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Calcium in PDB 6kka: Xylanase J Mutant From Bacillus Sp. 41M-1

Enzymatic activity of Xylanase J Mutant From Bacillus Sp. 41M-1

All present enzymatic activity of Xylanase J Mutant From Bacillus Sp. 41M-1:
3.2.1.8;

Protein crystallography data

The structure of Xylanase J Mutant From Bacillus Sp. 41M-1, PDB code: 6kka was solved by M.Suzuki, T.Takita, K.Nakatani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.25 / 2.36
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 125.436, 125.436, 318.154, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 21.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Xylanase J Mutant From Bacillus Sp. 41M-1 (pdb code 6kka). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Xylanase J Mutant From Bacillus Sp. 41M-1, PDB code: 6kka:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 6kka

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Calcium binding site 1 out of 7 in the Xylanase J Mutant From Bacillus Sp. 41M-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xylanase J Mutant From Bacillus Sp. 41M-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:61.0
occ:1.00
 OE2 A:GLU213 2.4 42.3 1.0
O A:ASN232 2.5 42.8 1.0
OD1 A:ASP322 2.5 43.7 1.0
O A:ASP322 2.5 39.4 1.0
OE2 A:GLU215 2.6 44.2 1.0
OE1 A:GLU215 3.3 43.2 1.0
C A:ASP322 3.3 42.2 1.0
CD A:GLU215 3.3 44.4 1.0
C A:ASN232 3.6 42.6 1.0
CD A:GLU213 3.6 39.2 1.0
CG A:ASP322 3.7 36.1 1.0
CA A:ASP322 3.8 32.7 1.0
CB A:GLU213 3.8 36.5 1.0
N A:ALA214 4.1 34.5 1.0
CA A:GLU213 4.2 38.1 1.0
CA A:GLY233 4.2 38.1 1.0
CG A:GLU213 4.3 43.6 1.0
N A:TYR323 4.3 35.3 1.0
CB A:ASP322 4.3 36.5 1.0
N A:GLY233 4.4 39.2 1.0
CB A:TYR323 4.5 37.4 1.0
C A:GLU213 4.5 41.6 1.0
OE1 A:GLU213 4.6 51.5 1.0
OD2 A:ASP322 4.6 38.2 1.0
CB A:ASN232 4.6 44.8 1.0
CA A:ASN232 4.7 41.4 1.0
CA A:TYR323 4.7 41.5 1.0
N A:GLU215 4.8 34.5 1.0
CG A:GLU215 4.8 29.0 1.0

Calcium binding site 2 out of 7 in 6kka

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Calcium binding site 2 out of 7 in the Xylanase J Mutant From Bacillus Sp. 41M-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xylanase J Mutant From Bacillus Sp. 41M-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:61.1
occ:1.00
 O A:TRP317 2.3 42.9 1.0
O A:TYR237 2.3 48.3 1.0
OD1 A:ASP313 2.4 41.2 1.0
OD1 A:ASP318 2.5 40.2 1.0
O A:HOH519 2.8 45.0 1.0
C A:TRP317 3.3 37.7 1.0
CG A:ASP313 3.4 45.2 1.0
C A:TYR237 3.4 42.0 1.0
CG A:ASP318 3.6 40.6 1.0
CA A:ASP318 3.8 37.5 1.0
CA A:TYR237 3.8 36.2 1.0
N A:ASP318 3.9 38.9 1.0
OD2 A:ASP313 4.0 44.6 1.0
O A:HOH557 4.0 42.1 1.0
CB A:ASP318 4.2 34.2 1.0
CB A:ASP313 4.3 42.5 1.0
N A:TRP317 4.5 37.6 1.0
N A:ALA238 4.5 46.5 1.0
O A:LEU236 4.5 43.8 1.0
CA A:TRP317 4.6 38.0 1.0
CB A:TYR237 4.6 40.7 1.0
OD2 A:ASP318 4.7 50.0 1.0
CA A:GLY315 4.7 41.4 1.0
N A:GLY315 4.7 38.3 1.0
CA A:ALA238 4.9 40.2 1.0
CE3 A:TRP317 4.9 37.5 1.0
C A:GLY315 5.0 50.7 1.0

Calcium binding site 3 out of 7 in 6kka

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Calcium binding site 3 out of 7 in the Xylanase J Mutant From Bacillus Sp. 41M-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Xylanase J Mutant From Bacillus Sp. 41M-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:73.6
occ:1.00
 O A:HOH620 2.4 42.5 1.0
O A:HOH505 2.4 40.4 1.0
ND2 A:ASN44 2.5 32.1 1.0
OE1 A:GLU183 2.6 36.6 1.0
CG A:ASN44 3.5 42.0 1.0
CD A:GLU183 3.7 35.1 1.0
OD1 A:ASN44 3.8 40.7 1.0
O A:HOH559 3.8 41.0 1.0
CD1 A:LEU46 3.9 35.0 1.0
O A:HOH555 4.0 44.3 1.0
OH A:TYR95 4.0 36.6 1.0
O A:HOH529 4.1 44.9 1.0
OE2 A:GLU183 4.1 38.6 1.0
OE2 A:GLU93 4.5 39.1 1.0
C5 A:MPD412 4.7 48.0 1.0
CB A:ASN44 4.8 32.7 1.0
CG A:GLU183 4.9 36.7 1.0

Calcium binding site 4 out of 7 in 6kka

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Calcium binding site 4 out of 7 in the Xylanase J Mutant From Bacillus Sp. 41M-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Xylanase J Mutant From Bacillus Sp. 41M-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:92.0
occ:1.00
 O A:HOH512 2.7 48.9 1.0
O A:HOH572 2.8 41.9 1.0
OE1 A:GLN186 2.9 46.3 1.0
OD1 A:ASN41 3.8 56.3 1.0
CD A:GLN186 4.1 42.9 1.0
OD1 A:ASN43 4.6 46.8 1.0
O A:VAL42 4.6 38.7 1.0
NE2 A:GLN186 4.8 48.5 1.0
CG A:ASN41 4.9 61.6 1.0
CB A:GLN186 4.9 37.3 1.0
CA A:GLN186 5.0 44.2 1.0

Calcium binding site 5 out of 7 in 6kka

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Calcium binding site 5 out of 7 in the Xylanase J Mutant From Bacillus Sp. 41M-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Xylanase J Mutant From Bacillus Sp. 41M-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:59.5
occ:1.00
 O B:ASN232 2.4 40.2 1.0
OD1 B:ASP322 2.4 45.6 1.0
OE2 B:GLU215 2.5 44.8 1.0
O B:ASP322 2.6 38.5 1.0
OE2 B:GLU213 2.6 39.4 1.0
OE1 B:GLU215 3.2 49.8 1.0
CD B:GLU215 3.2 44.6 1.0
C B:ASP322 3.3 37.7 1.0
C B:ASN232 3.6 44.0 1.0
CG B:ASP322 3.6 41.9 1.0
CA B:ASP322 3.8 37.6 1.0
CD B:GLU213 3.8 50.7 1.0
CB B:GLU213 4.0 40.9 1.0
N B:ALA214 4.1 36.7 1.0
CA B:GLY233 4.1 34.1 1.0
CA B:GLU213 4.3 40.9 1.0
N B:GLY233 4.3 36.5 1.0
CB B:ASP322 4.3 35.9 1.0
N B:TYR323 4.3 37.7 1.0
CG B:GLU213 4.4 42.8 1.0
CB B:ASN232 4.6 47.9 1.0
CB B:TYR323 4.6 36.2 1.0
OD2 B:ASP322 4.6 43.7 1.0
CA B:ASN232 4.6 42.9 1.0
C B:GLU213 4.6 43.1 1.0
CG B:GLU215 4.7 36.2 1.0
CA B:TYR323 4.7 36.4 1.0
OE1 B:GLU213 4.7 64.2 1.0
N B:GLU215 4.8 41.5 1.0

Calcium binding site 6 out of 7 in 6kka

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Calcium binding site 6 out of 7 in the Xylanase J Mutant From Bacillus Sp. 41M-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Xylanase J Mutant From Bacillus Sp. 41M-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:63.5
occ:1.00
 O B:TRP317 2.3 38.3 1.0
OD1 B:ASP313 2.3 43.3 1.0
OD1 B:ASP318 2.4 38.3 1.0
O B:TYR237 2.4 43.3 1.0
O B:HOH541 2.7 40.9 1.0
CG B:ASP313 3.3 44.6 1.0
C B:TRP317 3.3 40.1 1.0
C B:TYR237 3.5 38.8 1.0
CG B:ASP318 3.6 40.7 1.0
CA B:ASP318 3.8 33.0 1.0
N B:ASP318 3.9 32.4 1.0
OD2 B:ASP313 3.9 40.5 1.0
CA B:TYR237 3.9 34.7 1.0
O B:HOH519 4.0 48.8 1.0
O B:HOH551 4.1 39.8 1.0
CB B:ASP318 4.2 37.2 1.0
CB B:ASP313 4.3 38.3 1.0
N B:TRP317 4.5 37.0 1.0
CA B:TRP317 4.5 37.9 1.0
N B:ALA238 4.6 43.4 1.0
OD2 B:ASP318 4.6 47.9 1.0
CB B:TYR237 4.6 35.7 1.0
N B:GLY315 4.7 41.4 1.0
O B:LEU236 4.7 37.7 1.0
CA B:GLY315 4.7 34.1 1.0
O B:HOH596 4.9 52.6 1.0
CE3 B:TRP317 4.9 36.0 1.0
CA B:ALA238 4.9 36.4 1.0

Calcium binding site 7 out of 7 in 6kka

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Calcium binding site 7 out of 7 in the Xylanase J Mutant From Bacillus Sp. 41M-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Xylanase J Mutant From Bacillus Sp. 41M-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:84.2
occ:1.00
 OD1 B:ASN44 2.3 42.4 1.0
O B:HOH565 2.4 54.3 1.0
O B:HOH552 2.5 51.8 1.0
OE1 B:GLU183 3.0 46.8 1.0
CG B:ASN44 3.3 42.7 1.0
O B:HOH562 3.7 48.7 1.0
ND2 B:ASN44 3.7 38.7 1.0
O B:HOH537 3.9 48.8 1.0
CD1 B:LEU46 3.9 37.0 1.0
CD B:GLU183 4.1 44.4 1.0
O3 B:CIT405 4.3 60.9 1.0
OH B:TYR95 4.4 41.0 1.0
OE2 B:GLU183 4.6 45.7 1.0
O4 B:CIT405 4.6 73.3 1.0
CB B:ASN44 4.7 39.9 1.0
OE1 B:GLU93 4.8 48.5 1.0
C5 B:CIT405 4.8 75.7 1.0
NH2 B:ARG128 4.9 55.7 1.0

Reference:

T.Takita, K.Nakatani, Y.Katano, M.Suzuki, K.Kojima, N.Saka, B.Mikami, R.Yatsunami, S.Nakamura, K.Yasukawa. Increase in the Thermostability of GH11 Xylanase Xynj From Bacillus Sp. Strain 41M-1 Using Site Saturation Mutagenesis. Enzyme.Microb.Technol. V. 130 09363 2019.
ISSN: ISSN 0141-0229
PubMed: 31421720
DOI: 10.1016/J.ENZMICTEC.2019.109363
Page generated: Tue Jul 16 10:30:46 2024

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