Atomistry » Calcium » PDB 4ytz-4z6z » 4yzq
Atomistry »
  Calcium »
    PDB 4ytz-4z6z »
      4yzq »

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

Go back to Calcium Binding Sites List in 4yzq
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

Go back to Calcium Binding Sites List in 4yzq
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

Go back to Calcium Binding Sites List in 4yzq
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

Go back to Calcium Binding Sites List in 4yzq
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

Go back to Calcium Binding Sites List in 4yzq
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

Go back to Calcium Binding Sites List in 4yzq
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

Go back to Calcium Binding Sites List in 4yzq
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

Go back to Calcium Binding Sites List in 4yzq
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: Sun Jul 14 15:23:43 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy