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Calcium in PDB 4yzq: C. Bescii Family 3 Pectate Lyase Double Mutant K108A/Q111N in Complex with Trigalacturonic Acid

Enzymatic activity of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/Q111N in Complex with Trigalacturonic Acid

All present enzymatic activity of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/Q111N in Complex with Trigalacturonic Acid:
4.2.2.2;

Protein crystallography data

The structure of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/Q111N in Complex with Trigalacturonic Acid, PDB code: 4yzq 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) 49.63 / 1.48
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.730, 36.210, 99.470, 90.00, 132.39, 90.00
R / Rfree (%) 16.2 / 19.9

Calcium Binding Sites:

The binding sites of Calcium atom in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/Q111N in Complex with Trigalacturonic Acid (pdb code 4yzq). 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/Q111N in Complex with Trigalacturonic Acid, PDB code: 4yzq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4yzq

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Calcium binding site 1 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/Q111N 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/Q111N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:15.2
occ:0.76
 OE1 A:GLN37 2.2 15.8 1.0
OE1 A:GLU84 2.4 14.0 1.0
O6A A:ADA209 2.4 15.9 0.6
O6B A:ADA212 2.4 17.7 0.5
O A:HOH402 2.5 25.5 1.0
O A:HOH385 2.5 17.9 1.0
OD2 A:ASP107 2.5 22.0 1.0
O A:HOH378 2.8 14.2 1.0
C6 A:ADA209 2.9 17.9 0.6
O6B A:ADA209 3.0 17.6 0.6
C6 A:ADA212 3.0 19.2 0.5
O6A A:ADA212 3.1 19.2 0.5
CD A:GLN37 3.4 14.8 1.0
CG A:ASP107 3.5 17.1 1.0
CD A:GLU84 3.6 12.9 1.0
CB A:ASP107 3.7 14.4 1.0
CA A:CA202 3.7 14.0 1.0
OE1 A:GLU39 3.9 19.4 1.0
O A:HOH362 4.2 14.8 1.0
NE2 A:GLN37 4.2 14.9 1.0
C5 A:ADA209 4.3 15.9 0.6
C5 A:ADA212 4.3 17.4 0.5
O A:GLU84 4.3 9.8 1.0
CG A:GLN37 4.4 13.4 1.0
CG A:GLU84 4.4 12.6 1.0
CB A:GLN37 4.5 13.2 1.0
OE2 A:GLU84 4.5 13.0 1.0
O A:GLN37 4.7 13.7 1.0
OD1 A:ASP107 4.7 17.9 1.0
O2 A:ADA208 4.7 25.1 0.6
O2 A:GTR211 4.7 21.7 0.5
CD A:GLU39 4.8 19.3 1.0
O A:HOH319 4.8 20.6 0.8
C2 A:ADA208 4.9 23.8 0.6
CA A:GLN37 5.0 13.2 1.0
C2 A:GTR211 5.0 21.5 0.5

Calcium binding site 2 out of 8 in 4yzq

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Calcium binding site 2 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/Q111N 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/Q111N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:14.0
occ:0.96
 O6A A:ADA209 2.2 15.9 0.6
O6B A:ADA212 2.2 17.7 0.5
O6A A:ADA213 2.3 14.3 0.5
O6A A:ADA210 2.3 12.2 0.6
O5 A:ADA213 2.4 15.9 0.5
O5 A:ADA210 2.4 13.8 0.6
OE1 A:GLU84 2.4 14.0 1.0
O A:HOH362 2.4 14.8 1.0
OE2 A:GLU39 2.4 20.1 1.0
OE2 A:GLU84 2.5 13.0 1.0
OE1 A:GLU39 2.5 19.4 1.0
CD A:GLU84 2.7 12.9 1.0
CD A:GLU39 2.8 19.3 1.0
C6 A:ADA213 3.2 15.9 0.5
C6 A:ADA210 3.2 13.8 0.6
C6 A:ADA209 3.3 17.9 0.6
C6 A:ADA212 3.3 19.2 0.5
C5 A:ADA213 3.3 15.9 0.5
C5 A:ADA210 3.3 13.7 0.6
C1 A:ADA213 3.4 16.7 0.5
C1 A:ADA210 3.4 14.6 0.6
CA A:CA201 3.7 15.2 0.8
CA A:CA203 3.9 12.3 1.0
O A:HOH378 4.0 14.2 1.0
OD2 A:ASP85 4.0 13.7 1.0
O6B A:ADA209 4.0 17.6 0.6
O6A A:ADA212 4.0 19.2 0.5
O A:HOH424 4.1 14.7 1.0
C4 A:ADA209 4.1 14.4 0.6
O A:HOH385 4.1 17.9 1.0
C4 A:ADA212 4.1 16.1 0.5
CG A:GLU84 4.1 12.6 1.0
O4 A:ADA209 4.2 14.4 0.6
O4 A:ADA212 4.2 16.3 0.5
C5 A:ADA209 4.2 15.9 0.6
C5 A:ADA212 4.3 17.4 0.5
O6B A:ADA210 4.4 13.6 0.6
O6B A:ADA213 4.4 15.7 0.5
CG A:GLU39 4.4 17.8 1.0
O4 A:ADA213 4.4 20.3 0.5
C2 A:ADA213 4.5 17.6 0.5
C4 A:ADA213 4.5 17.5 0.5
O4 A:ADA210 4.5 18.5 0.6
C2 A:ADA210 4.5 15.5 0.6
C4 A:ADA210 4.5 15.4 0.6
O A:HOH319 4.7 20.6 0.8
CG A:ASP85 4.8 13.6 1.0

Calcium binding site 3 out of 8 in 4yzq

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Calcium binding site 3 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/Q111N 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/Q111N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:12.3
occ:0.98
 O A:HOH424 2.3 14.7 1.0
OE2 A:GLU84 2.3 13.0 1.0
O A:HOH342 2.4 13.2 1.0
OD1 A:ASP64 2.5 15.2 1.0
OD1 A:ASP85 2.5 13.4 1.0
O6A A:ADA210 2.6 12.2 0.6
OD2 A:ASP85 2.6 13.7 1.0
OD2 A:ASP64 2.6 13.8 1.0
O6A A:ADA213 2.6 14.3 0.5
CG A:ASP85 2.9 13.6 1.0
CG A:ASP64 2.9 12.8 1.0
C6 A:ADA210 3.6 13.8 0.6
C6 A:ADA213 3.6 15.9 0.5
CD A:GLU84 3.6 12.9 1.0
CA A:CA202 3.9 14.0 1.0
O6B A:ADA210 3.9 13.6 0.6
O6B A:ADA213 3.9 15.7 0.5
OE2 A:GLU39 4.0 20.1 1.0
OG1 A:THR88 4.2 12.4 1.0
O A:HOH362 4.2 14.8 1.0
O A:HOH475 4.3 24.4 1.0
CB A:ASP85 4.3 11.1 1.0
CB A:ASP64 4.4 12.0 1.0
CG A:GLU84 4.4 12.6 1.0
CB A:GLU84 4.4 11.2 1.0
O A:HOH399 4.5 14.2 1.0
OE1 A:GLU84 4.5 14.0 1.0
O A:HOH390 4.6 11.5 1.0
N A:ASP85 4.6 9.3 1.0
O A:HOH413 4.7 19.9 0.8
O A:HOH330 4.7 41.6 0.9
NE2 A:HIS67 4.9 13.2 1.0
C5 A:ADA210 4.9 13.7 0.6
C5 A:ADA213 5.0 15.9 0.5
C A:GLU84 5.0 10.1 1.0
CA A:ASP64 5.0 11.3 1.0
CA A:ASP85 5.0 10.3 1.0

Calcium binding site 4 out of 8 in 4yzq

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Calcium binding site 4 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/Q111N 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/Q111N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:11.4
occ:0.97
 O A:GLU104 2.3 10.0 1.0
OD1 A:ASP81 2.3 11.7 1.0
O A:HOH476 2.4 15.3 1.0
O A:HOH341 2.4 14.0 1.0
O A:VAL82 2.4 10.3 1.0
O A:HOH357 2.5 17.2 1.0
O A:HOH354 2.6 9.7 1.0
CG A:ASP81 3.4 12.5 1.0
C A:GLU104 3.5 10.3 1.0
C A:VAL82 3.6 9.8 1.0
OD2 A:ASP81 4.0 14.3 1.0
CB A:GLU104 4.0 13.3 1.0
N A:VAL82 4.1 8.9 1.0
O A:HOH403 4.2 11.7 0.9
C A:ASP81 4.3 9.8 1.0
CA A:GLU104 4.4 10.7 1.0
CA A:VAL82 4.4 9.7 1.0
N A:ALA105 4.4 9.4 1.0
N A:ALA106 4.4 10.1 1.0
O A:HOH398 4.4 12.3 1.0
O A:HOH469 4.5 16.9 0.8
CA A:ALA105 4.5 9.1 1.0
O A:GLY35 4.5 13.9 1.0
O A:GLY83 4.6 9.4 1.0
CB A:ASP81 4.6 11.3 1.0
O A:ASP81 4.6 10.2 1.0
N A:GLY83 4.7 9.4 1.0
CA A:ASP81 4.7 10.1 1.0
O A:HOH443 4.7 32.8 0.8
CA A:GLY83 4.8 9.5 1.0
CB A:VAL82 4.8 9.3 1.0
C A:ALA105 4.9 9.8 1.0
O A:HOH533 4.9 42.6 0.8

