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Calcium in PDB 8y1m: Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose.

Enzymatic activity of Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose.

All present enzymatic activity of Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose.:
3.2.1.8;

Protein crystallography data

The structure of Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose., PDB code: 8y1m was solved by T.Nakamura, K.Kuwata, T.Takita, K.Mizutani, B.Mikami, S.Nakamura, K.Yasukawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.26 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.702, 53.335, 96.567, 90, 93.58, 90
R / Rfree (%) 16.6 / 20.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose. (pdb code 8y1m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose., PDB code: 8y1m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 8y1m

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Calcium binding site 1 out of 9 in the Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:24.3
occ:1.00
 OD1 A:ASP289 2.3 21.3 1.0
O A:ARG348 2.3 24.9 1.0
OE1 A:GLU353 2.4 27.8 1.0
O A:HOH757 2.4 22.7 1.0
O A:HOH619 2.5 29.6 1.0
O A:HOH692 2.5 25.7 1.0
OD1 A:ASP351 2.6 29.7 1.0
CD A:GLU353 3.1 28.6 1.0
OE2 A:GLU353 3.2 30.6 1.0
CG A:ASP289 3.3 22.0 1.0
C A:ARG348 3.4 27.3 1.0
CG A:ASP351 3.5 36.0 1.0
OD2 A:ASP351 3.7 28.2 1.0
OD2 A:ASP289 4.1 26.5 1.0
CB A:ASP289 4.2 18.1 1.0
CA A:ILE349 4.2 23.8 1.0
CA A:ARG348 4.2 24.2 1.0
N A:ILE349 4.2 22.0 1.0
O A:HOH664 4.3 23.5 1.0
CA A:ASP289 4.3 19.2 1.0
CA A:CA504 4.3 23.1 1.0
O A:HOH638 4.3 29.3 1.0
OE2 A:GLU293 4.4 23.6 1.0
CG A:GLU353 4.4 28.1 1.0
CG A:GLU293 4.5 20.6 1.0
O A:ASP289 4.5 22.5 1.0
O A:ASP351 4.7 23.9 1.0
CB A:ARG348 4.8 26.0 1.0
C A:ASP289 4.8 20.1 1.0
CD A:GLU293 4.8 28.6 1.0
C A:ILE349 4.9 22.6 1.0
CB A:ASP351 4.9 25.2 1.0

Calcium binding site 2 out of 9 in 8y1m

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Calcium binding site 2 out of 9 in the Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:22.7
occ:0.66
 OD2 A:ASP21 2.3 33.6 1.0
O A:HOH781 2.4 32.1 1.0
O A:HOH827 2.4 34.7 1.0
OE2 A:GLU82 2.4 30.8 1.0
O A:HOH684 2.5 31.8 1.0
OE1 A:GLU82 2.6 36.6 1.0
CD A:GLU82 2.8 35.9 1.0
OD1 A:ASP21 2.9 33.3 1.0
CG A:ASP21 3.0 31.2 1.0
O A:SER303 4.0 21.4 1.0
O A:HOH661 4.2 32.0 1.0
O A:HOH644 4.3 33.5 1.0
CG A:GLU82 4.4 29.9 1.0
O A:HOH633 4.4 28.5 1.0
CB A:ASP21 4.4 22.6 1.0
O A:HOH865 4.5 50.1 1.0
O A:HOH687 4.5 23.8 1.0
CB A:SER303 4.9 22.8 1.0
C A:SER303 5.0 20.6 1.0
O1 A:PEG515 5.0 55.8 1.0

