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Calcium in PDB 7xrv: Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate

Protein crystallography data

The structure of Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate, PDB code: 7xrv was solved by G.M.Du, Y.L.Wang, F.J.Xin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 109.86 / 2.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 146.854, 153.548, 165.548, 90, 90, 90
R / Rfree (%) 17.9 / 22.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate (pdb code 7xrv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate, PDB code: 7xrv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 7xrv

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Calcium binding site 1 out of 10 in the Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:48.5
occ:0.00
 OD2 A:ASP235 2.2 100.2 1.0
OE2 B:GLU257 2.3 78.2 1.0
OE1 B:GLU257 2.4 76.2 1.0
OD1 A:ASP262 2.5 57.5 1.0
CD B:GLU257 2.6 72.0 1.0
CG A:ASP235 3.0 88.2 1.0
OD1 A:ASP235 3.0 92.6 1.0
CG A:ASP262 3.7 61.8 1.0
OD1 A:ASP234 3.7 47.1 1.0
OD2 A:ASP234 3.9 57.7 1.0
CG B:GLU257 4.2 51.6 1.0
OD2 A:ASP262 4.2 66.0 1.0
CG A:ASP234 4.3 45.3 1.0
CB A:ASP235 4.5 63.1 1.0
NH2 B:ARG259 4.8 48.5 1.0
CB A:ASP262 4.9 36.9 1.0

Calcium binding site 2 out of 10 in 7xrv

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Calcium binding site 2 out of 10 in the Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:39.0
occ:0.00
 OD2 B:ASP235 2.2 88.2 1.0
OE2 A:GLU257 2.2 64.9 1.0
OD1 B:ASP235 2.4 95.3 1.0
OE1 A:GLU257 2.5 62.4 1.0
CD A:GLU257 2.6 56.2 1.0
CG B:ASP235 2.6 90.6 1.0
OD2 B:ASP234 2.7 60.9 1.0
OD1 B:ASP262 2.9 61.5 1.0
OD1 B:ASP234 3.0 56.9 1.0
CG B:ASP234 3.2 50.7 1.0
CG A:GLU257 4.0 30.7 1.0
CG B:ASP262 4.1 65.4 1.0
CB B:ASP235 4.1 71.5 1.0
NH1 A:ARG259 4.4 29.2 1.0
O B:HOH412 4.4 42.3 1.0
N B:ASP235 4.5 40.7 1.0
CA A:GLU257 4.6 30.6 1.0
CB A:GLU257 4.6 27.3 1.0
CB B:ASP234 4.7 40.6 1.0
O A:HIS256 4.7 51.0 1.0
CA B:ASP235 4.8 50.6 1.0
OD2 B:ASP262 4.8 65.4 1.0
NH2 A:ARG259 4.8 38.0 1.0
C B:ASP234 5.0 40.3 1.0
CA B:ASP262 5.0 54.0 1.0
N B:GLY263 5.0 44.1 1.0

Calcium binding site 3 out of 10 in 7xrv

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Calcium binding site 3 out of 10 in the Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:51.3
occ:0.00
 OE1 E:GLU257 2.3 66.7 1.0
OD2 C:ASP235 2.4 110.7 1.0
CG C:ASP235 3.2 101.4 1.0
OD1 C:ASP235 3.4 112.4 1.0
CD E:GLU257 3.4 59.0 1.0
OE2 E:GLU257 3.9 60.6 1.0
OD1 C:ASP262 4.0 57.0 1.0
CB C:ASP235 4.5 67.5 1.0
CG E:GLU257 4.7 28.9 1.0

Calcium binding site 4 out of 10 in 7xrv

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Calcium binding site 4 out of 10 in the Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:32.8
occ:0.00
 OD2 D:ASP235 2.2 86.7 1.0
OE1 G:GLU257 2.3 63.8 1.0
OE2 G:GLU257 2.3 62.3 1.0
OD1 D:ASP235 2.4 90.4 1.0
OD1 D:ASP262 2.4 64.9 1.0
CD G:GLU257 2.6 57.3 1.0
CG D:ASP235 2.6 84.5 1.0
OD1 D:ASP234 3.0 54.5 1.0
OD2 D:ASP234 3.1 60.7 1.0
CG D:ASP234 3.4 46.4 1.0
CG D:ASP262 3.6 61.8 1.0
CG G:GLU257 4.0 42.9 1.0
CB D:ASP235 4.1 64.1 1.0
OD2 D:ASP262 4.2 65.6 1.0
NH1 G:ARG259 4.3 32.8 1.0
CA G:GLU257 4.5 36.2 1.0
N D:ASP235 4.6 47.5 1.0
O G:HIS256 4.6 49.1 1.0
CB G:GLU257 4.7 35.1 1.0
NH2 G:ARG259 4.7 35.5 1.0
CB D:ASP262 4.8 44.0 1.0
CA D:ASP235 4.8 51.8 1.0
CB D:ASP234 4.9 42.8 1.0
CA D:ASP262 4.9 44.1 1.0
CZ G:ARG259 5.0 37.0 1.0

Calcium binding site 5 out of 10 in 7xrv

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Calcium binding site 5 out of 10 in the Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:28.9
occ:0.00
 OD1 E:ASP235 2.3 93.2 1.0
OE1 C:GLU257 2.3 67.7 1.0
OD2 E:ASP235 2.3 86.6 1.0
OE2 C:GLU257 2.5 68.1 1.0
CD C:GLU257 2.5 63.7 1.0
OD2 E:ASP234 2.6 63.2 1.0
CG E:ASP235 2.6 88.5 1.0
CG E:ASP234 3.3 53.4 1.0
OD1 E:ASP234 3.4 59.8 1.0
OD1 E:ASP262 3.8 62.2 1.0
CG C:GLU257 3.8 30.5 1.0
O C:HIS256 3.9 48.2 1.0
CB E:ASP235 4.2 73.8 1.0
CA C:GLU257 4.2 27.9 1.0
CB C:GLU257 4.4 26.7 1.0
NH1 C:ARG259 4.5 40.2 1.0
N E:ASP235 4.6 37.3 1.0
C C:HIS256 4.7 35.8 1.0
CB E:ASP234 4.7 33.3 1.0
NH2 C:ARG259 4.7 32.7 1.0
N C:GLU257 4.8 34.9 1.0
CA E:ASP235 4.8 54.0 1.0
C E:ASP234 4.9 43.8 1.0
CG E:ASP262 4.9 57.6 1.0

Calcium binding site 6 out of 10 in 7xrv

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Calcium binding site 6 out of 10 in the Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca301

b:38.2
occ:0.00
 OD2 F:ASP235 2.1 85.3 1.0
OE2 H:GLU257 2.2 66.6 1.0
OD1 F:ASP234 2.3 53.0 1.0
OD1 F:ASP262 2.4 59.9 1.0
OE1 H:GLU257 2.4 61.5 1.0
OD2 F:ASP234 2.5 51.5 1.0
CD H:GLU257 2.6 60.8 1.0
CG F:ASP234 2.7 45.7 1.0
CG F:ASP235 2.7 84.2 1.0
OD1 F:ASP235 3.0 88.0 1.0
CG F:ASP262 3.6 55.5 1.0
CB F:ASP235 4.0 70.5 1.0
NH1 H:ARG259 4.1 51.3 1.0
N F:ASP235 4.1 46.7 1.0
CG H:GLU257 4.1 34.0 1.0
CB F:ASP234 4.2 32.3 1.0
CA F:ASP262 4.3 42.7 1.0
O F:HOH454 4.3 38.4 1.0
N F:GLY263 4.3 34.6 1.0
NH2 H:ARG259 4.4 34.8 1.0
CB F:ASP262 4.4 42.8 1.0
OD2 F:ASP262 4.4 58.5 1.0
C F:ASP234 4.5 48.2 1.0
CA F:ASP235 4.6 56.4 1.0
CZ H:ARG259 4.7 34.1 1.0
CB H:GLU257 4.8 32.5 1.0
CA H:GLU257 4.8 40.8 1.0
CA F:ASP234 4.8 34.5 1.0
C F:ASP262 4.8 47.2 1.0
O F:GLY263 4.9 39.4 1.0
O H:HIS256 5.0 49.0 1.0

Calcium binding site 7 out of 10 in 7xrv

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Calcium binding site 7 out of 10 in the Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca301

b:28.9
occ:0.00
 OD2 G:ASP235 1.7 94.3 1.0
OE2 D:GLU257 2.2 55.7 1.0
OD1 G:ASP262 2.4 66.8 1.0
CG G:ASP235 2.6 90.1 1.0
OD1 G:ASP235 2.8 97.7 1.0
OD1 G:ASP234 2.9 38.6 1.0
CD D:GLU257 3.0 56.5 1.0
OE1 D:GLU257 3.1 59.6 1.0
OD2 G:ASP234 3.3 38.4 1.0
CG G:ASP234 3.5 38.7 1.0
CG G:ASP262 3.6 61.4 1.0
CB G:ASP235 4.0 67.8 1.0
OD2 G:ASP262 4.3 67.1 1.0
CG D:GLU257 4.5 30.4 1.0
NH1 D:ARG259 4.6 32.6 1.0
N G:ASP235 4.6 48.0 1.0
CB G:ASP262 4.7 56.9 1.0
CA G:ASP262 4.7 48.0 1.0
N G:GLY263 4.7 45.4 1.0
NH2 D:ARG259 4.8 35.3 1.0
CA G:ASP235 4.9 53.7 1.0
CA D:GLU257 5.0 27.3 1.0
CB D:GLU257 5.0 28.2 1.0

