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Calcium in PDB 3axd: The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form

Enzymatic activity of The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form

All present enzymatic activity of The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form:
3.2.1.73;

Protein crystallography data

The structure of The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form, PDB code: 3axd was solved by J.W.Huang, Y.S.Cheng, T.P.Ko, C.Y.Lin, H.L.Lai, C.C.Chen, Y.Ma, C.H.Huang, Y.Zheng, J.R.Liu, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.53
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.391, 69.963, 81.242, 90.00, 100.98, 90.00
R / Rfree (%) 17.3 / 19.3

Calcium Binding Sites:

The binding sites of Calcium atom in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form (pdb code 3axd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form, PDB code: 3axd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3axd

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Calcium binding site 1 out of 8 in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3001

b:13.4
occ:1.00
 O A:PHE152 2.3 12.1 1.0
O A:HOH301 2.4 13.9 1.0
O A:HOH303 2.4 18.8 1.0
OE2 A:GLU154 2.5 13.2 1.0
O A:HOH302 2.5 14.6 1.0
OE1 A:GLU154 2.6 11.7 1.0
CD A:GLU154 2.9 10.2 1.0
C A:PHE152 3.5 11.3 1.0
O A:HOH561 3.9 24.4 1.0
CA A:PHE152 4.2 10.7 1.0
CB A:PHE152 4.3 11.9 1.0
N A:PHE152 4.4 10.6 1.0
CG A:GLU154 4.4 10.8 1.0
O A:HOH377 4.5 15.5 1.0
N A:ASP153 4.6 10.9 1.0
O A:HOH897 4.6 28.9 1.0
O A:HOH689 4.7 22.6 1.0
N A:GLU154 4.7 11.0 1.0
CA A:ASP153 4.8 11.5 1.0
O A:HOH663 4.8 32.5 1.0
O A:HOH840 4.8 30.9 1.0
OE1 A:GLN151 4.9 23.6 1.0
CG A:PHE152 5.0 12.1 1.0

Calcium binding site 2 out of 8 in 3axd

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Calcium binding site 2 out of 8 in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3002

b:8.4
occ:1.00
 O A:HOH305 2.3 13.0 1.0
O A:GLY222 2.3 11.5 1.0
O A:ASN189 2.4 10.2 1.0
O A:HOH306 2.4 16.1 1.0
O A:ASN164 2.4 8.9 1.0
OD1 A:ASN164 2.4 10.5 1.0
O A:HOH304 2.5 13.7 1.0
C A:GLY222 3.4 12.0 1.0
C A:ASN164 3.5 8.5 1.0
C A:ASN189 3.5 8.5 1.0
CG A:ASN164 3.5 8.4 1.0
CA A:GLY222 3.9 13.3 1.0
CA A:ASN164 4.0 6.6 1.0
CA A:ASN189 4.1 7.5 1.0
CB A:ASN189 4.2 10.6 1.0
CB A:ASN164 4.3 7.2 1.0
CG A:MET223 4.4 19.5 1.0
ND2 A:ASN164 4.5 11.1 1.0
N A:MET223 4.5 11.7 1.0
N A:PHE190 4.6 8.7 1.0
N A:TRP165 4.6 7.3 1.0
CB A:PHE190 4.7 9.5 1.0
O A:HOH556 4.8 34.8 1.0
CA A:MET223 4.8 10.9 1.0
OD1 A:ASP191 4.8 20.5 1.0
CB A:TRP165 4.8 7.9 1.0
C A:PHE190 4.9 11.8 1.0
CA A:PHE190 4.9 9.9 1.0

Calcium binding site 3 out of 8 in 3axd

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Calcium binding site 3 out of 8 in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3003

b:17.3
occ:1.00
 O A:LYS200 2.2 12.0 1.0
OD1 A:ASP202 2.3 18.8 1.0
O A:HOH307 2.4 23.9 1.0
O A:HOH887 2.4 29.3 1.0
O A:HOH991 2.5 31.4 1.0
O A:HOH308 2.5 23.5 1.0
O A:HOH309 2.8 23.1 1.0
C A:LYS200 3.4 11.6 1.0
CG A:ASP202 3.4 16.2 1.0
O A:HOH985 3.7 37.1 1.0
CB A:ASP202 4.1 13.3 1.0
N A:LYS200 4.2 10.6 1.0
CA A:LYS200 4.2 10.1 1.0
N A:ASP202 4.3 11.8 1.0
CB A:LYS200 4.3 11.8 1.0
O A:HOH668 4.4 35.4 1.0
C A:GLY201 4.4 12.4 1.0
N A:GLY201 4.4 10.3 1.0
OD2 A:ASP202 4.5 19.0 1.0
OH A:TYR13 4.5 13.1 1.0
CA A:GLY201 4.5 11.5 1.0
OD2 A:ASP214 4.8 19.6 1.0
CB A:ASP214 4.8 16.0 1.0
CA A:ASP202 4.8 12.9 1.0
O A:HOH711 4.8 25.9 1.0
O A:GLY201 4.8 11.8 1.0

Calcium binding site 4 out of 8 in 3axd

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Calcium binding site 4 out of 8 in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3004

b:24.0
occ:1.00
 OD1 A:ASP185 2.3 18.9 1.0
O A:HOH311 2.4 36.4 1.0
O A:HOH310 2.4 33.4 1.0
O A:ASP185 2.5 11.8 1.0
C A:ASP185 3.4 10.5 1.0
CG A:ASP185 3.6 18.0 1.0
CA A:ASP185 3.8 11.2 1.0
O A:HOH957 4.1 37.2 1.0
CB A:ASP185 4.3 14.5 1.0
N A:TRP186 4.5 9.4 1.0
OD2 A:ASP185 4.5 20.9 1.0
NZ A:LYS170 4.7 29.8 1.0
CB A:TRP186 4.8 8.8 1.0
CA A:TRP186 4.9 8.2 1.0

Calcium binding site 5 out of 8 in 3axd

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Calcium binding site 5 out of 8 in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3005

b:25.7
occ:1.00
 O A:HOH654 2.2 26.3 1.0
O A:HOH948 2.3 34.4 1.0
O A:HOH989 2.3 22.1 1.0
O A:MET4 2.3 20.1 1.0
OD1 A:ASP6 2.5 17.9 1.0
O A:HOH946 2.7 28.5 1.0
C A:MET4 3.4 19.1 1.0
CG A:ASP6 3.6 14.1 1.0
OD2 A:ASP6 4.1 16.0 1.0
C A:LYS5 4.1 12.1 1.0
O A:LYS5 4.2 13.2 1.0
CA A:MET4 4.3 22.2 1.0
N A:LYS5 4.3 15.3 1.0
CA A:LYS5 4.4 13.5 1.0
N A:ASP6 4.5 11.2 1.0
CB A:ASP6 4.8 13.1 1.0
CA A:ASP6 4.9 11.5 1.0
CB A:MET4 5.0 27.1 1.0

Calcium binding site 6 out of 8 in 3axd

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Calcium binding site 6 out of 8 in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3006

b:24.8
occ:1.00
 O A:HOH874 2.3 32.8 1.0
OD1 A:ASN129 2.3 13.2 1.0
O A:HOH876 2.4 28.1 1.0
O A:HOH873 2.5 39.8 1.0
O A:HOH682 2.7 33.9 1.0
O A:HOH875 2.8 28.3 1.0
CG A:ASN129 3.4 11.7 1.0
ND2 A:ASN129 3.9 14.0 1.0
CB A:ASN129 4.7 8.9 1.0
O A:SER128 4.8 10.2 1.0
O A:HOH532 4.8 35.8 1.0
CA A:ASN129 4.9 8.6 1.0