Calcium binding site 3 out of 9 in 8y1m

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Calcium binding site 3 out of 9 in the Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:25.6
occ:0.64
 O A:ALA299 2.3 25.9 1.0
O A:GLN19 2.3 23.9 1.0
O2 A:PEG515 2.3 55.0 1.0
O A:ILE302 2.4 21.8 1.0
O A:HOH790 2.5 33.3 1.0
C2 A:PEG515 2.7 42.6 1.0
C3 A:PEG515 2.7 29.9 1.0
C1 A:PEG515 3.1 57.1 1.0
C A:ALA299 3.4 26.8 1.0
C A:ILE302 3.4 22.0 1.0
C A:GLN19 3.5 26.3 1.0
CA A:SER303 4.1 22.6 1.0
O1 A:PEG515 4.1 55.8 1.0
C4 A:PEG515 4.2 46.0 1.0
N A:SER303 4.2 19.2 1.0
N A:ILE302 4.2 23.6 1.0
CA A:ALA299 4.2 23.8 1.0
N A:ALA300 4.4 25.3 1.0
CA A:GLN19 4.4 22.1 1.0
CB A:PHE20 4.4 18.4 1.0
CA A:PHE20 4.4 21.9 1.0
CA A:ILE302 4.4 19.5 1.0
N A:PHE20 4.4 21.9 1.0
O A:HOH783 4.4 41.7 1.0
CA A:ALA300 4.5 24.6 1.0
C A:ALA300 4.5 25.7 1.0
CB A:ALA299 4.5 24.0 1.0
O A:ALA300 4.7 27.5 1.0
CD2 A:PHE20 4.8 25.8 1.0
C A:SER303 4.9 20.6 1.0
N A:ASP301 4.9 23.3 1.0

Calcium binding site 4 out of 9 in 8y1m

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Calcium binding site 4 out of 9 in the Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:23.1
occ:0.96
 OE2 A:GLU353 2.3 30.6 1.0
OE2 A:GLU293 2.3 23.6 1.0
OE2 B:GLU14 2.4 25.2 1.0
OD2 A:ASP289 2.4 26.5 1.0
OE1 B:GLN17 2.5 26.1 1.0
O A:HOH770 2.5 29.3 1.0
OE1 B:GLU14 2.7 25.9 1.0
CD B:GLU14 2.9 28.9 1.0
OD1 A:ASP289 2.9 21.3 1.0
CG A:ASP289 3.0 22.0 1.0
CD A:GLU353 3.3 28.6 1.0
CD B:GLN17 3.4 29.9 1.0
CD A:GLU293 3.5 28.6 1.0
NE2 B:GLN17 3.7 25.7 1.0
O A:HOH619 3.8 29.6 1.0
OE1 A:GLU353 3.9 27.8 1.0
O B:HOH785 4.2 30.7 1.0
O B:HOH726 4.3 38.2 1.0
O A:HOH728 4.3 29.7 1.0
CA A:CA501 4.3 24.3 1.0
OE1 A:GLU293 4.4 29.8 1.0
CG B:GLU14 4.4 24.8 1.0
CG A:GLU353 4.4 28.1 1.0
CG A:GLU293 4.4 20.6 1.0
CB A:ASP289 4.5 18.1 1.0
O B:HOH799 4.7 29.6 1.0
NH2 A:ARG348 4.8 23.4 1.0
CG B:GLN17 4.8 30.2 1.0

Calcium binding site 5 out of 9 in 8y1m

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Calcium binding site 5 out of 9 in the Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:23.4
occ:0.55
 O A:ASP312 2.3 20.6 1.0
O A:ASP331 2.4 22.9 1.0
OD1 A:ASP318 2.4 23.5 1.0
OH A:TYR273 2.4 23.7 1.0
OD2 A:ASP318 2.6 25.3 1.0
CG A:ASP318 2.8 22.9 1.0
CG2 A:THR315 3.3 20.5 1.0
CZ A:TYR273 3.4 27.5 1.0
C A:ASP312 3.5 18.1 1.0
C A:ASP331 3.5 22.0 1.0
CE1 A:TYR273 3.6 23.5 1.0
N A:ASP331 3.8 19.2 1.0
O A:HOH603 3.9 36.0 1.0
CA A:ASP331 4.3 16.9 1.0
CA A:ASP312 4.3 20.4 1.0
CB A:ASP318 4.3 21.0 1.0
CB A:ILE330 4.4 23.3 1.0
CB A:ASP312 4.4 20.1 1.0
N A:ASN313 4.5 18.3 1.0
N A:ALA332 4.6 19.8 1.0
CA A:ASN313 4.6 24.0 1.0
CG2 A:ILE330 4.6 24.5 1.0
C A:ASN313 4.7 25.7 1.0
CE2 A:TYR273 4.7 24.7 1.0
O A:HOH624 4.8 23.8 1.0
CB A:THR315 4.8 20.2 1.0
CA A:ALA332 4.8 16.9 1.0
C A:ILE330 4.8 23.9 1.0
CA A:ILE330 4.8 22.3 1.0
CD A:PRO333 4.9 21.4 1.0
N A:HIS314 4.9 22.4 1.0
CB A:ASP331 5.0 20.8 1.0
N A:THR315 5.0 19.5 1.0
CD1 A:TYR273 5.0 25.5 1.0

Calcium binding site 6 out of 9 in 8y1m

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Calcium binding site 6 out of 9 in the Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:23.0
occ:1.00
 O B:HOH617 2.3 29.8 1.0
OE2 B:GLU353 2.4 34.3 1.0
O B:ARG348 2.4 23.5 1.0
O B:HOH620 2.4 22.0 1.0
O B:HOH725 2.4 24.6 1.0
OD1 B:ASP351 2.4 27.2 0.7
OD1 B:ASP289 2.5 24.5 1.0
OD1 B:ASP351 2.5 30.4 0.3
OD2 B:ASP351 2.8 28.3 0.7
CG B:ASP351 3.0 29.7 0.7
CG B:ASP351 3.4 31.0 0.3
CG B:ASP289 3.4 25.6 1.0
C B:ARG348 3.4 23.8 1.0
OD2 B:ASP351 3.5 29.1 0.3
CD B:GLU353 3.6 49.4 1.0
OD2 B:ASP289 4.0 27.3 1.0
O B:HOH692 4.2 22.8 1.0
CA B:ARG348 4.3 23.5 1.0
CA B:ILE349 4.3 17.7 1.0
N B:ILE349 4.3 21.3 1.0
CG B:GLU353 4.3 34.5 1.0
O B:HOH628 4.4 40.4 1.0
CB B:ASP289 4.5 21.7 1.0
CB B:ASP351 4.5 28.6 0.7
CA B:ASP289 4.5 19.4 1.0
OE1 B:GLU353 4.5 49.6 1.0
O B:ASP351 4.6 25.8 1.0
O B:ASP289 4.6 21.2 1.0
OE2 B:GLU293 4.7 38.7 1.0
CB B:ASP351 4.8 28.2 0.3
CG B:GLU293 4.8 23.4 1.0
CB B:ARG348 4.9 24.1 1.0
C B:ILE349 4.9 23.8 1.0
C B:ASP289 5.0 22.8 1.0
N B:ASP351 5.0 23.2 1.0

Calcium binding site 7 out of 9 in 8y1m

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Calcium binding site 7 out of 9 in the Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:22.2
occ:0.96
 OD2 B:ASP21 2.3 23.2 1.0
O B:HOH693 2.3 26.3 1.0
OE2 B:GLU82 2.4 23.8 1.0
O B:HOH810 2.5 24.5 1.0
O B:HOH804 2.5 32.5 1.0
OE1 B:GLU82 2.5 27.7 1.0
O A:HOH784 2.5 26.0 1.0
OD1 B:ASP21 2.7 22.9 1.0
CD B:GLU82 2.8 23.1 1.0
CG B:ASP21 2.9 27.3 1.0
O B:HOH669 4.2 29.9 1.0
O B:SER303 4.2 18.4 1.0
CG B:GLU82 4.3 29.2 1.0
CB B:ASP21 4.3 21.3 1.0
O B:HOH634 4.4 24.7 1.0
O B:HOH690 4.5 27.5 1.0
CH3 A:ACT506 4.6 31.7 1.0
O A:HOH852 4.6 51.1 1.0
O B:HOH865 4.6 41.7 1.0
ND1 A:HIS357 4.6 25.1 1.0
O B:HOH710 4.6 21.4 1.0
O A:ACT506 4.8 39.6 1.0
CG2 B:THR143 5.0 26.2 0.6
CE1 A:HIS357 5.0 25.8 1.0
CB B:GLU82 5.0 20.9 1.0

Calcium binding site 8 out of 9 in 8y1m

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Calcium binding site 8 out of 9 in the Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:22.9
occ:0.68
 O B:GLN19 2.3 24.0 1.0
O B:ALA299 2.3 25.4 1.0
O B:ILE302 2.3 22.9 1.0
O B:HOH834 2.4 36.1 1.0
O B:HOH818 2.5 34.6 1.0
O B:HOH823 2.5 35.6 1.0
C B:ILE302 3.4 19.1 1.0
C B:GLN19 3.5 25.6 1.0
C B:ALA299 3.5 28.5 1.0
CA B:SER303 4.1 20.8 1.0
N B:SER303 4.2 20.3 1.0
N B:ILE302 4.3 21.9 1.0
CA B:GLN19 4.3 24.4 1.0
CA B:ALA299 4.3 19.5 1.0
N B:PHE20 4.4 21.2 1.0
N B:ALA300 4.4 27.2 1.0
CA B:ILE302 4.4 19.1 1.0
CB B:PHE20 4.4 23.7 1.0
CA B:PHE20 4.4 22.6 1.0
CA B:ALA300 4.5 24.2 1.0
C B:ALA300 4.5 23.7 1.0
O B:HOH719 4.6 38.0 1.0
CB B:ALA299 4.6 23.1 1.0
CH3 A:ACT506 4.6 31.7 1.0
CD2 B:PHE20 4.7 28.2 1.0
O B:ALA300 4.7 26.3 1.0
OXT A:ACT506 4.9 50.6 1.0
C B:SER303 4.9 21.8 1.0
N B:ASP301 5.0 21.2 1.0

Calcium binding site 9 out of 9 in 8y1m

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Calcium binding site 9 out of 9 in the Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Xylanase R From Bacillus Sp. Tar-1 Complexed with Xylobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:25.6
occ:0.56
 O B:ASP312 2.3 20.6 1.0
OH B:TYR273 2.3 25.7 1.0
OD1 B:ASP318 2.4 27.1 1.0
O B:ASP331 2.4 24.8 1.0
OD2 B:ASP318 2.6 25.6 1.0
CG B:ASP318 2.9 24.7 1.0
CZ B:TYR273 3.4 28.4 1.0
CG2 B:THR315 3.4 23.1 1.0
C B:ASP312 3.5 19.0 1.0
CE1 B:TYR273 3.6 27.6 1.0
C B:ASP331 3.6 21.6 1.0
N B:ASP331 3.8 22.2 1.0
O B:HOH627 4.0 38.7 1.0
CA B:ASP331 4.3 22.9 1.0
CA B:ASP312 4.3 20.5 1.0
CB B:ILE330 4.4 25.8 1.0
CB B:ASP318 4.4 25.1 1.0
CB B:ASP312 4.4 19.9 1.0
N B:ASN313 4.5 20.8 1.0
CA B:ASN313 4.5 22.9 1.0
N B:ALA332 4.6 19.0 1.0
CE2 B:TYR273 4.6 31.2 1.0
CG2 B:ILE330 4.7 28.9 1.0
C B:ASN313 4.7 27.1 1.0
C B:ILE330 4.8 28.3 1.0
O B:HOH630 4.8 27.5 1.0
CA B:ILE330 4.8 27.4 1.0
CA B:ALA332 4.9 23.0 1.0
CB B:THR315 4.9 19.4 1.0
N B:HIS314 4.9 19.9 1.0
CD1 B:TYR273 4.9 33.5 1.0
CD B:PRO333 5.0 20.2 1.0

Reference:

T.Nakamura, T.Takita, K.Kuwata, K.Mizutani, B.Mikami, S.Nakamura, K.Yasukawa. Activity-Stability Trade-Off Observed in Variants at Position 315 of the GH10 Xylanase Xynr. Sci Rep V. 14 7767 2024.
ISSN: ESSN 2045-2322
PubMed: 38565938
DOI: 10.1038/S41598-024-57819-Z
Page generated: Thu Jul 10 08:30:22 2025

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