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Calcium in PDB 5vol: BACINT_04212 Ferulic Acid Esterase

Protein crystallography data

The structure of BACINT_04212 Ferulic Acid Esterase, PDB code: 5vol was solved by N.M.Koropatkin, I.Cann, R.I.Mackie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.65 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 127.920, 135.790, 172.590, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19.8

Calcium Binding Sites:

The binding sites of Calcium atom in the BACINT_04212 Ferulic Acid Esterase (pdb code 5vol). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the BACINT_04212 Ferulic Acid Esterase, PDB code: 5vol:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5vol

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Calcium binding site 1 out of 8 in the BACINT_04212 Ferulic Acid Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of BACINT_04212 Ferulic Acid Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:28.4
occ:1.00
 OD1 A:ASP262 2.4 19.3 1.0
OE1 B:GLN257 2.5 19.8 1.0
O A:HOH554 2.5 24.4 1.0
OD1 A:ASP234 2.5 19.5 1.0
OD2 A:ASP234 2.5 19.3 1.0
O A:HOH418 2.6 22.4 1.0
OD2 A:ASP235 2.6 33.9 1.0
CG A:ASP234 2.9 18.9 1.0
CG A:ASP235 3.3 28.1 1.0
CD B:GLN257 3.4 23.3 1.0
OD1 A:ASP235 3.4 28.3 1.0
CG A:ASP262 3.6 20.7 1.0
NE2 B:GLN257 3.6 24.2 1.0
NH1 B:ARG259 3.9 17.3 1.0
N A:GLY263 4.1 20.7 1.0
O A:HOH468 4.1 20.8 1.0
O A:HOH580 4.4 35.5 1.0
OD2 A:ASP262 4.4 22.1 1.0
CA A:ASP262 4.4 18.7 1.0
CB A:ASP234 4.4 17.1 1.0
CB A:ASP262 4.5 18.1 1.0
NH2 B:ARG259 4.5 20.2 1.0
CZ B:ARG259 4.6 22.3 1.0
CB A:ASP235 4.7 23.1 1.0
CG B:GLN257 4.7 20.9 1.0
CA B:GLN257 4.7 19.9 1.0
C A:ASP262 4.8 20.3 1.0
N A:ASP235 4.8 18.6 1.0
CB B:GLN257 4.9 22.0 1.0
O B:CYS256 5.0 21.7 1.0

Calcium binding site 2 out of 8 in 5vol

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Calcium binding site 2 out of 8 in the BACINT_04212 Ferulic Acid Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of BACINT_04212 Ferulic Acid Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:29.2
occ:1.00
 OD1 B:ASP262 2.3 22.4 1.0
O B:HOH521 2.5 21.5 1.0
OD2 B:ASP234 2.5 18.4 1.0
OD1 B:ASP234 2.6 18.8 1.0
OE1 A:GLN257 2.6 21.8 1.0
O B:HOH428 2.7 24.0 1.0
OD2 B:ASP235 2.7 36.3 1.0
CG B:ASP234 2.9 20.2 1.0
CG B:ASP235 3.4 29.0 1.0
CD A:GLN257 3.5 21.9 1.0
OD1 B:ASP235 3.5 30.8 1.0
CG B:ASP262 3.6 23.5 1.0
NE2 A:GLN257 3.7 23.6 1.0
NH1 A:ARG259 3.9 20.5 1.0
O C:HOH457 4.1 19.5 1.0
N B:GLY263 4.2 20.2 1.0
CA B:ASP262 4.3 19.7 1.0
OD2 B:ASP262 4.4 22.4 1.0
CB B:ASP234 4.4 20.4 1.0
NH2 A:ARG259 4.4 18.6 1.0
CB B:ASP262 4.5 18.2 1.0
O B:HOH582 4.5 38.5 1.0
CZ A:ARG259 4.6 20.2 1.0
CA A:GLN257 4.7 19.4 1.0
CB B:ASP235 4.7 21.9 1.0
C B:ASP262 4.8 20.6 1.0
CG A:GLN257 4.8 20.8 1.0
N B:ASP235 4.9 20.9 1.0
CB A:GLN257 4.9 18.4 1.0
O A:CYS256 4.9 20.9 1.0