Calcium binding site 7 out of 8 in 3axd

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Calcium binding site 7 out of 8 in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4002

b:7.6
occ:1.00
 O B:GLY222 2.3 9.7 1.0
OD1 B:ASN164 2.4 10.2 1.0
O B:ASN189 2.4 8.0 1.0
O B:ASN164 2.4 7.5 1.0
O B:HOH312 2.4 7.2 1.0
O B:HOH313 2.4 10.2 1.0
O B:HOH314 2.5 9.6 1.0
C B:GLY222 3.4 10.1 1.0
C B:ASN164 3.4 6.4 1.0
C B:ASN189 3.5 7.7 1.0
CG B:ASN164 3.5 9.6 1.0
CA B:GLY222 3.9 10.9 1.0
CA B:ASN164 3.9 6.7 1.0
CA B:ASN189 4.0 8.7 1.0
CB B:ASN189 4.1 9.9 1.0
CB B:ASN164 4.3 7.9 1.0
O B:HOH445 4.5 18.2 1.0
ND2 B:ASN164 4.5 11.5 1.0
N B:MET223 4.5 8.8 1.0
N B:TRP165 4.6 4.9 1.0
O B:HOH386 4.6 14.5 1.0
N B:PHE190 4.6 7.3 1.0
OD1 B:ASN189 4.7 10.3 1.0
CB B:PHE190 4.8 8.3 1.0
CB B:TRP165 4.8 7.6 1.0
CA B:MET223 4.9 8.7 1.0
OD1 B:ASP191 4.9 12.9 1.0
C B:PHE190 4.9 8.5 1.0
O B:PHE190 4.9 12.6 1.0
CG B:ASN189 4.9 9.3 1.0
CA B:PHE190 5.0 8.9 1.0
O B:HOH446 5.0 21.4 1.0
CA B:TRP165 5.0 7.1 1.0

Calcium binding site 8 out of 8 in 3axd

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Calcium binding site 8 out of 8 in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Apo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4003

b:13.2
occ:1.00
 O B:LYS200 2.2 9.0 1.0
OD1 B:ASP202 2.3 15.8 1.0
O B:HOH317 2.3 23.8 1.0
O B:HOH316 2.4 19.8 1.0
O B:HOH315 2.4 19.8 1.0
O B:HOH862 2.4 18.2 1.0
O B:HOH318 2.5 17.1 1.0
C B:LYS200 3.5 8.9 1.0
CG B:ASP202 3.5 12.5 1.0
CB B:ASP202 4.2 12.4 1.0
N B:LYS200 4.2 8.6 1.0
CA B:LYS200 4.3 8.2 1.0
O B:HOH739 4.3 26.8 1.0
CB B:LYS200 4.3 7.8 1.0
N B:ASP202 4.3 10.9 1.0
C B:GLY201 4.4 10.5 1.0
N B:GLY201 4.5 9.5 1.0
O B:HOH863 4.5 42.0 1.0
OD2 B:ASP202 4.5 13.0 1.0
CA B:GLY201 4.6 9.8 1.0
OH B:TYR13 4.6 12.2 1.0
OD2 B:ASP214 4.6 15.1 1.0
CB B:ASP214 4.7 9.2 1.0
O B:HOH885 4.8 23.1 1.0
O B:HOH478 4.8 23.8 1.0
CA B:ASP202 4.9 11.1 1.0
O B:GLY201 4.9 10.3 1.0

Reference:

J.W.Huang, Y.S.Cheng, T.P.Ko, C.Y.Lin, H.L.Lai, C.C.Chen, Y.Ma, Y.Zheng, C.H.Huang, P.Zou, J.R.Liu, R.T.Guo. Rational Design to Improve Thermostability and Specific Activity of the Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase Appl.Microbiol.Biotechnol. V. 94 111 2012.
ISSN: ISSN 0175-7598
PubMed: 21959377
DOI: 10.1007/S00253-011-3586-7
Page generated: Sat Jul 13 08:02:21 2024

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