Atomistry » Calcium » PDB 4elg-4fa1 » 4ew9
Atomistry »
  Calcium »
    PDB 4elg-4fa1 »
      4ew9 »

Calcium in PDB 4ew9: The Liganded Structure of C. Bescii Family 3 Pectate Lyase

Enzymatic activity of The Liganded Structure of C. Bescii Family 3 Pectate Lyase

All present enzymatic activity of The Liganded Structure of C. Bescii Family 3 Pectate Lyase:
4.2.2.2;

Protein crystallography data

The structure of The Liganded Structure of C. Bescii Family 3 Pectate Lyase, PDB code: 4ew9 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) 33.85 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.946, 35.898, 98.687, 90.00, 132.00, 90.00
R / Rfree (%) 16.4 / 20.4

Calcium Binding Sites:

The binding sites of Calcium atom in the The Liganded Structure of C. Bescii Family 3 Pectate Lyase (pdb code 4ew9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the The Liganded Structure of C. Bescii Family 3 Pectate Lyase, PDB code: 4ew9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4ew9

Go back to Calcium Binding Sites List in 4ew9
Calcium binding site 1 out of 9 in the The Liganded Structure of C. Bescii Family 3 Pectate Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Liganded Structure of C. Bescii Family 3 Pectate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:17.3
occ:1.00
O A:VAL82 2.3 18.2 1.0
O A:HOH353 2.4 19.6 1.0
OD1 A:ASP81 2.4 20.0 1.0
O A:HOH336 2.4 22.1 1.0
O A:GLU104 2.4 16.0 1.0
O A:HOH331 2.4 22.9 1.0
O A:HOH310 2.5 16.1 1.0
CG A:ASP81 3.5 20.6 1.0
C A:VAL82 3.6 15.7 1.0
C A:GLU104 3.6 16.4 1.0
CB A:GLU104 4.0 19.2 1.0
N A:VAL82 4.0 14.3 1.0
OD2 A:ASP81 4.0 22.5 1.0
O A:HOH327 4.1 19.2 1.0
C A:ASP81 4.2 16.7 1.0
CA A:VAL82 4.3 14.6 1.0
N A:ALA106 4.4 14.7 1.0
CA A:GLU104 4.5 15.5 1.0
O A:HOH454 4.5 27.4 0.5
O A:HOH301 4.5 17.5 1.0
O A:GLY35 4.5 19.9 1.0
N A:ALA105 4.5 15.2 1.0
O A:HOH429 4.5 38.5 1.0
CA A:ALA105 4.6 14.6 1.0
N A:GLY83 4.6 16.0 1.0
CA A:ASP81 4.6 15.6 1.0
O A:GLY83 4.6 15.4 1.0
CB A:ASP81 4.6 18.5 1.0
O A:HOH430 4.7 28.6 1.0
CA A:GLY83 4.7 16.0 1.0
O A:ASP81 4.7 17.4 1.0
CB A:VAL82 4.8 14.1 1.0
C A:ALA105 5.0 13.1 1.0
O A:LYS103 5.0 14.4 1.0

Calcium binding site 2 out of 9 in 4ew9

Go back to Calcium Binding Sites List in 4ew9
Calcium binding site 2 out of 9 in the The Liganded Structure of C. Bescii Family 3 Pectate Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Liganded Structure of C. Bescii Family 3 Pectate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:17.8
occ:1.00
OE1 A:GLU84 2.4 18.6 1.0
O A:HOH482 2.4 18.2 1.0
O A:HOH352 2.5 19.8 1.0
OD1 A:ASP85 2.5 16.7 1.0
OD1 A:ASP64 2.6 20.1 1.0
OD2 A:ASP85 2.6 16.7 1.0
OD2 A:ASP64 2.6 17.7 1.0
OAM A:DGU210 2.6 16.4 0.8
CG A:ASP85 2.9 14.9 1.0
CG A:ASP64 2.9 15.1 1.0
CAJ A:DGU210 3.5 19.2 0.8
CD A:GLU84 3.6 18.7 1.0
OAD A:DGU210 3.8 16.8 0.8
CA A:CA204 3.9 20.0 1.0
OE1 A:GLU39 4.1 19.7 1.0
OG1 A:THR88 4.1 18.0 1.0
O A:HOH483 4.3 16.6 1.0
O A:HOH440 4.3 27.1 1.0
CB A:ASP85 4.3 14.1 1.0
CB A:ASP64 4.3 16.1 1.0
CB A:GLU84 4.4 16.8 1.0
CG A:GLU84 4.4 17.5 1.0
O A:HOH484 4.5 18.2 1.0
O A:HOH332 4.5 17.8 1.0
OE2 A:GLU84 4.6 18.3 1.0
N A:ASP85 4.6 14.6 1.0
O A:HOH469 4.7 33.9 1.0
NE2 A:HIS67 4.8 16.6 1.0
CAI A:DGU210 4.9 22.9 0.8
CA A:ASP64 4.9 16.4 1.0
C A:GLU84 5.0 17.4 1.0

Calcium binding site 3 out of 9 in 4ew9

Go back to Calcium Binding Sites List in 4ew9
Calcium binding site 3 out of 9 in the The Liganded Structure of C. Bescii Family 3 Pectate Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Liganded Structure of C. Bescii Family 3 Pectate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:20.2
occ:1.00
OE1 A:GLN37 2.1 19.6 1.0
OE2 A:GLU84 2.4 18.3 1.0
OD2 A:ASP107 2.4 19.4 1.0
O A:HOH409 2.5 20.1 1.0
O A:HOH444 2.5 21.5 1.0
O A:HOH309 2.5 15.6 1.0
O6 A:UNG209 2.5 22.2 1.0
OAN A:UNG209 2.7 22.2 1.0
C6 A:UNG209 2.9 23.3 1.0
CD A:GLN37 3.4 18.8 1.0
CG A:ASP107 3.4 17.1 1.0
CD A:GLU84 3.6 18.7 1.0
CB A:ASP107 3.7 15.9 1.0
CA A:CA204 3.8 20.0 1.0
OE2 A:GLU39 3.9 19.2 1.0
CG A:GLN37 4.3 20.1 1.0
O A:HOH483 4.3 16.6 1.0
NE2 A:GLN37 4.3 19.0 1.0
C5 A:UNG209 4.3 23.8 1.0
CG A:GLU84 4.4 17.5 1.0
O A:GLU84 4.4 16.5 1.0
CB A:GLN37 4.4 18.4 1.0
OE1 A:GLU84 4.5 18.6 1.0
OD1 A:ASP107 4.6 19.3 1.0
O A:GLN37 4.7 17.8 1.0
O2' A:UNG209 4.8 30.4 1.0
O A:HOH516 4.8 39.7 1.0
CD A:GLU39 4.8 18.7 1.0
CE A:LYS108 4.9 24.0 1.0
O A:HOH485 4.9 17.9 1.0
C2' A:UNG209 4.9 26.1 1.0
NZ A:LYS108 4.9 21.4 1.0
O5 A:UNG209 5.0 22.6 1.0
CA A:GLN37 5.0 19.0 1.0

Calcium binding site 4 out of 9 in 4ew9

Go back to Calcium Binding Sites List in 4ew9
Calcium binding site 4 out of 9 in the The Liganded Structure of C. Bescii Family 3 Pectate Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Liganded Structure of C. Bescii Family 3 Pectate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:20.0
occ:1.00
O6 A:UNG209 2.3 22.2 1.0
OAM A:DGU210 2.3 16.4 0.8
OE2 A:GLU84 2.4 18.3 1.0
OAC A:DGU210 2.4 17.9 0.8
OE2 A:GLU39 2.5 19.2 1.0
O A:HOH483 2.5 16.6 1.0
OE1 A:GLU84 2.5 18.6 1.0
OE1 A:GLU39 2.5 19.7 1.0
CD A:GLU84 2.8 18.7 1.0
CD A:GLU39 2.9 18.7 1.0
CAJ A:DGU210 3.1 19.2 0.8
C6 A:UNG209 3.3 23.3 1.0
CAI A:DGU210 3.3 22.9 0.8
CA A:CA203 3.8 20.2 1.0
CA A:CA202 3.9 17.8 1.0
OD1 A:ASP85 3.9 16.7 1.0
O A:HOH309 3.9 15.6 1.0
O A:HOH482 4.1 18.2 1.0
OAN A:UNG209 4.2 22.2 1.0
O A:HOH409 4.2 20.1 1.0
C5 A:UNG209 4.2 23.8 1.0
CG A:GLU84 4.3 17.5 1.0
OAK A:DGU210 4.3 52.5 0.8
OAD A:DGU210 4.3 16.8 0.8
C4 A:UNG209 4.4 21.5 1.0
CG A:GLU39 4.4 21.0 1.0
CAH A:DGU210 4.4 32.0 0.8
OAL A:DGU210 4.5 41.4 0.8
OE1 A:GLN111 4.5 16.9 1.0
O A:HOH486 4.8 26.0 1.0
CD A:GLN111 4.8 15.6 1.0
CG A:ASP85 4.9 14.9 1.0
O A:HOH487 4.9 32.8 1.0
CAG A:DGU210 5.0 38.8 0.8

Calcium binding site 5 out of 9 in 4ew9

Go back to Calcium Binding Sites List in 4ew9
Calcium binding site 5 out of 9 in the The Liganded Structure of C. Bescii Family 3 Pectate Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Liganded Structure of C. Bescii Family 3 Pectate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:22.5
occ:0.70
O A:HOH492 2.2 23.6 0.7
O6A A:ADA211 2.3 30.1 1.0
OE2 A:GLU167 2.3 24.3 1.0
O5 A:ADA211 2.3 23.4 1.0
O A:HOH506 2.4 24.9 0.5
O A:HOH505 2.5 23.7 0.5
O A:HOH367 2.6 21.4 1.0
C6 A:ADA211 3.1 30.1 1.0
C1 A:ADA211 3.3 27.9 1.0
C5 A:ADA211 3.4 26.0 1.0
CD A:GLU167 3.4 22.4 1.0
O1 A:ADA211 4.1 25.3 1.0
O A:HOH363 4.2 19.3 1.0
OE1 A:GLU167 4.2 21.6 1.0
CG A:GLU167 4.3 16.1 1.0
O6B A:ADA211 4.4 33.6 1.0
NZ A:LYS141 4.4 24.6 1.0
O4 A:ADA211 4.4 26.1 1.0
O A:HOH404 4.5 22.2 0.7
C4 A:ADA211 4.5 24.6 1.0
O A:HOH343 4.5 20.1 1.0
C2 A:ADA211 4.5 27.1 1.0
O A:HOH371 4.6 39.4 1.0
O A:VAL165 4.8 14.0 1.0