Calcium binding site 8 out of 10 in 7xrv

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Calcium binding site 8 out of 10 in the Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca301

b:47.3
occ:0.00
 OD2 H:ASP235 2.1 91.3 1.0
OE2 F:GLU257 2.2 76.3 1.0
OD1 H:ASP262 2.4 66.7 1.0
OE1 F:GLU257 2.5 79.3 1.0
OD1 H:ASP234 2.5 44.0 1.0
OD2 H:ASP234 2.5 50.9 1.0
CD F:GLU257 2.6 68.7 1.0
CG H:ASP235 2.7 82.4 1.0
OD1 H:ASP235 2.7 87.7 1.0
CG H:ASP234 2.9 43.1 1.0
CG H:ASP262 3.6 63.9 1.0
O F:HOH433 3.8 45.5 1.0
CG F:GLU257 4.0 41.7 1.0
NH1 F:ARG259 4.0 35.1 1.0
CB H:ASP235 4.1 54.5 1.0
N H:ASP235 4.3 45.0 1.0
OD2 H:ASP262 4.4 71.8 1.0
CB H:ASP234 4.4 36.6 1.0
NH2 F:ARG259 4.5 34.5 1.0
CA F:GLU257 4.5 29.8 1.0
CB F:GLU257 4.5 32.7 1.0
CB H:ASP262 4.6 53.5 1.0
CA H:ASP262 4.6 39.1 1.0
CZ F:ARG259 4.7 35.8 1.0
N H:GLY263 4.8 37.5 1.0
CA H:ASP235 4.8 48.1 1.0
C H:ASP234 4.8 35.8 1.0
O F:HIS256 4.8 41.0 1.0

Calcium binding site 9 out of 10 in 7xrv

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Calcium binding site 9 out of 10 in the Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca301

b:39.3
occ:0.00
 OD2 I:ASP235 2.0 85.7 1.0
OE2 J:GLU257 2.1 64.5 1.0
OD1 I:ASP262 2.2 59.8 1.0
OE1 J:GLU257 2.2 66.8 1.0
CD J:GLU257 2.5 61.3 1.0
CG I:ASP235 2.8 83.7 1.0
OD1 I:ASP235 2.8 85.7 1.0
CG I:ASP262 3.3 58.2 1.0
OD1 I:ASP234 3.4 43.1 1.0
OD2 I:ASP234 3.5 51.5 1.0
OD2 I:ASP262 3.8 60.1 1.0
CG I:ASP234 3.9 40.0 1.0
CG J:GLU257 4.1 40.4 1.0
CB I:ASP235 4.3 64.3 1.0
NH2 J:ARG259 4.5 40.6 1.0
CB I:ASP262 4.6 48.4 1.0
NH1 J:ARG259 4.6 31.0 1.0
N I:GLY263 4.7 32.6 1.0
CA I:ASP262 4.8 46.9 1.0
N I:ASP235 5.0 43.1 1.0
CZ J:ARG259 5.0 39.5 1.0
CB J:GLU257 5.0 35.9 1.0

Calcium binding site 10 out of 10 in 7xrv

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Calcium binding site 10 out of 10 in the Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Bacteroides Thetaiotaomicron Ferulic Acid Esterase - S150A (BT_4077- S150A) Complex with Trans-Methylferulate within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca303

b:49.1
occ:0.00
 OE1 I:GLU257 2.2 74.1 1.0
OD2 J:ASP235 2.3 97.4 1.0
OE2 I:GLU257 2.6 73.5 1.0
CD I:GLU257 2.8 62.6 1.0
OD1 J:ASP262 3.1 53.7 1.0
CG J:ASP235 3.4 96.0 1.0
OD1 J:ASP235 3.8 103.0 1.0
CG J:ASP262 4.1 49.4 1.0
CG I:GLU257 4.3 38.8 1.0
OD2 J:ASP262 4.4 60.3 1.0
OD1 J:ASP234 4.5 33.1 1.0
CB J:ASP235 4.7 77.2 1.0
OD2 J:ASP234 4.8 51.3 1.0
NH2 I:ARG259 4.8 58.6 1.0

Reference:

G.M.Du, Y.L.Wang, F.J.Xin. Insights Into the Regulatory Mechanism of Btfae Activity By Oligomerization and A Distinct Substrate Binding Pocket Adjacent to the Active Site To Be Published.
Page generated: Thu Dec 28 01:32:25 2023

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