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Calcium in PDB 4yz0: C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid

Enzymatic activity of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid

All present enzymatic activity of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid:
4.2.2.2;

Protein crystallography data

The structure of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid, PDB code: 4yz0 was solved by P.M.Alahuhta, V.V.Lunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 138.290, 36.470, 100.070, 90.00, 132.63, 90.00
R / Rfree (%) 11.6 / 14.8

Calcium Binding Sites:

The binding sites of Calcium atom in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid (pdb code 4yz0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid, PDB code: 4yz0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4yz0

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Calcium binding site 1 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:16.8
occ:0.75
 OE1 A:GLN37 2.2 10.7 1.0
OE1 A:GLU84 2.3 9.8 1.0
O6A A:ADA216 2.3 14.0 0.6
O6A A:ADA213 2.3 12.6 0.4
OD2 A:ASP107 2.4 11.2 1.0
O A:HOH399 2.8 9.9 1.0
O A:HOH428 2.8 24.4 1.0
C6 A:ADA216 3.0 14.3 0.6
C6 A:ADA213 3.1 13.8 0.4
O6B A:ADA216 3.3 25.9 0.6
NE2 A:GLN39 3.4 27.6 1.0
CG A:ASP107 3.4 9.3 1.0
CD A:GLN37 3.4 9.5 1.0
O6B A:ADA213 3.5 18.7 0.4
CD A:GLU84 3.5 8.7 1.0
CA A:CA202 3.5 11.1 0.6
CB A:ASP107 3.5 7.8 1.0
NH2 A:ARG133 3.9 9.3 0.5
O2 A:X1X212 4.0 28.7 0.4
NE2 A:GLN37 4.0 9.0 1.0
O A:HOH349 4.0 9.0 1.0
O A:GLU84 4.1 6.4 1.0
CG A:GLU84 4.2 8.1 1.0
C5 A:ADA216 4.3 15.0 0.6
C5 A:ADA213 4.3 9.7 0.4
OE2 A:GLU84 4.4 9.7 1.0
O A:HOH328 4.4 35.6 1.0
CD A:GLN39 4.4 19.6 1.0
O A:HOH437 4.5 13.6 0.5
OE1 A:GLN39 4.5 15.9 1.0
OD1 A:ASP107 4.5 11.8 1.0
CG A:GLN37 4.5 9.9 1.0
C2 A:X1X212 4.8 45.0 0.4
CB A:GLN37 4.8 9.1 1.0
O2 A:GTR215 4.9 21.6 0.6
C A:GLU84 5.0 5.3 1.0
CZ A:ARG133 5.0 7.3 0.5

Calcium binding site 2 out of 8 in 4yz0

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Calcium binding site 2 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:11.1
occ:0.63
 OE1 A:GLU84 2.3 9.8 1.0
O6B A:ADA214 2.4 11.0 0.4
O6A A:ADA216 2.4 14.0 0.6
O6A A:ADA213 2.4 12.6 0.4
O6B A:ADA217 2.4 8.1 0.6
O5 A:ADA217 2.4 9.4 0.6
O5 A:ADA214 2.4 10.1 0.4
O A:HOH349 2.6 9.0 1.0
OE1 A:GLN39 2.6 15.9 1.0
OE2 A:GLU84 2.7 9.7 1.0
CD A:GLU84 2.8 8.7 1.0
C6 A:ADA214 3.1 8.5 0.4
C6 A:ADA217 3.1 8.7 0.6
C5 A:ADA217 3.3 9.1 0.6
C5 A:ADA214 3.3 9.1 0.4
C6 A:ADA213 3.3 13.8 0.4
C6 A:ADA216 3.4 14.3 0.6
C1 A:ADA217 3.4 11.0 0.6
C1 A:ADA214 3.4 10.4 0.4
CD A:GLN39 3.5 19.6 1.0
CA A:CA201 3.5 16.8 0.8
NE2 A:GLN39 3.7 27.6 1.0
O A:HOH317 3.8 22.9 1.0
OD2 A:ASP85 3.8 8.0 1.0
CA A:CA203 3.8 8.2 1.0
C4 A:ADA213 4.0 10.6 0.4
C4 A:ADA216 4.0 12.5 0.6
O A:HOH399 4.0 9.9 1.0
O6B A:ADA213 4.1 18.7 0.4
O4 A:ADA216 4.2 12.3 0.6
O6B A:ADA216 4.2 25.9 0.6
O4 A:ADA213 4.2 10.1 0.4
CG A:GLU84 4.2 8.1 1.0
C5 A:ADA216 4.2 15.0 0.6
C5 A:ADA213 4.2 9.7 0.4
O6A A:ADA214 4.3 8.3 0.4
O6A A:ADA217 4.3 10.3 0.6
O A:HOH483 4.3 12.9 1.0
C4 A:ADA217 4.5 12.7 0.6
C4 A:ADA214 4.6 10.4 0.4
NH2 A:ARG133 4.6 9.3 0.5
C2 A:ADA214 4.6 11.1 0.4
C2 A:ADA217 4.6 13.5 0.6
CG A:ASP85 4.7 7.5 1.0
OE1 A:GLN111 4.7 7.2 1.0
O4 A:ADA214 4.8 12.3 0.4
O4 A:ADA217 4.8 22.3 0.6
O A:HOH437 4.8 13.6 0.5
CG A:GLN39 5.0 20.4 1.0

