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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Sun Jul 14 00:05:22 2024

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