Atomistry » Calcium » PDB 5vlk-5w4t » 5vol
Atomistry »
  Calcium »
    PDB 5vlk-5w4t »
      5vol »

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

Go back to Calcium Binding Sites List in 5vol
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

Go back to Calcium Binding Sites List in 5vol
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

Go back to Calcium Binding Sites List in 5vol
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

Go back to Calcium Binding Sites List in 5vol
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

Go back to Calcium Binding Sites List in 5vol
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

Go back to Calcium Binding Sites List in 5vol
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

Go back to Calcium Binding Sites List in 5vol
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

Go back to Calcium Binding Sites List in 5vol
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: Mon Jul 15 12:34:32 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