Calcium binding site 3 out of 8 in 5vol

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Calcium binding site 3 out of 8 in the BACINT_04212 Ferulic Acid Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of BACINT_04212 Ferulic Acid Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:30.2
occ:1.00
 OD1 C:ASP262 2.3 22.8 1.0
OD2 C:ASP234 2.4 23.2 1.0
OE1 F:GLN257 2.5 21.9 1.0
OD1 C:ASP234 2.5 21.2 1.0
O C:HOH544 2.5 24.3 1.0
OD2 C:ASP235 2.6 34.7 1.0
O C:HOH413 2.6 25.6 1.0
CG C:ASP234 2.8 22.8 1.0
CG C:ASP235 3.3 32.3 1.0
OD1 C:ASP235 3.4 32.2 1.0
CD F:GLN257 3.4 25.4 1.0
CG C:ASP262 3.6 25.3 1.0
NE2 F:GLN257 3.7 23.5 1.0
NH1 F:ARG259 3.9 21.5 1.0
O B:HOH451 4.1 21.4 1.0
N C:GLY263 4.2 22.3 1.0
CB C:ASP234 4.3 20.9 1.0
O C:HOH560 4.3 36.1 1.0
CA C:ASP262 4.4 21.4 1.0
OD2 C:ASP262 4.4 22.0 1.0
NH2 F:ARG259 4.4 24.1 1.0
CB C:ASP262 4.5 19.9 1.0
CZ F:ARG259 4.6 23.8 1.0
CB C:ASP235 4.7 25.9 1.0
CA F:GLN257 4.7 23.5 1.0
CG F:GLN257 4.8 21.7 1.0
C C:ASP262 4.8 23.0 1.0
N C:ASP235 4.8 22.6 1.0
O F:CYS256 4.9 23.6 1.0
CB F:GLN257 5.0 23.2 1.0

Calcium binding site 4 out of 8 in 5vol

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Calcium binding site 4 out of 8 in the BACINT_04212 Ferulic Acid Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of BACINT_04212 Ferulic Acid Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:29.8
occ:1.00
 OD1 D:ASP262 2.4 25.0 1.0
O D:HOH558 2.5 22.4 1.0
O D:HOH451 2.5 26.1 1.0
OE1 E:GLN257 2.6 21.8 1.0
OD2 D:ASP235 2.6 34.4 1.0
OD2 D:ASP234 2.6 21.5 1.0
OD1 D:ASP234 2.6 21.3 1.0
CG D:ASP234 3.0 22.2 1.0
CG D:ASP235 3.3 32.1 1.0
OD1 D:ASP235 3.3 28.4 1.0
CD E:GLN257 3.4 25.0 1.0
CG D:ASP262 3.6 24.9 1.0
NE2 E:GLN257 3.7 24.8 1.0
NH1 E:ARG259 4.0 21.4 1.0
O G:HOH460 4.1 26.1 1.0
N D:GLY263 4.1 23.8 1.0
O D:HOH572 4.2 39.0 1.0
OD2 D:ASP262 4.4 28.2 1.0
CA D:ASP262 4.4 22.1 1.0
CB D:ASP234 4.5 19.8 1.0
NH2 E:ARG259 4.5 23.1 1.0
CB D:ASP262 4.5 22.9 1.0
CB D:ASP235 4.7 24.0 1.0
CZ E:ARG259 4.7 23.7 1.0
CA E:GLN257 4.8 20.2 1.0
C D:ASP262 4.8 22.0 1.0
CG E:GLN257 4.8 21.2 1.0
N D:ASP235 4.9 20.3 1.0
O E:CYS256 5.0 22.1 1.0

Calcium binding site 5 out of 8 in 5vol

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Calcium binding site 5 out of 8 in the BACINT_04212 Ferulic Acid Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of BACINT_04212 Ferulic Acid Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:34.8
occ:1.00
 OD1 E:ASP262 2.4 24.4 1.0
OE1 D:GLN257 2.5 22.6 1.0
OD1 E:ASP234 2.5 22.7 1.0
O E:HOH522 2.5 27.2 1.0
OD2 E:ASP234 2.5 21.5 1.0
O E:HOH416 2.7 26.4 1.0
OD2 E:ASP235 2.8 33.7 1.0
CG E:ASP234 2.9 23.1 1.0
CD D:GLN257 3.3 26.5 1.0
CG E:ASP235 3.4 31.3 1.0
OD1 E:ASP235 3.5 29.9 1.0
NE2 D:GLN257 3.6 29.1 1.0
CG E:ASP262 3.6 24.7 1.0
NH1 D:ARG259 3.9 21.0 1.0
O H:HOH439 4.1 26.3 1.0
N E:GLY263 4.2 25.0 1.0
CA E:ASP262 4.4 21.4 1.0
CB E:ASP234 4.4 20.4 1.0
NH2 D:ARG259 4.5 23.1 1.0
OD2 E:ASP262 4.5 24.8 1.0
CB E:ASP262 4.5 22.6 1.0
CZ D:ARG259 4.6 24.4 1.0
CG D:GLN257 4.7 21.7 1.0
CB E:ASP235 4.7 24.0 1.0
CA D:GLN257 4.8 25.0 1.0
C E:ASP262 4.8 27.1 1.0
N E:ASP235 4.8 23.1 1.0
O D:CYS256 4.9 29.1 1.0

Calcium binding site 6 out of 8 in 5vol

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Calcium binding site 6 out of 8 in the BACINT_04212 Ferulic Acid Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of BACINT_04212 Ferulic Acid Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca301

b:31.1
occ:1.00
 OD1 F:ASP262 2.3 25.6 1.0
OE1 C:GLN257 2.4 22.6 1.0
O F:HOH503 2.5 22.3 1.0
OD2 F:ASP234 2.5 21.1 1.0
OD1 F:ASP234 2.6 21.7 1.0
O F:HOH426 2.6 28.8 1.0
OD2 F:ASP235 2.7 36.0 1.0
CG F:ASP234 2.9 24.4 1.0
CD C:GLN257 3.3 24.3 1.0
CG F:ASP235 3.4 30.1 1.0
OD1 F:ASP235 3.5 34.0 1.0
CG F:ASP262 3.6 24.2 1.0
NE2 C:GLN257 3.6 25.1 1.0
NH1 C:ARG259 3.9 20.7 1.0
O F:HOH433 4.0 22.4 1.0
N F:GLY263 4.2 23.5 1.0
O F:HOH532 4.3 44.2 1.0
OD2 F:ASP262 4.4 24.8 1.0
CA F:ASP262 4.4 21.9 1.0
CB F:ASP234 4.4 20.0 1.0
NH2 C:ARG259 4.4 20.7 1.0
CB F:ASP262 4.4 20.7 1.0
CZ C:ARG259 4.6 22.8 1.0
CG C:GLN257 4.7 21.5 1.0
CA C:GLN257 4.7 21.6 1.0
CB F:ASP235 4.7 28.1 1.0
C F:ASP262 4.8 22.9 1.0
N F:ASP235 4.9 23.5 1.0
CB C:GLN257 4.9 20.6 1.0
O C:CYS256 4.9 24.2 1.0

Calcium binding site 7 out of 8 in 5vol

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Calcium binding site 7 out of 8 in the BACINT_04212 Ferulic Acid Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of BACINT_04212 Ferulic Acid Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca301

b:39.0
occ:1.00
 OD1 G:ASP262 2.4 31.9 1.0
O G:HOH459 2.4 27.8 1.0
OE1 H:GLN257 2.5 30.6 1.0
O G:HOH440 2.5 34.2 1.0
OD2 G:ASP234 2.6 30.4 1.0
OD1 G:ASP234 2.7 29.3 1.0
OD2 G:ASP235 2.8 45.0 1.0
CG G:ASP234 3.0 30.9 1.0
CD H:GLN257 3.4 31.8 1.0
CG G:ASP235 3.4 41.2 1.0
OD1 G:ASP235 3.4 37.0 1.0
CG G:ASP262 3.6 34.1 1.0
NE2 H:GLN257 3.7 30.0 1.0
NH1 H:ARG259 3.9 26.8 1.0
O D:HOH458 4.1 26.9 1.0
N G:GLY263 4.1 28.9 1.0
NH2 H:ARG259 4.4 27.2 1.0
CA G:ASP262 4.4 29.9 1.0
OD2 G:ASP262 4.4 30.0 1.0
CB G:ASP234 4.5 26.2 1.0
CB G:ASP262 4.5 24.2 1.0
CZ H:ARG259 4.6 27.8 1.0
CG H:GLN257 4.7 31.0 1.0
CB G:ASP235 4.7 35.8 1.0
CA H:GLN257 4.7 30.4 1.0
C G:ASP262 4.8 30.1 1.0
N G:ASP235 4.8 32.1 1.0
O H:CYS256 4.9 30.8 1.0
CB H:GLN257 5.0 28.8 1.0

Calcium binding site 8 out of 8 in 5vol

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Calcium binding site 8 out of 8 in the BACINT_04212 Ferulic Acid Esterase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of BACINT_04212 Ferulic Acid Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca301

b:37.8
occ:1.00
 OD1 H:ASP262 2.4 29.1 1.0
OD2 H:ASP234 2.5 26.8 1.0
OE1 G:GLN257 2.5 27.8 1.0
O G:HOH518 2.5 27.3 1.0
O H:HOH423 2.6 32.3 1.0
OD1 H:ASP234 2.6 31.6 1.0
OD2 H:ASP235 2.7 39.1 1.0
CG H:ASP234 2.9 30.7 1.0
CD G:GLN257 3.4 29.6 1.0
CG H:ASP235 3.4 36.8 1.0
OD1 H:ASP235 3.5 38.6 1.0
CG H:ASP262 3.6 29.9 1.0
NE2 G:GLN257 3.6 30.1 1.0
NH1 G:ARG259 4.0 23.2 1.0
N H:GLY263 4.2 29.2 1.0
O E:HOH475 4.2 29.5 1.0
OD2 H:ASP262 4.4 28.1 1.0
CA H:ASP262 4.4 26.8 1.0
CB H:ASP234 4.4 27.2 1.0
CB H:ASP262 4.5 27.5 1.0
NH2 G:ARG259 4.5 24.9 1.0
CZ G:ARG259 4.7 27.3 1.0
CB H:ASP235 4.7 33.0 1.0
CG G:GLN257 4.8 25.7 1.0
CA G:GLN257 4.8 30.7 1.0
C H:ASP262 4.8 29.8 1.0
O G:HOH528 4.8 46.7 1.0
O G:CYS256 4.9 34.4 1.0
N H:ASP235 4.9 31.8 1.0

Reference:

D.Wefers, J.J.V.Cavalcante, R.R.Schendel, J.Deveryshetty, K.Wang, Z.Wawrzak, R.I.Mackie, N.M.Koropatkin, I.Cann. Biochemical and Structural Analyses of Two Cryptic Esterases in Bacteroides Intestinalis and Their Synergistic Activities with Cognate Xylanases. J. Mol. Biol. V. 429 2509 2017.
ISSN: ESSN 1089-8638
PubMed: 28669823
DOI: 10.1016/J.JMB.2017.06.017
Page generated: Wed Jul 9 10:51:07 2025

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