Atomistry » Calcium » PDB 4ytz-4z6z » 4z06
Atomistry »
  Calcium »
    PDB 4ytz-4z6z »
      4z06 »

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

Go back to Calcium Binding Sites List in 4z06
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

Go back to Calcium Binding Sites List in 4z06
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

Go back to Calcium Binding Sites List in 4z06
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

Go back to Calcium Binding Sites List in 4z06
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

Go back to Calcium Binding Sites List in 4z06
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

Go back to Calcium Binding Sites List in 4z06
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

Go back to Calcium Binding Sites List in 4z06
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

Go back to Calcium Binding Sites List in 4z06
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: Sun Jul 14 15:27:19 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy