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Calcium in PDB 4z03: C. Bescii Family 3 Pectate Lyase Double Mutant K108A in Complex with Trigalacturonic Acid

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

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

Protein crystallography data

The structure of C. Bescii Family 3 Pectate Lyase Double Mutant K108A in Complex with Trigalacturonic Acid, PDB code: 4z03 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 / 1.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.872, 36.361, 99.555, 90.00, 132.44, 90.00
R / Rfree (%) 12.2 / 18.4

Calcium Binding Sites:

The binding sites of Calcium atom in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A in Complex with Trigalacturonic Acid (pdb code 4z03). 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 in Complex with Trigalacturonic Acid, PDB code: 4z03:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4z03

Go back to Calcium Binding Sites List in 4z03
Calcium binding site 1 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A 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 in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:12.6
occ:1.00
 O6A A:ADA210 2.3 21.0 0.3
O6A A:ADA207 2.3 11.9 0.7
O6B A:ADA211 2.3 13.2 0.3
O6B A:ADA208 2.3 9.7 0.7
OE2 A:GLU84 2.4 12.7 1.0
O5 A:ADA211 2.4 13.2 0.3
O5 A:ADA208 2.4 10.1 0.7
O A:HOH364 2.4 13.3 1.0
OE2 A:GLU39 2.5 14.5 1.0
OE1 A:GLU39 2.5 14.8 1.0
OE1 A:GLU84 2.5 11.1 1.0
CD A:GLU84 2.7 12.9 1.0
CD A:GLU39 2.8 14.1 1.0
C6 A:ADA208 3.2 9.9 0.7
C6 A:ADA211 3.2 13.0 0.3
C6 A:ADA207 3.3 11.0 0.7
C6 A:ADA210 3.3 19.6 0.3
C5 A:ADA208 3.3 10.4 0.7
C5 A:ADA211 3.3 13.2 0.3
C1 A:ADA208 3.4 11.2 0.7
C1 A:ADA211 3.4 15.4 0.3
CA A:CA202 3.7 14.6 0.9
CA A:CA203 3.8 11.3 1.0
OD2 A:ASP85 3.9 12.1 1.0
O A:HOH417 4.0 13.2 1.0
O6B A:ADA207 4.0 14.3 0.7
O6B A:ADA210 4.0 22.8 0.3
O A:HOH370 4.1 15.9 1.0
O A:HOH426 4.1 14.1 1.0
CG A:GLU84 4.2 9.9 1.0
C4 A:ADA207 4.2 9.2 0.7
O4 A:ADA207 4.2 11.8 0.7
C4 A:ADA210 4.2 15.6 0.3
O4 A:ADA210 4.3 16.4 0.3
C5 A:ADA207 4.3 12.0 0.7
CG A:GLU39 4.3 14.4 1.0
C5 A:ADA210 4.4 18.6 0.3
O6A A:ADA208 4.4 10.7 0.7
O6A A:ADA211 4.4 13.9 0.3
O4 A:ADA208 4.5 15.4 0.7
O4 A:ADA211 4.5 17.4 0.3
C4 A:ADA208 4.5 11.5 0.7
C4 A:ADA211 4.5 14.9 0.3
C2 A:ADA208 4.5 10.5 0.7
C2 A:ADA211 4.6 16.2 0.3
NH1 A:ARG133 4.6 7.7 0.2
OE1 A:GLN111 4.7 13.2 1.0
CG A:ASP85 4.8 10.7 1.0
O A:HOH301 5.0 21.5 0.8

Calcium binding site 2 out of 8 in 4z03

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Calcium binding site 2 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A 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 in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:14.6
occ:0.87
 OE1 A:GLN37 2.3 15.3 1.0
O A:HOH370 2.4 15.9 1.0
OE2 A:GLU84 2.4 12.7 1.0
OD2 A:ASP107 2.5 19.2 1.0
O6A A:ADA207 2.5 11.9 0.7
O6A A:ADA210 2.5 21.0 0.3
O A:HOH350 2.6 19.8 1.0
O6B A:ADA207 2.8 14.3 0.7
O6B A:ADA210 2.8 22.8 0.3
O A:HOH417 2.8 13.2 1.0
C6 A:ADA207 2.9 11.0 0.7
C6 A:ADA210 2.9 19.6 0.3
CG A:ASP107 3.4 15.7 1.0
CD A:GLN37 3.4 12.0 1.0
CB A:ASP107 3.6 12.2 1.0
CD A:GLU84 3.7 12.9 1.0
CA A:CA201 3.7 12.6 1.0
OE1 A:GLU39 3.9 14.8 1.0
C5 A:ADA207 4.2 12.0 0.7
O A:HOH364 4.2 13.3 1.0
NE2 A:GLN37 4.3 13.6 1.0
C5 A:ADA210 4.3 18.6 0.3
CG A:GLN37 4.4 13.5 1.0
O A:GLU84 4.4 8.9 1.0
CG A:GLU84 4.4 9.9 1.0
CB A:GLN37 4.5 13.0 1.0
O2 A:ADA206 4.5 33.7 0.7
OD1 A:ASP107 4.5 15.8 1.0
OE1 A:GLU84 4.5 11.1 1.0
O A:GLN37 4.6 14.4 1.0
NH1 A:ARG133 4.6 7.7 0.2
O A:HOH301 4.6 21.5 0.8
O2 A:GTR209 4.7 15.6 0.3
CD A:GLU39 4.8 14.1 1.0
C2 A:ADA206 4.9 22.9 0.7
C2 A:GTR209 5.0 13.4 0.3
CA A:GLN37 5.0 11.3 1.0

Calcium binding site 3 out of 8 in 4z03

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Calcium binding site 3 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A 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 in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:11.3
occ:1.00
 O A:HOH426 2.4 14.1 1.0
OE1 A:GLU84 2.4 11.1 1.0
O A:HOH355 2.4 12.6 1.0
OD2 A:ASP85 2.5 12.1 1.0
OD1 A:ASP64 2.5 12.8 1.0
OD1 A:ASP85 2.5 11.9 1.0
OD2 A:ASP64 2.6 13.2 1.0
O6B A:ADA208 2.6 9.7 0.7
O6B A:ADA211 2.6 13.2 0.3
CG A:ASP85 2.9 10.7 1.0
CG A:ASP64 2.9 11.3 1.0
CD A:GLU84 3.6 12.9 1.0
C6 A:ADA208 3.6 9.9 0.7
C6 A:ADA211 3.6 13.0 0.3
CA A:CA201 3.8 12.6 1.0
O6A A:ADA208 3.9 10.7 0.7
OE2 A:GLU39 3.9 14.5 1.0
O6A A:ADA211 4.0 13.9 0.3
OG1 A:THR88 4.1 12.2 1.0
O A:HOH364 4.1 13.3 1.0
CB A:ASP85 4.3 10.4 1.0
O A:HOH354 4.4 29.1 1.0
CB A:GLU84 4.4 9.0 1.0
CG A:GLU84 4.4 9.9 1.0
CB A:ASP64 4.4 12.2 1.0
O A:HOH362 4.5 13.9 1.0
OE2 A:GLU84 4.5 12.7 1.0
O A:HOH387 4.6 10.7 1.0
N A:ASP85 4.6 10.4 1.0
O A:HOH409 4.7 21.2 1.0
NE2 A:HIS67 4.9 12.2 1.0
C A:GLU84 5.0 8.9 1.0

Calcium binding site 4 out of 8 in 4z03

Go back to Calcium Binding Sites List in 4z03
Calcium binding site 4 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A 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 in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:10.8
occ:1.00
 O A:GLU104 2.3 8.6 1.0
OD1 A:ASP81 2.3 11.7 1.0
O A:HOH379 2.4 13.8 1.0
O A:VAL82 2.4 8.8 1.0
O A:HOH486 2.4 16.7 1.0
O A:HOH382 2.5 16.4 1.0
O A:HOH372 2.5 8.9 1.0
C A:GLU104 3.5 8.3 1.0
CG A:ASP81 3.5 10.6 1.0
C A:VAL82 3.6 9.6 1.0
CB A:GLU104 4.0 12.4 1.0
OD2 A:ASP81 4.0 15.5 1.0
N A:VAL82 4.0 8.8 1.0
O A:HOH419 4.2 12.7 1.0
C A:ASP81 4.2 8.7 1.0
CA A:VAL82 4.4 8.7 1.0
CA A:GLU104 4.4 9.2 1.0
N A:ALA105 4.4 7.8 1.0
O A:HOH398 4.4 10.8 1.0
O A:HOH584 4.5 35.9 1.0
N A:ALA106 4.5 8.9 1.0
CA A:ALA105 4.5 8.9 1.0
O A:GLY35 4.5 13.3 1.0
O A:HOH456 4.5 25.9 1.0
O A:GLY83 4.6 10.0 1.0
O A:HOH563 4.6 43.5 1.0
N A:GLY83 4.6 8.9 1.0
O A:ASP81 4.6 10.1 1.0
CA A:ASP81 4.7 8.9 1.0
CB A:ASP81 4.7 11.5 1.0
CA A:GLY83 4.8 8.6 1.0
CB A:VAL82 4.8 8.5 1.0
O A:HOH345 4.8 25.5 0.6
C A:ALA105 5.0 9.4 1.0

