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Calcium in PDB 4yzx: C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid

Enzymatic activity of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid

All present enzymatic activity of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid:
4.2.2.2;

Protein crystallography data

The structure of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid, PDB code: 4yzx 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) 34.58 / 1.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 138.334, 36.352, 100.106, 90.00, 132.67, 90.00
R / Rfree (%) 11 / 15.6

Other elements in 4yzx:

The structure of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid (pdb code 4yzx). 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/D107N in Complex with Trigalacturonic Acid, PDB code: 4yzx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4yzx

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Calcium binding site 1 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N 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/D107N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:16.8
occ:0.50
 OE1 A:GLN37 2.1 17.5 1.0
OE1 A:GLU84 2.3 12.8 1.0
O A:HOH424 2.4 18.6 1.0
O6B A:ADA212 2.4 14.6 1.0
OD1 A:ASN107 2.5 19.6 1.0
O A:HOH401 2.9 13.0 1.0
C6 A:ADA212 3.0 14.8 1.0
O6A A:ADA212 3.1 16.9 1.0
O A:HOH361 3.2 33.9 1.0
CD A:GLN37 3.3 15.8 1.0
CG A:ASN107 3.4 14.6 1.0
CA A:CA202 3.5 12.8 1.0
CB A:ASN107 3.5 13.2 1.0
CD A:GLU84 3.6 12.5 1.0
NE2 A:GLN37 3.9 15.1 1.0
OE2 A:GLU39 4.0 15.5 1.0
O A:HOH338 4.0 12.6 1.0
O A:GLU84 4.1 10.6 1.0
C5 A:ADA212 4.3 13.8 1.0
OE2 A:GLU84 4.4 12.3 1.0
CG A:GLN37 4.4 15.3 1.0
CG A:GLU84 4.5 11.9 1.0
O A:HOH402 4.5 15.2 1.0
CB A:GLN37 4.6 13.1 1.0
ND2 A:ASN107 4.6 15.3 1.0
O A:GLN37 4.7 15.0 1.0
CD A:GLU39 4.8 15.5 1.0
CA A:GLN37 5.0 11.3 1.0
O2 A:ADA211 5.0 24.5 1.0

Calcium binding site 2 out of 8 in 4yzx

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Calcium binding site 2 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N 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/D107N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:12.8
occ:1.00
 O6B A:ADA212 2.3 14.6 1.0
O6A A:ADA213 2.3 12.6 1.0
OE1 A:GLU84 2.4 12.8 1.0
O5 A:ADA213 2.4 12.4 1.0
OE1 A:GLU39 2.4 16.3 1.0
O A:HOH338 2.5 12.6 1.0
OE2 A:GLU39 2.5 15.5 1.0
OE2 A:GLU84 2.6 12.3 1.0
CD A:GLU84 2.8 12.5 1.0
CD A:GLU39 2.8 15.5 1.0
C6 A:ADA213 3.2 11.3 1.0
C6 A:ADA212 3.3 14.8 1.0
C5 A:ADA213 3.3 12.3 1.0
C1 A:ADA213 3.4 12.6 1.0
CA A:CA201 3.5 16.8 0.5
CA A:CA203 3.9 11.6 1.0
OD2 A:ASP85 3.9 12.1 1.0
O A:HOH424 4.0 18.6 1.0
O6A A:ADA212 4.0 16.9 1.0
O A:HOH388 4.1 14.2 1.0
O A:HOH401 4.1 13.0 1.0
CG A:GLU84 4.2 11.9 1.0
C4 A:ADA212 4.2 11.7 1.0
O4 A:ADA212 4.3 12.7 1.0
C5 A:ADA212 4.3 13.8 1.0
CG A:GLU39 4.3 16.7 1.0
O6B A:ADA213 4.4 11.9 1.0
O4 A:ADA213 4.4 18.5 1.0
C4 A:ADA213 4.5 14.2 1.0
C2 A:ADA213 4.6 14.5 1.0
OE1 A:GLN111 4.7 12.3 1.0
CG A:ASP85 4.8 10.8 1.0
O A:HOH402 4.8 15.2 1.0

Calcium binding site 3 out of 8 in 4yzx

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Calcium binding site 3 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N 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/D107N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:11.6
occ:1.00
 OE2 A:GLU84 2.4 12.3 1.0
O A:HOH375 2.4 12.8 1.0
O A:HOH388 2.4 14.2 1.0
OD2 A:ASP85 2.5 12.1 1.0
OD1 A:ASP64 2.5 12.5 1.0
OD1 A:ASP85 2.6 12.4 1.0
OD2 A:ASP64 2.6 12.5 1.0
O6A A:ADA213 2.6 12.6 1.0
CG A:ASP85 2.9 10.8 1.0
CG A:ASP64 2.9 10.6 1.0
CD A:GLU84 3.6 12.5 1.0
C6 A:ADA213 3.6 11.3 1.0
CA A:CA202 3.9 12.8 1.0
O6B A:ADA213 3.9 11.9 1.0
OE1 A:GLU39 3.9 16.3 1.0
O A:HOH338 4.1 12.6 1.0
OG1 A:THR88 4.2 11.9 1.0
C1 A:MRD209 4.2 17.9 0.3
CB A:ASP85 4.3 10.0 1.0
CG A:GLU84 4.3 11.9 1.0
CB A:GLU84 4.4 10.2 1.0
CB A:ASP64 4.4 11.1 1.0
O A:HOH354 4.4 14.5 1.0
OE1 A:GLU84 4.5 12.8 1.0
O A:HOH331 4.6 23.2 0.7
O A:HOH384 4.6 11.8 1.0
N A:ASP85 4.6 9.5 1.0
O2 A:MRD209 4.7 25.3 0.3
O A:HOH412 4.8 24.0 0.9
NE2 A:HIS67 4.9 13.8 1.0
C A:GLU84 4.9 9.5 1.0
CA A:ASP64 5.0 10.0 1.0
C5 A:ADA213 5.0 12.3 1.0

Calcium binding site 4 out of 8 in 4yzx

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Calcium binding site 4 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N 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/D107N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:11.0
occ:1.00
 O A:GLU104 2.3 9.9 1.0
OD1 A:ASP81 2.4 13.1 1.0
O A:HOH359 2.4 15.2 1.0
O A:VAL82 2.4 9.8 1.0
O A:HOH505 2.4 17.8 1.0
O A:HOH356 2.5 17.5 1.0
O A:HOH423 2.5 9.9 1.0
C A:GLU104 3.5 10.5 1.0
CG A:ASP81 3.5 11.0 1.0
C A:VAL82 3.6 9.0 1.0
CB A:GLU104 4.0 11.7 1.0
OD2 A:ASP81 4.0 14.8 1.0
N A:VAL82 4.1 8.6 1.0
O A:HOH397 4.2 12.7 1.0
C A:ASP81 4.2 9.7 1.0
CA A:VAL82 4.4 9.7 1.0
CA A:GLU104 4.4 10.3 1.0
N A:ALA105 4.4 9.7 1.0
N A:ALA106 4.4 9.6 1.0
O A:HOH404 4.5 14.1 1.0
CA A:ALA105 4.5 9.5 1.0
O A:HOH574 4.5 26.5 0.5
O A:GLY35 4.5 13.7 1.0
O A:HOH480 4.5 24.2 0.9
O A:GLY83 4.6 10.6 1.0
N A:GLY83 4.6 8.5 1.0
O A:HOH428 4.6 30.4 0.7
O A:ASP81 4.6 10.6 1.0
CA A:ASP81 4.7 9.5 1.0
CB A:ASP81 4.7 12.0 1.0
CA A:GLY83 4.8 9.5 1.0
CB A:VAL82 4.8 9.7 1.0
C A:ALA105 4.9 9.6 1.0

Calcium binding site 5 out of 8 in 4yzx

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Calcium binding site 5 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N 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/D107N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:13.0
occ:0.56
 OE1 B:GLN37 2.2 15.2 1.0
O6A B:ADA210 2.3 11.0 0.7
OE1 B:GLU84 2.3 12.8 1.0
OD1 B:ASN107 2.4 18.1 1.0
O B:HOH413 2.4 16.9 1.0
O6A B:ADA213 2.5 17.5 0.3
O B:HOH401 2.8 13.6 1.0
C6 B:ADA210 3.0 9.9 0.7
O6B B:ADA210 3.0 11.6 0.7
C6 B:ADA213 3.0 19.1 0.3
O B:HOH360 3.0 30.0 1.0
O6B B:ADA213 3.0 29.2 0.3
CG B:ASN107 3.3 16.0 1.0
CD B:GLN37 3.4 12.2 1.0
CA B:CA203 3.5 12.1 1.0
CB B:ASN107 3.5 12.3 1.0
CD B:GLU84 3.6 10.1 1.0
OE2 B:GLU39 4.0 12.8 1.0
O B:HOH343 4.0 12.0 1.0
NE2 B:GLN37 4.1 11.6 1.0
O B:GLU84 4.3 10.3 1.0
C5 B:ADA210 4.3 9.3 0.7
C5 B:ADA213 4.3 20.1 0.3
OE2 B:GLU84 4.4 11.2 1.0
CG B:GLU84 4.5 10.9 1.0
O B:HOH423 4.5 12.7 1.0
CG B:GLN37 4.5 11.7 1.0
ND2 B:ASN107 4.6 16.5 1.0
CB B:GLN37 4.6 11.4 1.0
O2 B:ADA209 4.6 15.1 0.7
O A:HOH325 4.6 19.9 0.3
NZ A:LYS103 4.7 19.2 1.0
O B:GLN37 4.7 13.8 1.0
CD B:GLU39 4.8 13.0 1.0
C2 B:ADA209 4.8 13.3 0.7

Calcium binding site 6 out of 8 in 4yzx

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Calcium binding site 6 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N 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/D107N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:12.1
occ:1.00
 O6A B:ADA213 2.2 17.5 0.3
O6A B:ADA210 2.3 11.0 0.7
O6B B:ADA211 2.3 10.6 0.7
O5 B:ADA214 2.4 17.4 0.3
O6B B:ADA214 2.4 16.7 0.3
OE1 B:GLU84 2.4 12.8 1.0
O5 B:ADA211 2.4 10.3 0.7
OE1 B:GLU39 2.5 14.8 1.0
O B:HOH343 2.5 12.0 1.0
OE2 B:GLU84 2.5 11.2 1.0
OE2 B:GLU39 2.5 12.8 1.0
CD B:GLU84 2.8 10.1 1.0
CD B:GLU39 2.9 13.0 1.0
C6 B:ADA214 3.2 16.2 0.3
C6 B:ADA213 3.2 19.1 0.3
C6 B:ADA211 3.2 9.4 0.7
C5 B:ADA214 3.3 18.1 0.3
C6 B:ADA210 3.3 9.9 0.7
C1 B:ADA211 3.4 10.9 0.7
C1 B:ADA214 3.4 17.0 0.3
C5 B:ADA211 3.4 10.9 0.7
CA B:CA202 3.5 13.0 0.6
O6B B:ADA213 3.9 29.2 0.3
CA B:CA204 3.9 11.6 1.0
OD2 B:ASP85 4.0 11.5 1.0
O6B B:ADA210 4.0 11.6 0.7
O B:HOH413 4.1 16.9 1.0
O B:HOH401 4.1 13.6 1.0
O B:HOH410 4.1 13.9 1.0
CG B:GLU84 4.2 10.9 1.0
C4 B:ADA210 4.2 10.3 0.7
C4 B:ADA213 4.2 17.5 0.3
O4 B:ADA210 4.3 10.9 0.7
C5 B:ADA210 4.3 9.3 0.7
C5 B:ADA213 4.3 20.1 0.3
O4 B:ADA213 4.3 17.8 0.3
CG B:GLU39 4.3 11.9 1.0
O6A B:ADA214 4.4 18.8 0.3
O6A B:ADA211 4.4 10.7 0.7
O4 B:ADA214 4.5 21.5 0.3
O4 B:ADA211 4.5 13.5 0.7
C4 B:ADA214 4.5 18.9 0.3
C2 B:ADA214 4.5 18.9 0.3
C2 B:ADA211 4.6 11.1 0.7
C4 B:ADA211 4.6 12.2 0.7
OE1 B:GLN111 4.7 11.0 1.0
CG B:ASP85 4.8 11.4 1.0
O B:HOH423 4.9 12.7 1.0

Calcium binding site 7 out of 8 in 4yzx

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Calcium binding site 7 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N 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/D107N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:11.6
occ:1.00
 OE2 B:GLU84 2.4 11.2 1.0
O B:HOH349 2.4 12.0 1.0
O B:HOH410 2.4 13.9 1.0
OD2 B:ASP85 2.5 11.5 1.0
OD1 B:ASP64 2.5 13.0 1.0
OD2 B:ASP64 2.5 13.3 1.0
O6B B:ADA214 2.6 16.7 0.3
OD1 B:ASP85 2.6 12.6 1.0
O6B B:ADA211 2.6 10.6 0.7
CG B:ASP85 2.9 11.4 1.0
CG B:ASP64 2.9 11.2 1.0
C6 B:ADA214 3.6 16.2 0.3
CD B:GLU84 3.6 10.1 1.0
C6 B:ADA211 3.6 9.4 0.7
O6A B:ADA214 3.9 18.8 0.3
O6A B:ADA211 3.9 10.7 0.7
CA B:CA203 3.9 12.1 1.0
OE1 B:GLU39 4.1 14.8 1.0
O B:HOH343 4.1 12.0 1.0
OG1 B:THR88 4.1 11.7 1.0
CB B:ASP85 4.3 10.9 1.0
CG B:GLU84 4.3 10.9 1.0
CB B:GLU84 4.3 11.0 1.0
CB B:ASP64 4.4 11.8 1.0
O B:HOH375 4.4 18.7 0.9
O B:HOH325 4.4 13.6 1.0
O B:HOH354 4.5 20.7 0.7
OE1 B:GLU84 4.6 12.8 1.0
N B:ASP85 4.6 9.6 1.0
O B:HOH364 4.6 12.7 1.0
NE2 B:HIS67 4.9 13.7 1.0
O B:HOH390 5.0 25.6 0.9
CA B:ASP64 5.0 11.7 1.0
C5 B:ADA214 5.0 18.1 0.3
C B:GLU84 5.0 9.4 1.0

Calcium binding site 8 out of 8 in 4yzx

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Calcium binding site 8 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N 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/D107N in Complex with Trigalacturonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca205

b:11.2
occ:1.00
 O B:GLU104 2.3 10.5 1.0
OD1 B:ASP81 2.3 13.4 1.0
O B:HOH377 2.4 14.9 1.0
O B:VAL82 2.4 10.5 1.0
O B:HOH502 2.4 16.3 1.0
O B:HOH376 2.5 16.6 1.0
O B:HOH388 2.5 10.5 1.0
C B:GLU104 3.5 9.6 1.0
CG B:ASP81 3.5 13.4 1.0
C B:VAL82 3.5 10.0 1.0
OD2 B:ASP81 4.0 17.1 1.0
CB B:GLU104 4.0 11.7 1.0
N B:VAL82 4.1 9.8 1.0
O B:HOH424 4.2 13.8 1.0
C B:ASP81 4.3 10.6 1.0
CA B:VAL82 4.3 9.0 1.0
CA B:GLU104 4.3 10.2 1.0
O B:HOH586 4.4 32.1 1.0
O B:HOH562 4.4 42.4 0.9
O B:HOH398 4.4 12.1 1.0
N B:ALA105 4.4 9.2 1.0
N B:ALA106 4.5 9.9 1.0
CA B:ALA105 4.5 9.4 1.0
O B:GLY35 4.5 12.3 1.0
O B:HOH495 4.5 22.1 0.7
O B:GLY83 4.6 10.3 1.0
N B:GLY83 4.6 9.4 1.0
O B:HOH517 4.6 44.5 1.0
O B:HOH481 4.7 27.9 0.8
O B:ASP81 4.7 10.8 1.0
CB B:ASP81 4.7 13.1 1.0
CB B:VAL82 4.7 9.3 1.0
CA B:GLY83 4.8 9.5 1.0
CA B:ASP81 4.8 11.3 1.0
O B:LYS103 4.9 9.7 0.5
C B:ALA105 5.0 8.8 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 15:23:54 2024

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