Calcium binding site 6 out of 9 in 4ew9

Go back to Calcium Binding Sites List in 4ew9
Calcium binding site 6 out of 9 in the The Liganded Structure of C. Bescii Family 3 Pectate Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Liganded Structure of C. Bescii Family 3 Pectate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:19.0
occ:1.00
O B:GLU104 2.3 16.7 1.0
O B:HOH303 2.3 19.8 1.0
O B:HOH334 2.4 22.2 1.0
O B:VAL82 2.4 17.9 1.0
O B:HOH337 2.4 21.5 1.0
OD1 B:ASP81 2.4 23.2 1.0
O B:HOH322 2.5 18.9 1.0
C B:GLU104 3.4 16.7 1.0
CG B:ASP81 3.6 25.2 1.0
C B:VAL82 3.6 16.6 1.0
CB B:GLU104 3.9 19.8 1.0
N B:VAL82 4.0 17.5 1.0
OD2 B:ASP81 4.1 22.4 1.0
O B:HOH319 4.1 21.0 1.0
C B:ASP81 4.3 18.2 1.0
O B:HOH375 4.3 39.6 1.0
CA B:GLU104 4.3 18.1 1.0
CA B:VAL82 4.3 17.5 1.0
N B:ALA105 4.4 15.7 1.0
O B:HOH320 4.5 22.0 1.0
N B:ALA106 4.5 17.5 1.0
CA B:ALA105 4.5 15.8 1.0
O B:GLY35 4.5 21.1 1.0
O B:GLY83 4.6 17.6 1.0
N B:GLY83 4.6 18.3 1.0
O B:HOH326 4.7 32.7 1.0
CB B:VAL82 4.7 18.4 1.0
O B:ASP81 4.7 20.4 1.0
CB B:ASP81 4.8 19.5 1.0
CA B:ASP81 4.8 19.7 1.0
O B:HOH402 4.8 30.0 0.5
CA B:GLY83 4.8 19.0 1.0
C B:ALA105 5.0 16.6 1.0

Calcium binding site 7 out of 9 in 4ew9

Go back to Calcium Binding Sites List in 4ew9
Calcium binding site 7 out of 9 in the The Liganded Structure of C. Bescii Family 3 Pectate Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Liganded Structure of C. Bescii Family 3 Pectate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:19.6
occ:1.00
OE1 B:GLN37 2.3 17.5 1.0
O6 B:UNG206 2.3 17.9 1.0
OD2 B:ASP107 2.4 21.7 1.0
O B:HOH317 2.5 21.2 1.0
OE2 B:GLU84 2.5 19.5 1.0
O B:HOH432 2.6 16.3 1.0
OAN B:UNG206 2.6 23.1 1.0
O B:HOH429 2.6 23.7 1.0
C6 B:UNG206 2.7 19.5 1.0
CG B:ASP107 3.4 20.6 1.0
CD B:GLN37 3.5 20.1 1.0
CD B:GLU84 3.7 19.7 1.0
CB B:ASP107 3.7 17.5 1.0
CA B:CA204 3.7 18.8 1.0
OE2 B:GLU39 3.8 19.1 1.0
C5 B:UNG206 4.2 21.7 1.0
O B:HOH431 4.2 19.8 1.0
CG B:GLU84 4.4 19.7 1.0
O B:GLU84 4.4 17.8 1.0
NE2 B:GLN37 4.4 19.9 1.0
CG B:GLN37 4.5 20.1 1.0
CB B:GLN37 4.5 21.3 1.0
OE1 B:GLU84 4.5 20.5 1.0
OD1 B:ASP107 4.6 21.5 1.0
O B:GLN37 4.6 19.8 1.0
CD B:GLU39 4.7 18.4 1.0
CE B:LYS108 4.8 22.2 1.0
NZ B:LYS108 4.8 21.0 1.0
C4 B:UNG206 4.9 21.1 1.0
O5 B:UNG206 5.0 19.7 1.0
O B:HOH444 5.0 40.1 1.0

Calcium binding site 8 out of 9 in 4ew9

Go back to Calcium Binding Sites List in 4ew9
Calcium binding site 8 out of 9 in the The Liganded Structure of C. Bescii Family 3 Pectate Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Liganded Structure of C. Bescii Family 3 Pectate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:19.5
occ:1.00
O B:HOH341 2.3 20.5 1.0
OE1 B:GLU84 2.4 20.5 1.0
O B:HOH422 2.4 18.7 1.0
OD1 B:ASP64 2.5 20.6 1.0
OD1 B:ASP85 2.5 20.3 1.0
OD2 B:ASP85 2.5 16.2 1.0
OAM B:DGU207 2.5 18.0 0.8
OD2 B:ASP64 2.6 23.0 1.0
CG B:ASP85 2.8 18.1 1.0
CG B:ASP64 2.9 18.0 1.0
CAJ B:DGU207 3.5 18.8 0.8
CD B:GLU84 3.6 19.7 1.0
OAD B:DGU207 3.9 17.1 0.8
CA B:CA204 3.9 18.8 1.0
OE1 B:GLU39 4.1 21.7 1.0
OG1 B:THR88 4.1 17.6 1.0
O B:HOH431 4.1 19.8 1.0
O B:HOH330 4.3 32.2 1.0
CB B:ASP85 4.3 16.4 1.0
CG B:GLU84 4.4 19.7 1.0
CB B:GLU84 4.4 19.8 1.0
CB B:ASP64 4.4 18.6 1.0
O B:HOH428 4.5 20.6 1.0
OE2 B:GLU84 4.5 19.5 1.0
O B:HOH308 4.5 17.5 1.0
N B:ASP85 4.6 17.6 1.0
NE2 B:HIS67 4.8 22.5 1.0
CAI B:DGU207 4.9 21.0 0.8
CA B:ASP64 5.0 19.3 1.0
C B:GLU84 5.0 17.0 1.0

Calcium binding site 9 out of 9 in 4ew9

Go back to Calcium Binding Sites List in 4ew9
Calcium binding site 9 out of 9 in the The Liganded Structure of C. Bescii Family 3 Pectate Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The Liganded Structure of C. Bescii Family 3 Pectate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:18.8
occ:1.00
OAC B:DGU207 2.3 16.9 0.8
OE2 B:GLU84 2.3 19.5 1.0
O6 B:UNG206 2.4 17.9 1.0
OE1 B:GLU39 2.5 21.7 1.0
OE2 B:GLU39 2.5 19.1 1.0
OAM B:DGU207 2.5 18.0 0.8
O B:HOH431 2.5 19.8 1.0
OE1 B:GLU84 2.7 20.5 1.0
CD B:GLU39 2.8 18.4 1.0
CD B:GLU84 2.8 19.7 1.0
CAJ B:DGU207 3.1 18.8 0.8
CAI B:DGU207 3.2 21.0 0.8
C6 B:UNG206 3.4 19.5 1.0
CA B:CA202 3.7 19.6 1.0
CA B:CA203 3.9 19.5 1.0
O B:HOH432 4.0 16.3 1.0
OD1 B:ASP85 4.0 20.3 1.0
O B:HOH422 4.1 18.7 1.0
OAN B:UNG206 4.2 23.1 1.0
O B:HOH317 4.2 21.2 1.0
CG B:GLU84 4.2 19.7 1.0
C5 B:UNG206 4.3 21.7 1.0
OAD B:DGU207 4.3 17.1 0.8
C4 B:UNG206 4.3 21.1 1.0
CAH B:DGU207 4.4 29.6 0.8
CG B:GLU39 4.4 20.0 1.0
OE1 B:GLN111 4.6 16.9 1.0
OAL B:DGU207 4.7 38.9 0.8
CD B:GLN111 4.8 19.0 1.0
CAG B:DGU207 4.8 27.8 0.8
CG B:ASP85 4.9 18.1 1.0

Reference:

M.Alahuhta, R.Brunecky, P.Chandrayan, I.Kataeva, M.W.Adams, M.E.Himmel, V.V.Lunin. The Structure and Mode of Action of Caldicellulosiruptor Bescii Family 3 Pectate Lyase in Biomass Deconstruction. Acta Crystallogr. D Biol. V. 69 534 2013CRYSTALLOGR..
ISSN: ESSN 1399-0047
PubMed: 23519661
DOI: 10.1107/S0907444912050512
Page generated: Sat Dec 12 04:45:36 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy