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

Go back to Calcium Binding Sites List in 8y1m
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

Go back to Calcium Binding Sites List in 8y1m
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

Go back to Calcium Binding Sites List in 8y1m
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

Go back to Calcium Binding Sites List in 8y1m
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

Go back to Calcium Binding Sites List in 8y1m
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

Go back to Calcium Binding Sites List in 8y1m
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

Go back to Calcium Binding Sites List in 8y1m
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

Go back to Calcium Binding Sites List in 8y1m
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

Go back to Calcium Binding Sites List in 8y1m
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: Fri Jul 19 12:47:19 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy