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Calcium in PDB 4z06: C. Bescii Family 3 Pectate Lyase Double Mutant K108A/R133A in Complex with Alpha-D-Galactopyranuronic Acid

Enzymatic activity of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/R133A in Complex with Alpha-D-Galactopyranuronic Acid

All present enzymatic activity of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/R133A in Complex with Alpha-D-Galactopyranuronic Acid:
4.2.2.2;

Protein crystallography data

The structure of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/R133A in Complex with Alpha-D-Galactopyranuronic Acid, PDB code: 4z06 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) 49.80 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.680, 36.240, 99.820, 90.00, 132.53, 90.00
R / Rfree (%) 16 / 20

Calcium Binding Sites:

The binding sites of Calcium atom in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/R133A in Complex with Alpha-D-Galactopyranuronic Acid (pdb code 4z06). 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/R133A in Complex with Alpha-D-Galactopyranuronic Acid, PDB code: 4z06:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4z06

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Calcium binding site 1 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/R133A in Complex with Alpha-D-Galactopyranuronic 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/R133A in Complex with Alpha-D-Galactopyranuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:19.7
occ:0.56
 OE1 A:GLN37 2.2 19.1 1.0
OE1 A:GLU84 2.4 21.7 1.0
O A:HOH469 2.4 27.2 1.0
O A:HOH366 2.4 33.2 0.7
O A:HOH376 2.5 14.4 1.0
OD2 A:ASP107 2.5 22.2 1.0
CG A:ASP107 3.4 18.0 1.0
CD A:GLN37 3.4 18.6 1.0
CB A:ASP107 3.4 14.5 1.0
CD A:GLU84 3.5 21.2 1.0
CA A:CA202 3.5 20.0 0.7
O A:HOH374 3.7 36.4 0.9
O A:HOH324 3.9 16.6 0.9
O A:GLU84 4.0 13.8 1.0
NE2 A:GLN37 4.0 18.0 1.0
OE1 A:GLU39 4.1 26.6 0.5
OE2 A:GLU84 4.3 21.2 1.0
CG A:GLU84 4.4 17.1 1.0
OD1 A:ASP107 4.5 19.6 1.0
CG A:GLN37 4.6 18.5 1.0
O A:HOH337 4.8 31.4 0.9
O A:HOH450 4.8 44.4 1.0
CD A:GLU39 4.9 25.6 0.5
CA A:ASP107 4.9 13.3 1.0
N A:ALA108 4.9 10.6 1.0
CB A:GLN37 4.9 19.2 1.0
C A:GLU84 4.9 13.4 1.0

Calcium binding site 2 out of 8 in 4z06

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Calcium binding site 2 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/R133A in Complex with Alpha-D-Galactopyranuronic 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/R133A in Complex with Alpha-D-Galactopyranuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:20.0
occ:0.71
 O5 A:ADA205 2.3 19.5 0.7
O6A A:ADA205 2.3 16.0 0.7
O A:HOH469 2.4 27.2 1.0
OE1 A:GLU84 2.4 21.7 1.0
OE1 A:GLU39 2.6 26.6 0.5
O A:HOH324 2.6 16.6 0.9
OE2 A:GLU39 2.6 25.4 0.5
OE2 A:GLU84 2.6 21.2 1.0
CD A:GLU84 2.8 21.2 1.0
CD A:GLU39 3.0 25.6 0.5
C6 A:ADA205 3.1 16.5 0.7
C5 A:ADA205 3.2 19.0 0.7
C1 A:ADA205 3.4 22.6 0.7
CA A:CA201 3.5 19.7 0.6
CA A:CA203 3.9 16.1 0.8
OD2 A:ASP85 3.9 17.7 1.0
O A:HOH366 3.9 33.2 0.7
O A:HOH376 4.0 14.4 1.0
O1 A:ADA205 4.1 27.0 0.7
O A:HOH363 4.1 28.2 1.0
CG A:GLU84 4.2 17.1 1.0
O6B A:ADA205 4.3 15.9 0.7
CG A:GLU39 4.5 25.6 0.5
C4 A:ADA205 4.5 20.8 0.7
C2 A:ADA205 4.6 24.3 0.7
O4 A:ADA205 4.6 21.9 0.7
OE1 A:GLN111 4.7 12.9 1.0
O A:HOH337 4.8 31.4 0.9
CG A:ASP85 4.8 18.9 1.0
CD A:GLN111 4.9 13.0 1.0
O A:HOH450 5.0 44.4 1.0

Calcium binding site 3 out of 8 in 4z06

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Calcium binding site 3 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/R133A in Complex with Alpha-D-Galactopyranuronic 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/R133A in Complex with Alpha-D-Galactopyranuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:16.1
occ:0.80
 O A:HOH339 2.3 18.8 1.0
OE2 A:GLU84 2.4 21.2 1.0
OD1 A:ASP64 2.5 23.7 1.0
O A:HOH363 2.5 28.2 1.0
OD2 A:ASP85 2.5 17.7 1.0
O6A A:ADA205 2.5 16.0 0.7
OD1 A:ASP85 2.6 19.2 1.0
OD2 A:ASP64 2.7 18.8 1.0
CG A:ASP85 2.9 18.9 1.0
CG A:ASP64 2.9 17.7 1.0
C6 A:ADA205 3.5 16.5 0.7
CD A:GLU84 3.6 21.2 1.0
O6B A:ADA205 3.9 15.9 0.7
CA A:CA202 3.9 20.0 0.7
OG1 A:THR88 4.1 12.8 1.0
OE2 A:GLU39 4.1 25.4 0.5
O A:HOH324 4.2 16.6 0.9
CB A:GLU84 4.2 16.1 1.0
O A:HOH445 4.3 26.9 1.0
CB A:ASP85 4.3 15.3 1.0
CG A:GLU84 4.4 17.1 1.0
O A:HOH399 4.4 19.2 0.9
N A:ASP85 4.4 12.0 1.0
CB A:ASP64 4.4 15.9 1.0
OE1 A:GLU84 4.5 21.7 1.0
O A:HOH370 4.6 13.9 1.0
C A:GLU84 4.8 13.4 1.0
C5 A:ADA205 4.8 19.0 0.7
CA A:ASP85 4.9 12.4 1.0
CA A:ASP64 5.0 13.8 1.0

Calcium binding site 4 out of 8 in 4z06

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Calcium binding site 4 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/R133A in Complex with Alpha-D-Galactopyranuronic 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/R133A in Complex with Alpha-D-Galactopyranuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:11.4
occ:0.58
 O A:GLU104 2.3 10.7 1.0
O A:HOH478 2.3 21.2 1.0
O A:VAL82 2.3 11.6 1.0
OD1 A:ASP81 2.3 14.1 1.0
O A:HOH389 2.4 15.5 0.9
O A:HOH371 2.5 12.4 1.0
C A:GLU104 3.4 11.2 1.0
O A:HOH411 3.5 31.5 0.8
C A:VAL82 3.5 10.5 1.0
CG A:ASP81 3.5 13.9 1.0
N A:VAL82 3.9 9.4 1.0
CB A:GLU104 4.0 13.7 1.0
C A:ASP81 4.1 10.5 1.0
CA A:VAL82 4.2 9.6 1.0
O A:HOH386 4.2 13.1 0.9
OD2 A:ASP81 4.2 18.2 1.0
N A:ALA105 4.4 9.1 1.0
CA A:GLU104 4.4 11.0 1.0
N A:ALA106 4.4 10.8 1.0
O A:ASP81 4.4 11.3 1.0
CA A:ALA105 4.4 9.7 1.0
CA A:ASP81 4.5 10.5 1.0
O A:GLY35 4.5 16.4 1.0
O A:HOH390 4.5 16.0 1.0
N A:GLY83 4.6 11.0 1.0
O A:HOH475 4.6 41.0 1.0
CB A:ASP81 4.6 12.9 1.0
O A:GLY83 4.6 12.2 1.0
CB A:VAL82 4.7 8.7 1.0
O A:HOH452 4.7 28.9 0.6
CA A:GLY83 4.8 11.3 1.0
C A:ALA105 4.9 10.1 1.0
O A:LYS103 5.0 10.9 1.0

Calcium binding site 5 out of 8 in 4z06

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Calcium binding site 5 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/R133A in Complex with Alpha-D-Galactopyranuronic 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/R133A in Complex with Alpha-D-Galactopyranuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:15.2
occ:0.69
 OE1 B:GLN37 2.3 13.2 1.0
O B:HOH469 2.3 13.0 1.0
OE1 B:GLU84 2.4 11.2 1.0
OD2 B:ASP107 2.5 19.1 1.0
O B:HOH437 2.5 20.6 1.0
O B:HOH368 2.6 10.4 1.0
CG B:ASP107 3.4 15.5 1.0
CD B:GLN37 3.4 12.8 1.0
CA B:CA202 3.5 12.1 0.9
O A:HOH466 3.5 22.9 0.9
CB B:ASP107 3.5 12.7 1.0
CD B:GLU84 3.6 10.2 1.0
O B:HOH406 3.7 27.2 0.9
O B:HOH351 3.9 13.7 1.0
OE2 B:GLU39 4.1 14.5 1.0
NE2 B:GLN37 4.1 12.2 1.0
O B:GLU84 4.1 10.8 1.0
OE2 B:GLU84 4.4 13.9 1.0
CG B:GLU84 4.4 11.1 1.0
O B:HOH387 4.4 20.5 0.6
OD1 B:ASP107 4.6 16.8 1.0
CG B:GLN37 4.6 12.6 1.0
NZ A:LYS103 4.8 32.1 1.0
CB B:GLN37 4.8 13.5 1.0
O B:GLN37 4.8 15.1 1.0
CD B:GLU39 4.9 15.7 1.0
CA B:ASP107 5.0 10.4 1.0

Calcium binding site 6 out of 8 in 4z06

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Calcium binding site 6 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/R133A in Complex with Alpha-D-Galactopyranuronic 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/R133A in Complex with Alpha-D-Galactopyranuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:12.1
occ:0.91
 OE1 B:GLU84 2.2 11.2 1.0
O5 B:ADA205 2.4 14.1 0.9
O B:HOH469 2.4 13.0 1.0
OE1 B:GLU39 2.4 16.2 1.0
OE2 B:GLU39 2.5 14.5 1.0
O6B B:ADA205 2.5 10.5 0.9
O B:HOH351 2.5 13.7 1.0
OE2 B:GLU84 2.6 13.9 1.0
CD B:GLU84 2.7 10.2 1.0
CD B:GLU39 2.8 15.7 1.0
C6 B:ADA205 3.3 13.1 0.9
C5 B:ADA205 3.4 13.8 0.9
C1 B:ADA205 3.4 17.2 0.9
CA B:CA201 3.5 15.2 0.7
OD2 B:ASP85 3.9 12.6 1.0
CA B:CA203 3.9 11.3 0.9
O B:HOH437 4.0 20.6 1.0
O B:HOH380 4.1 13.4 0.9
O B:HOH368 4.1 10.4 1.0
CG B:GLU84 4.1 11.1 1.0
O A:HOH466 4.3 22.9 0.9
O1 B:ADA205 4.3 17.1 0.9
CG B:GLU39 4.4 15.5 1.0
O6A B:ADA205 4.4 11.1 0.9
O4 B:ADA205 4.5 15.6 0.9
C2 B:ADA205 4.6 17.0 0.9
C4 B:ADA205 4.6 15.4 0.9
OE1 B:GLN111 4.6 10.7 1.0
O B:HOH387 4.7 20.5 0.6
CG B:ASP85 4.8 13.4 1.0

Calcium binding site 7 out of 8 in 4z06

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Calcium binding site 7 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/R133A in Complex with Alpha-D-Galactopyranuronic 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/R133A in Complex with Alpha-D-Galactopyranuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:11.3
occ:0.92
 O B:HOH330 2.3 12.2 0.9
OE2 B:GLU84 2.3 13.9 1.0
OD2 B:ASP85 2.4 12.6 1.0
O B:HOH380 2.4 13.4 0.9
OD1 B:ASP85 2.5 14.0 1.0
OD1 B:ASP64 2.6 14.9 1.0
OD2 B:ASP64 2.6 15.3 1.0
O6B B:ADA205 2.6 10.5 0.9
CG B:ASP85 2.8 13.4 1.0
CG B:ASP64 2.9 14.4 1.0
CD B:GLU84 3.5 10.2 1.0
C6 B:ADA205 3.6 13.1 0.9
O6A B:ADA205 3.9 11.1 0.9
CA B:CA202 3.9 12.1 0.9
OE1 B:GLU39 4.1 16.2 1.0
OG1 B:THR88 4.1 10.8 1.0
O B:HOH351 4.2 13.7 1.0
CB B:ASP85 4.3 11.6 1.0
CG B:GLU84 4.3 11.1 1.0
O B:HOH381 4.4 14.6 0.9
CB B:GLU84 4.4 10.8 1.0
O B:HOH333 4.4 24.1 1.0
CB B:ASP64 4.4 13.6 1.0
OE1 B:GLU84 4.5 11.2 1.0
N B:ASP85 4.5 10.8 1.0
O B:HOH370 4.6 14.6 1.0
C B:GLU84 4.9 11.2 1.0
NE2 B:HIS67 4.9 15.0 1.0
CA B:ASP85 5.0 10.3 1.0
C5 B:ADA205 5.0 13.8 0.9

Calcium binding site 8 out of 8 in 4z06

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Calcium binding site 8 out of 8 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/R133A in Complex with Alpha-D-Galactopyranuronic 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/R133A in Complex with Alpha-D-Galactopyranuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:13.2
occ:0.75
 O B:HOH487 2.3 14.1 0.3
O B:GLU104 2.3 10.7 1.0
O B:VAL82 2.3 11.7 1.0
O B:HOH487 2.4 20.1 0.7
OD1 B:ASP81 2.4 15.2 1.0
O B:HOH369 2.4 11.5 0.8
O B:HOH400 2.6 10.2 1.0
C B:GLU104 3.5 10.4 1.0
C B:VAL82 3.5 11.7 1.0
CG B:ASP81 3.6 15.2 1.0
N B:VAL82 3.9 10.7 1.0
CB B:GLU104 4.0 12.4 1.0
O B:HOH539 4.0 18.2 0.5
C B:ASP81 4.2 13.1 1.0
O B:HOH497 4.2 6.5 0.2
OD2 B:ASP81 4.2 18.8 1.0
O B:HOH390 4.2 13.9 1.0
CA B:VAL82 4.2 11.5 1.0
CA B:GLU104 4.4 11.1 1.0
N B:ALA106 4.4 9.7 1.0
N B:ALA105 4.4 10.2 1.0
CA B:ALA105 4.5 9.7 1.0
O B:GLY35 4.5 15.0 1.0
O B:HOH378 4.5 13.8 1.0
O B:ASP81 4.5 11.8 1.0
N B:GLY83 4.6 10.6 1.0
O B:HOH485 4.6 31.2 0.9
O B:GLY83 4.6 11.8 1.0
CA B:ASP81 4.6 12.3 1.0
CB B:VAL82 4.7 10.6 1.0
O B:HOH539 4.7 22.5 0.5
CB B:ASP81 4.7 13.7 1.0
O B:HOH445 4.8 29.3 0.7
CA B:GLY83 4.9 12.1 1.0
C B:ALA105 4.9 9.3 1.0
O B:LYS103 5.0 11.0 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: Wed Jul 9 03:28:44 2025

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