Calcium binding site 3 out of 8 in 4yz0

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Calcium binding site 3 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:8.2
occ:1.00
 OE2 A:GLU84 2.3 9.7 1.0
O A:HOH483 2.4 12.9 1.0
O A:HOH346 2.4 8.8 1.0
OD1 A:ASP64 2.5 8.8 1.0
O6B A:ADA217 2.5 8.1 0.6
OD2 A:ASP85 2.5 8.0 1.0
O6B A:ADA214 2.5 11.0 0.4
OD2 A:ASP64 2.6 9.3 1.0
OD1 A:ASP85 2.6 8.1 1.0
CG A:ASP85 2.9 7.5 1.0
CG A:ASP64 2.9 8.1 1.0
C6 A:ADA217 3.5 8.7 0.6
C6 A:ADA214 3.5 8.5 0.4
CD A:GLU84 3.6 8.7 1.0
CA A:CA202 3.8 11.1 0.6
O6A A:ADA214 3.8 8.3 0.4
O6A A:ADA217 3.8 10.3 0.6
OG1 A:THR88 4.2 7.4 1.0
O A:HOH349 4.3 9.0 1.0
CB A:ASP85 4.3 6.5 1.0
O A:HOH448 4.4 16.1 1.0
O A:HOH417 4.4 10.4 1.0
CB A:ASP64 4.4 7.4 1.0
CG A:GLU84 4.4 8.1 1.0
OE1 A:GLU84 4.4 9.8 1.0
CB A:GLU84 4.5 7.0 1.0
O A:HOH317 4.6 22.9 1.0
N A:ASP85 4.6 5.8 1.0
O A:HOH389 4.7 7.8 1.0
OE1 A:GLN39 4.9 15.9 1.0
C5 A:ADA217 4.9 9.1 0.6
C5 A:ADA214 4.9 9.1 0.4
O A:HOH400 4.9 25.8 1.0
O A:HOH531 4.9 36.3 1.0
NE2 A:HIS67 5.0 8.8 1.0
C A:GLU84 5.0 5.3 1.0

Calcium binding site 4 out of 8 in 4yz0

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Calcium binding site 4 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:8.1
occ:1.00
 O A:GLU104 2.3 6.7 1.0
OD1 A:ASP81 2.3 9.6 1.0
O A:HOH392 2.4 11.8 1.0
O A:HOH497 2.4 16.8 1.0
O A:VAL82 2.4 5.9 1.0
O A:HOH423 2.5 6.4 1.0
O A:HOH372 2.5 15.6 1.0
C A:GLU104 3.5 5.6 1.0
CG A:ASP81 3.5 7.6 1.0
C A:VAL82 3.6 5.0 1.0
N A:VAL82 4.0 5.3 1.0
CB A:GLU104 4.0 8.4 1.0
OD2 A:ASP81 4.1 11.4 1.0
O A:HOH422 4.2 8.8 1.0
C A:ASP81 4.2 5.7 1.0
CA A:VAL82 4.3 5.8 1.0
CA A:GLU104 4.4 6.5 1.0
N A:ALA105 4.4 5.2 1.0
O A:HOH403 4.4 23.5 0.6
N A:ALA106 4.5 6.1 1.0
O A:HOH447 4.5 18.9 1.0
O A:GLY35 4.5 9.3 1.0
O A:HOH414 4.5 9.3 1.0
CA A:ALA105 4.5 6.0 1.0
O A:ASP81 4.6 6.3 1.0
O A:HOH567 4.6 24.6 0.5
O A:GLY83 4.6 6.6 1.0
N A:GLY83 4.6 5.2 1.0
CB A:ASP81 4.7 7.8 1.0
CA A:ASP81 4.7 5.7 1.0
CB A:VAL82 4.8 5.6 1.0
CA A:GLY83 4.8 5.9 1.0
C A:ALA105 4.9 5.8 1.0

Calcium binding site 5 out of 8 in 4yz0

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Calcium binding site 5 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:13.8
occ:0.83
 OE1 B:GLN37 2.2 10.0 1.0
OE1 B:GLU84 2.3 9.3 1.0
O6B B:ADA211 2.3 12.2 0.4
O6B B:ADA208 2.3 14.5 0.2
OD2 B:ASP107 2.3 11.7 1.0
O6B B:ADA214 2.4 11.8 0.3
O B:HOH352 2.5 19.3 0.7
O B:HOH352 2.6 14.6 0.3
O B:HOH385 2.6 10.2 0.4
O B:HOH379 2.9 9.6 1.0
C6 B:ADA208 3.1 15.0 0.2
C6 B:ADA211 3.2 13.4 0.4
C6 B:ADA214 3.2 10.8 0.3
CG B:ASP107 3.4 9.3 1.0
CD B:GLN37 3.4 8.5 1.0
CD B:GLU84 3.5 6.8 1.0
O6A B:ADA208 3.5 20.3 0.2
CA B:CA202 3.5 10.5 0.7
O6A B:ADA211 3.6 18.8 0.4
CB B:ASP107 3.6 7.4 1.0
O B:HOH391 3.7 24.1 0.6
NE2 B:GLN39 3.7 10.6 0.6
O6A B:ADA214 3.7 15.3 0.3
NH2 B:ARG133 4.0 7.8 0.5
NE2 B:GLN37 4.1 7.5 1.0
O B:HOH335 4.1 9.0 1.0
OE1 B:GLN39 4.2 6.9 0.4
O2 B:X0X207 4.2 13.8 0.2
O B:GLU84 4.2 6.2 1.0
CG B:GLU84 4.2 8.2 1.0
C5 B:ADA208 4.3 11.6 0.2
C5 B:ADA211 4.3 11.1 0.4
C5 B:ADA214 4.3 7.8 0.3
OE2 B:GLU84 4.4 8.9 1.0
OD1 B:ASP107 4.5 10.3 1.0
CG B:GLN37 4.5 7.0 1.0
O B:HOH462 4.5 13.4 0.5
CD B:GLN39 4.6 10.3 0.6
OE1 B:GLN39 4.7 11.1 0.6
O2 B:ADA210 4.7 24.8 0.4
CB B:GLN37 4.7 7.9 1.0
C2 B:ADA210 5.0 20.4 0.4
O B:GLN37 5.0 11.0 1.0

Calcium binding site 6 out of 8 in 4yz0

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Calcium binding site 6 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:10.5
occ:0.69
 O6B B:ADA208 2.4 14.5 0.2
O6A B:ADA215 2.4 7.6 0.3
O6A B:ADA212 2.4 8.2 0.4
O6A B:ADA209 2.4 7.7 0.2
O6B B:ADA211 2.4 12.2 0.4
OE1 B:GLU84 2.4 9.3 1.0
OE1 B:GLN39 2.4 6.9 0.4
O5 B:ADA209 2.4 8.4 0.2
O6B B:ADA214 2.4 11.8 0.3
O5 B:ADA212 2.4 8.9 0.4
O5 B:ADA215 2.4 7.9 0.3
O B:HOH335 2.5 9.0 1.0
OE1 B:GLN39 2.6 11.1 0.6
OE2 B:GLU84 2.7 8.9 1.0
CD B:GLU84 2.8 6.8 1.0
C6 B:ADA212 3.1 8.2 0.4
C6 B:ADA215 3.1 7.4 0.3
C6 B:ADA209 3.1 7.2 0.2
C5 B:ADA215 3.3 8.2 0.3
C5 B:ADA212 3.3 9.1 0.4
C5 B:ADA209 3.3 8.3 0.2
CD B:GLN39 3.3 10.6 0.4
C6 B:ADA208 3.3 15.0 0.2
C6 B:ADA211 3.4 13.4 0.4
C6 B:ADA214 3.4 10.8 0.3
C1 B:ADA209 3.4 10.1 0.2
C1 B:ADA215 3.5 6.8 0.3
C1 B:ADA212 3.5 11.3 0.4
CD B:GLN39 3.5 10.3 0.6
NE2 B:GLN39 3.5 8.8 0.4
CA B:CA201 3.5 13.8 0.8
NE2 B:GLN39 3.6 10.6 0.6
O B:HOH385 3.8 10.2 0.4
OD2 B:ASP85 3.8 8.8 1.0
CA B:CA203 3.8 8.0 1.0
C4 B:ADA208 4.0 10.4 0.2
C4 B:ADA211 4.0 11.4 0.4
C4 B:ADA214 4.0 6.3 0.3
O B:HOH319 4.1 10.5 0.6
O B:HOH379 4.1 9.6 1.0
O6A B:ADA208 4.1 20.3 0.2
O6A B:ADA211 4.2 18.8 0.4
O4 B:ADA214 4.2 6.0 0.3
C5 B:ADA211 4.2 11.1 0.4
O4 B:ADA211 4.2 12.7 0.4
O6A B:ADA214 4.2 15.3 0.3
O4 B:ADA208 4.2 9.9 0.2
C5 B:ADA214 4.2 7.8 0.3
C5 B:ADA208 4.2 11.6 0.2
O6B B:ADA215 4.3 7.9 0.3
CG B:GLU84 4.3 8.2 1.0
O6B B:ADA212 4.3 9.7 0.4
O6B B:ADA209 4.3 8.8 0.2
O B:HOH484 4.3 12.0 1.0
C4 B:ADA215 4.6 10.0 0.3
C4 B:ADA212 4.6 9.4 0.4
C4 B:ADA209 4.6 9.2 0.2
NH2 B:ARG133 4.6 7.8 0.5
C2 B:ADA209 4.7 10.4 0.2
C2 B:ADA212 4.7 13.5 0.4
C2 B:ADA215 4.7 8.3 0.3
CG B:GLN39 4.7 9.1 0.4
CG B:ASP85 4.7 7.6 1.0
O4 B:ADA215 4.7 14.1 0.3
O4 B:ADA212 4.8 10.4 0.4
O4 B:ADA209 4.8 8.7 0.2
OE1 B:GLN111 4.8 7.6 1.0
O B:HOH462 4.8 13.4 0.5
CG B:GLN39 4.9 9.5 0.6
O B:HOH352 5.0 19.3 0.7

Calcium binding site 7 out of 8 in 4yz0

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Calcium binding site 7 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:8.0
occ:1.00
 OE2 B:GLU84 2.3 8.9 1.0
O B:HOH354 2.4 9.1 1.0
O B:HOH484 2.4 12.0 1.0
OD2 B:ASP85 2.5 8.8 1.0
OD1 B:ASP64 2.5 9.0 1.0
OD2 B:ASP64 2.5 9.0 1.0
O6A B:ADA212 2.6 8.2 0.4
O6A B:ADA215 2.6 7.6 0.3
O6A B:ADA209 2.6 7.7 0.2
OD1 B:ASP85 2.6 8.4 1.0
CG B:ASP85 2.9 7.6 1.0
CG B:ASP64 2.9 7.1 1.0
C6 B:ADA212 3.5 8.2 0.4
C6 B:ADA215 3.5 7.4 0.3
C6 B:ADA209 3.5 7.2 0.2
CD B:GLU84 3.6 6.8 1.0
CA B:CA202 3.8 10.5 0.7
O6B B:ADA215 3.8 7.9 0.3
O6B B:ADA212 3.9 9.7 0.4
O6B B:ADA209 3.9 8.8 0.2
O B:HOH335 4.2 9.0 1.0
OG1 B:THR88 4.3 7.7 1.0
CB B:ASP85 4.3 6.7 1.0
O B:HOH440 4.3 13.6 1.0
CB B:ASP64 4.4 7.8 1.0
CG B:GLU84 4.4 8.2 1.0
CB B:GLU84 4.4 7.1 1.0
O B:HOH383 4.4 10.9 1.0
OE1 B:GLU84 4.4 9.3 1.0
O B:HOH319 4.6 10.5 0.6
N B:ASP85 4.6 6.0 1.0
O B:HOH384 4.7 8.3 1.0
NE2 B:GLN39 4.8 8.8 0.4
OE1 B:GLN39 4.8 11.1 0.6
NE2 B:HIS67 4.9 10.0 0.4
OE1 B:GLN39 4.9 6.9 0.4
C5 B:ADA215 4.9 8.2 0.3
C5 B:ADA212 4.9 9.1 0.4
C5 B:ADA209 4.9 8.3 0.2
NE2 B:HIS67 4.9 8.0 0.6
CA B:ASP64 5.0 8.0 1.0

Calcium binding site 8 out of 8 in 4yz0

Go back to Calcium Binding Sites List in 4yz0
Calcium binding site 8 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/E39Q in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:7.6
occ:1.00
 O B:GLU104 2.3 6.5 1.0
O B:HOH393 2.4 11.2 1.0
OD1 B:ASP81 2.4 8.8 1.0
O B:VAL82 2.4 6.3 1.0
O B:HOH495 2.4 13.8 1.0
O B:HOH408 2.5 6.7 1.0
O B:HOH406 2.5 13.8 1.0
C B:GLU104 3.5 5.7 1.0
CG B:ASP81 3.5 7.8 1.0
C B:VAL82 3.5 5.9 1.0
CB B:GLU104 4.0 7.4 1.0
N B:VAL82 4.0 6.0 1.0
OD2 B:ASP81 4.1 12.7 1.0
O B:HOH404 4.2 10.0 1.0
C B:ASP81 4.2 5.8 1.0
O B:HOH409 4.3 11.2 0.3
CA B:VAL82 4.3 5.5 1.0
CA B:GLU104 4.4 5.5 1.0
O B:HOH543 4.4 33.6 0.9
N B:ALA105 4.4 5.6 1.0
O B:HOH564 4.4 25.8 1.0
N B:ALA106 4.5 5.7 1.0
O B:HOH400 4.5 8.8 1.0
CA B:ALA105 4.5 5.5 1.0
O B:GLY35 4.5 8.8 1.0
O B:HOH499 4.6 22.6 1.0
N B:GLY83 4.6 6.1 1.0
O B:ASP81 4.6 6.7 1.0
O B:GLY83 4.6 6.3 1.0
O B:HOH478 4.7 26.5 1.0
CB B:ASP81 4.7 8.3 1.0
CA B:ASP81 4.7 6.1 1.0
CB B:VAL82 4.8 5.3 1.0
CA B:GLY83 4.8 6.9 1.0
C B:ALA105 5.0 5.5 1.0
O B:LYS103 5.0 6.6 0.3

Reference:

M.Alahuhta, L.E.Taylor, R.Brunecky, D.W.Sammond, W.Michener, M.W.Adams, M.E.Himmel, Y.J.Bomble, V.Lunin. The Catalytic Mechanism and Unique Low pH Optimum of Caldicellulosiruptor Bescii Family 3 Pectate Lyase. Acta Crystallogr.,Sect.D V. 71 1946 2015.
ISSN: ESSN 1399-0047
PubMed: 26327384
DOI: 10.1107/S1399004715013760
Page generated: Sun Jul 14 15:20:20 2024

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