Calcium binding site 5 out of 8 in 4z03

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Calcium binding site 5 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A 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 in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:11.0
occ:1.00
 O6B B:ADA209 2.3 11.2 1.0
OE2 B:GLU84 2.4 11.4 1.0
O6A B:ADA210 2.4 9.8 1.0
O5 B:ADA210 2.4 10.5 1.0
OE2 B:GLU39 2.5 13.6 1.0
OE1 B:GLU84 2.5 10.1 1.0
O B:HOH334 2.5 10.7 1.0
OE1 B:GLU39 2.5 11.4 1.0
CD B:GLU84 2.7 8.9 1.0
CD B:GLU39 2.8 13.5 1.0
C6 B:ADA210 3.2 9.5 1.0
C6 B:ADA209 3.3 10.8 1.0
C1 B:ADA210 3.4 12.9 1.0
C5 B:ADA210 3.4 10.9 1.0
CA B:CA202 3.7 12.5 1.0
CA B:CA203 3.9 11.2 1.0
O B:HOH416 3.9 11.1 1.0
OD2 B:ASP85 3.9 11.2 1.0
O B:HOH406 4.1 13.5 1.0
O6A B:ADA209 4.1 14.0 1.0
O B:HOH379 4.1 13.2 1.0
CG B:GLU84 4.1 10.1 1.0
C4 B:ADA209 4.2 9.8 1.0
O4 B:ADA209 4.3 10.4 1.0
C5 B:ADA209 4.3 10.4 1.0
CG B:GLU39 4.3 13.2 1.0
O6B B:ADA210 4.4 11.1 1.0
C4 B:ADA210 4.5 13.4 1.0
O4 B:ADA210 4.5 14.8 1.0
C2 B:ADA210 4.5 11.9 1.0
OE1 B:GLN111 4.7 10.9 1.0
CG B:ASP85 4.8 11.4 1.0

Calcium binding site 6 out of 8 in 4z03

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Calcium binding site 6 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A 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 in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:12.5
occ:1.00
 OE1 B:GLN37 2.2 10.8 1.0
OD2 B:ASP107 2.4 17.9 1.0
O6B B:ADA209 2.4 11.2 1.0
OE2 B:GLU84 2.4 11.4 1.0
O B:HOH379 2.5 13.2 1.0
O B:HOH400 2.5 16.5 1.0
O B:HOH416 2.7 11.1 1.0
O6A B:ADA209 2.7 14.0 1.0
C6 B:ADA209 2.9 10.8 1.0
CG B:ASP107 3.3 12.2 1.0
CD B:GLN37 3.5 9.7 1.0
CB B:ASP107 3.6 10.1 1.0
CD B:GLU84 3.7 8.9 1.0
CA B:CA201 3.7 11.0 1.0
OE1 B:GLU39 3.9 11.4 1.0
O B:HOH334 4.2 10.7 1.0
C5 B:ADA209 4.3 10.4 1.0
NE2 B:GLN37 4.3 12.4 1.0
O B:GLU84 4.4 9.8 1.0
CG B:GLN37 4.4 11.1 1.0
NZ A:LYS103 4.4 16.8 1.0
CG B:GLU84 4.5 10.1 1.0
O2 B:GTR208 4.5 20.4 1.0
OD1 B:ASP107 4.5 13.6 1.0
OE1 B:GLU84 4.5 10.1 1.0
O A:HOH357 4.6 22.5 0.6
CB B:GLN37 4.6 10.5 1.0
O B:HOH395 4.6 9.8 0.5
O B:GLN37 4.6 13.7 1.0
CD B:GLU39 4.8 13.5 1.0
O B:HOH549 4.8 22.8 0.6
C2 B:GTR208 4.8 15.4 1.0

Calcium binding site 7 out of 8 in 4z03

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Calcium binding site 7 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A 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 in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:11.2
occ:1.00
 OE1 B:GLU84 2.4 10.1 1.0
O B:HOH406 2.4 13.5 1.0
O B:HOH336 2.4 11.7 1.0
OD2 B:ASP64 2.5 12.2 1.0
OD1 B:ASP64 2.5 11.7 1.0
OD2 B:ASP85 2.5 11.2 1.0
OD1 B:ASP85 2.6 12.7 1.0
O6A B:ADA210 2.6 9.8 1.0
CG B:ASP64 2.9 9.8 1.0
CG B:ASP85 2.9 11.4 1.0
CD B:GLU84 3.6 8.9 1.0
C6 B:ADA210 3.6 9.5 1.0
CA B:CA201 3.9 11.0 1.0
O6B B:ADA210 3.9 11.1 1.0
OE2 B:GLU39 4.0 13.6 1.0
OG1 B:THR88 4.1 10.8 1.0
O B:HOH334 4.1 10.7 1.0
O B:HOH362 4.3 23.0 1.0
CB B:ASP85 4.3 10.3 1.0
CB B:GLU84 4.4 9.2 1.0
CG B:GLU84 4.4 10.1 1.0
CB B:ASP64 4.4 10.5 1.0
O B:HOH352 4.4 12.9 1.0
OE2 B:GLU84 4.5 11.4 1.0
O B:HOH363 4.5 12.2 1.0
N B:ASP85 4.6 9.4 1.0
O B:HOH347 4.7 30.2 1.0
NE2 B:HIS67 4.9 14.7 1.0
O B:HOH376 4.9 23.6 1.0
CA B:ASP64 5.0 10.9 1.0
C B:GLU84 5.0 8.0 1.0

Calcium binding site 8 out of 8 in 4z03

Go back to Calcium Binding Sites List in 4z03
Calcium binding site 8 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A 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 in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:10.8
occ:1.00
 O B:GLU104 2.3 9.6 1.0
OD1 B:ASP81 2.3 13.5 1.0
O B:HOH378 2.4 14.9 1.0
O B:VAL82 2.4 11.3 1.0
O B:HOH357 2.4 16.3 1.0
O B:HOH493 2.4 16.9 1.0
O B:HOH384 2.5 11.2 1.0
C B:GLU104 3.5 8.6 1.0
CG B:ASP81 3.5 13.3 1.0
C B:VAL82 3.6 10.5 1.0
CB B:GLU104 4.0 10.8 1.0
N B:VAL82 4.1 9.3 1.0
OD2 B:ASP81 4.1 18.0 1.0
O B:HOH423 4.2 13.4 1.0
C B:ASP81 4.2 10.3 1.0
O B:HOH570 4.3 40.1 0.7
CA B:VAL82 4.3 9.4 1.0
CA B:GLU104 4.4 8.8 1.0
O B:HOH588 4.4 35.7 1.0
O B:HOH391 4.4 13.1 1.0
N B:ALA105 4.4 9.3 1.0
CA B:ALA105 4.5 10.5 1.0
N B:ALA106 4.5 9.5 1.0
O B:HOH496 4.5 22.0 0.6
O B:HOH413 4.5 27.6 1.0
O B:GLY35 4.5 13.7 1.0
O B:GLY83 4.6 9.6 1.0
O B:HOH498 4.6 32.8 1.0
N B:GLY83 4.6 9.1 1.0
O B:ASP81 4.7 12.0 1.0
CB B:ASP81 4.7 11.7 1.0
CA B:ASP81 4.7 10.4 1.0
CB B:VAL82 4.8 9.5 1.0
CA B:GLY83 4.8 10.0 1.0
C B:ALA105 4.9 9.3 1.0
O B:LYS103 5.0 8.6 0.5

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 15:26:11 2024

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