.0
CG B:GLU330 4.4 18.0 1.0
O B:VAL346 4.4 26.7 1.0
N B:VAL348 4.5 21.5 1.0
CA B:VAL348 4.5 20.0 1.0
O B:HOH745 4.5 20.9 1.0
N B:ALA329 4.6 19.5 1.0
N B:TYR448 4.6 13.2 1.0
CA B:GLN328 4.6 19.9 1.0
CB B:PHE349 4.8 19.1 1.0
CB B:TYR448 4.9 16.1 1.0
CB B:VAL348 4.9 21.0 1.0

Reference:

P.Vishwakarma, P.Kaur, E.Sachdeva, A.S.Ethayathulla, U.Das, A.Goyal. Structure of GH43 Family Enzyme, Xylan 1, 4 Beta- Xylosidase From Pseudopedobacter Saltans To Be Published.
Page generated: Fri Jul 19 09:25:03 2024

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