Calcium binding site 5 out of 8 in 4yzq

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Calcium binding site 5 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/Q111N 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/Q111N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:12.4
occ:0.86
 OE1 B:GLN37 2.3 13.2 1.0
O6A B:ADA208 2.3 11.5 0.6
OD2 B:ASP107 2.4 15.3 1.0
OE1 B:GLU84 2.5 10.4 1.0
O B:HOH389 2.5 10.3 0.9
O6A B:ADA211 2.5 13.6 0.4
O B:HOH382 2.6 16.8 1.0
O6B B:ADA208 2.7 12.9 0.6
O B:HOH404 2.8 13.4 1.0
C6 B:ADA208 2.8 12.4 0.6
O6B B:ADA211 2.8 14.6 0.4
C6 B:ADA211 2.9 14.0 0.4
CG B:ASP107 3.4 14.0 1.0
CD B:GLN37 3.5 13.0 1.0
CB B:ASP107 3.7 12.2 1.0
CD B:GLU84 3.7 10.7 1.0
CA B:CA202 3.7 11.6 1.0
OE2 B:GLU39 4.0 12.9 1.0
O B:HOH330 4.2 12.3 1.0
C5 B:ADA208 4.2 11.7 0.6
C5 B:ADA211 4.3 13.8 0.4
NE2 B:GLN37 4.4 11.8 1.0
NZ A:LYS103 4.4 20.0 1.0
O B:GLU84 4.4 11.0 1.0
CG B:GLN37 4.4 11.6 1.0
CG B:GLU84 4.5 10.5 1.0
OE2 B:GLU84 4.5 12.4 1.0
O2 B:GTR210 4.5 17.6 0.4
CB B:GLN37 4.5 11.6 1.0
OD1 B:ASP107 4.6 14.1 1.0
O A:HOH376 4.6 29.9 0.7
O B:HOH350 4.6 16.0 0.6
O2 B:ADA207 4.6 18.4 0.6
O B:GLN37 4.6 13.3 1.0
C2 B:ADA207 4.7 15.9 0.6
CD B:GLU39 4.7 13.7 1.0
O B:HOH508 4.8 36.8 0.7
C2 B:GTR210 5.0 15.4 0.4

Calcium binding site 6 out of 8 in 4yzq

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Calcium binding site 6 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/Q111N 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/Q111N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:11.6
occ:1.00
 O6A B:ADA211 2.1 13.6 0.4
O5 B:ADA212 2.3 13.9 0.4
OE1 B:GLU84 2.3 10.4 1.0
O6B B:ADA209 2.4 10.0 0.6
O6A B:ADA208 2.4 11.5 0.6
OE1 B:GLU39 2.4 14.5 1.0
O5 B:ADA209 2.4 10.1 0.6
O B:HOH330 2.5 12.3 1.0
OE2 B:GLU84 2.5 12.4 1.0
O6B B:ADA212 2.5 13.9 0.4
OE2 B:GLU39 2.6 12.9 1.0
CD B:GLU84 2.7 10.7 1.0
CD B:GLU39 2.9 13.7 1.0
C5 B:ADA212 3.2 15.0 0.4
C6 B:ADA211 3.2 14.0 0.4
C6 B:ADA212 3.2 14.3 0.4
C6 B:ADA209 3.3 10.6 0.6
C1 B:ADA209 3.3 12.0 0.6
C6 B:ADA208 3.4 12.4 0.6
C5 B:ADA209 3.5 11.2 0.6
C1 B:ADA212 3.6 15.4 0.4
CA B:CA201 3.7 12.4 0.9
CA B:CA203 3.9 12.4 1.0
O6B B:ADA211 3.9 14.6 0.4
O B:HOH404 4.0 13.4 1.0
OD2 B:ASP85 4.0 12.5 1.0
C4 B:ADA208 4.1 11.2 0.6
O B:HOH415 4.1 13.1 1.0
O B:HOH389 4.1 10.3 0.9
CG B:GLU84 4.1 10.5 1.0
O6B B:ADA208 4.2 12.9 0.6
C4 B:ADA211 4.2 13.7 0.4
C5 B:ADA208 4.2 11.7 0.6
O4 B:ADA211 4.2 14.6 0.4
C5 B:ADA211 4.3 13.8 0.4
O4 B:ADA208 4.3 11.7 0.6
C2 B:ADA209 4.4 11.9 0.6
CG B:GLU39 4.4 14.0 1.0
O4 B:ADA209 4.4 13.5 0.6
O6A B:ADA209 4.4 11.3 0.6
O6A B:ADA212 4.4 15.5 0.4
C4 B:ADA212 4.5 15.2 0.4
C4 B:ADA209 4.6 11.6 0.6
O4 B:ADA212 4.6 17.1 0.4
O B:HOH350 4.7 16.0 0.6
CG B:ASP85 4.8 11.9 1.0
C2 B:ADA212 4.9 15.7 0.4
OD1 B:ASN111 4.9 15.7 1.0

Calcium binding site 7 out of 8 in 4yzq

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Calcium binding site 7 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/Q111N 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/Q111N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:12.4
occ:1.00
 O6B B:ADA212 2.3 13.9 0.4
OE2 B:GLU84 2.4 12.4 1.0
O B:HOH307 2.4 11.7 1.0
O B:HOH415 2.4 13.1 1.0
OD2 B:ASP64 2.5 14.7 1.0
OD1 B:ASP64 2.5 12.2 1.0
OD2 B:ASP85 2.5 12.5 1.0
O6B B:ADA209 2.6 10.0 0.6
OD1 B:ASP85 2.6 12.3 1.0
CG B:ASP85 2.9 11.9 1.0
CG B:ASP64 2.9 13.2 1.0
C6 B:ADA212 3.4 14.3 0.4
CD B:GLU84 3.6 10.7 1.0
C6 B:ADA209 3.6 10.6 0.6
O6A B:ADA212 3.8 15.5 0.4
CA B:CA202 3.9 11.6 1.0
O6A B:ADA209 3.9 11.3 0.6
OE1 B:GLU39 4.1 14.5 1.0
O B:HOH330 4.1 12.3 1.0
OG1 B:THR88 4.1 11.7 1.0
CB B:ASP85 4.3 11.6 1.0
O B:HOH384 4.3 21.6 1.0
CG B:GLU84 4.4 10.5 1.0
O B:HOH365 4.4 12.7 1.0
CB B:GLU84 4.4 11.2 1.0
CB B:ASP64 4.4 12.5 1.0
OE1 B:GLU84 4.5 10.4 1.0
O B:HOH340 4.5 13.0 1.0
N B:ASP85 4.7 10.3 1.0
C5 B:ADA212 4.8 15.0 0.4
O B:HOH363 4.9 27.7 1.0
NE2 B:HIS67 4.9 15.1 1.0
C B:GLU84 5.0 11.4 1.0

Calcium binding site 8 out of 8 in 4yzq

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Calcium binding site 8 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/Q111N 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/Q111N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:9.3
occ:0.89
 O B:GLU104 2.3 9.7 1.0
OD1 B:ASP81 2.4 13.0 1.0
O B:VAL82 2.4 10.1 1.0
O B:HOH480 2.4 14.6 1.0
O B:HOH324 2.4 12.6 1.0
O B:HOH362 2.4 15.6 1.0
O B:HOH359 2.5 11.2 1.0
C B:GLU104 3.5 10.2 1.0
CG B:ASP81 3.5 14.8 1.0
C B:VAL82 3.6 9.4 1.0
CB B:GLU104 4.0 11.7 1.0
N B:VAL82 4.0 10.8 1.0
OD2 B:ASP81 4.0 14.3 1.0
O B:HOH412 4.2 12.0 1.0
C B:ASP81 4.3 12.3 1.0
CA B:VAL82 4.3 10.6 1.0
N B:ALA105 4.4 10.1 1.0
CA B:GLU104 4.4 10.6 1.0
O B:HOH397 4.4 12.0 1.0
N B:ALA106 4.5 10.3 1.0
O B:GLY35 4.5 14.0 1.0
O B:HOH546 4.5 33.2 1.0
CA B:ALA105 4.5 10.6 1.0
O B:HOH433 4.5 33.7 0.8
O B:HOH434 4.5 23.3 0.6
O B:GLY83 4.6 10.6 1.0
O B:HOH472 4.6 36.2 0.8
N B:GLY83 4.6 9.5 1.0
O B:ASP81 4.7 11.1 1.0
CB B:ASP81 4.7 12.9 1.0
CB B:VAL82 4.8 9.9 1.0
CA B:ASP81 4.8 12.3 1.0
CA B:GLY83 4.8 10.3 1.0
C B:ALA105 5.0 10.8 1.0

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: Wed Jul 9 03:26:47 2025

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