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Calcium in PDB 3axe: The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Complex with Cellotetraose (Cellobiose Density Was Observed)

Enzymatic activity of The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Complex with Cellotetraose (Cellobiose Density Was Observed)

All present enzymatic activity of The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Complex with Cellotetraose (Cellobiose Density Was Observed):
3.2.1.73;

Protein crystallography data

The structure of The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Complex with Cellotetraose (Cellobiose Density Was Observed), PDB code: 3axe 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 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.091, 70.404, 76.589, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.1

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 Complex with Cellotetraose (Cellobiose Density Was Observed) (pdb code 3axe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Complex with Cellotetraose (Cellobiose Density Was Observed), PDB code: 3axe:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3axe

Go back to Calcium Binding Sites List in 3axe
Calcium binding site 1 out of 4 in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Complex with Cellotetraose (Cellobiose Density Was Observed)


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 Complex with Cellotetraose (Cellobiose Density Was Observed) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3001

b:14.7
occ:1.00
 O A:PHE152 2.3 14.1 1.0
O A:HOH324 2.4 16.6 1.0
O A:HOH311 2.4 16.4 1.0
O A:HOH368 2.4 18.0 1.0
OE2 A:GLU154 2.5 15.6 1.0
OE1 A:GLU154 2.5 15.0 1.0
CD A:GLU154 2.9 13.0 1.0
C A:PHE152 3.5 14.3 1.0
O A:HOH392 4.2 20.6 1.0
CA A:PHE152 4.2 14.4 1.0
CB A:PHE152 4.2 14.3 1.0
N A:PHE152 4.4 14.2 1.0
CG A:GLU154 4.4 13.3 1.0
N A:ASP153 4.5 13.2 1.0
O A:HOH315 4.6 18.6 1.0
O A:HOH394 4.6 27.6 1.0
N A:GLU154 4.6 12.1 1.0
CA A:ASP153 4.7 14.4 1.0
OE1 A:GLN151 4.7 25.5 1.0
O A:HOH409 4.9 30.3 1.0
CG A:PHE152 4.9 14.2 1.0

Calcium binding site 2 out of 4 in 3axe

Go back to Calcium Binding Sites List in 3axe
Calcium binding site 2 out of 4 in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Complex with Cellotetraose (Cellobiose Density Was Observed)


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 Complex with Cellotetraose (Cellobiose Density Was Observed) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3002

b:13.6
occ:1.00
 O A:GLY222 2.3 16.5 1.0
O A:HOH351 2.3 21.9 1.0
OD1 A:ASN164 2.4 16.1 1.0
O A:ASN189 2.4 16.2 1.0
O A:HOH426 2.4 22.1 1.0
O A:ASN164 2.5 12.5 1.0
O A:HOH318 2.5 19.0 1.0
C A:GLY222 3.4 16.4 1.0
CG A:ASN164 3.5 13.4 1.0
C A:ASN189 3.5 17.7 1.0
C A:ASN164 3.5 11.5 1.0
CA A:GLY222 3.9 17.2 1.0
CA A:ASN164 4.0 11.9 1.0
CA A:ASN189 4.1 17.9 1.0
CB A:ASN189 4.2 23.4 1.0
O A:HOH576 4.3 44.4 1.0
CB A:ASN164 4.3 13.1 1.0
ND2 A:ASN164 4.4 15.9 1.0
N A:MET223 4.5 15.2 1.0
O A:HOH397 4.6 27.0 1.0
N A:PHE190 4.6 15.7 1.0
N A:TRP165 4.6 10.9 1.0
CB A:PHE190 4.8 15.9 1.0
OD1 A:ASP191 4.8 32.5 1.0
CB A:TRP165 4.9 12.6 1.0
O A:HOH531 4.9 29.4 1.0
CA A:MET223 4.9 16.1 1.0
C A:PHE190 4.9 19.1 1.0
CA A:PHE190 4.9 16.6 1.0

Calcium binding site 3 out of 4 in 3axe

Go back to Calcium Binding Sites List in 3axe
Calcium binding site 3 out of 4 in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Complex with Cellotetraose (Cellobiose Density Was Observed)


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 Complex with Cellotetraose (Cellobiose Density Was Observed) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3003

b:20.3
occ:1.00
 O A:LYS200 2.2 12.8 1.0
O A:HOH468 2.3 25.7 1.0
O A:HOH369 2.4 26.6 1.0
OD1 A:ASP202 2.4 21.9 1.0
O A:HOH470 2.5 34.7 1.0
O A:HOH469 2.7 30.3 1.0
C A:LYS200 3.4 12.6 1.0
CG A:ASP202 3.6 20.1 1.0
CB A:ASP202 4.1 16.9 1.0
N A:ASP202 4.2 13.0 1.0
N A:LYS200 4.2 11.7 1.0
CA A:LYS200 4.2 10.4 1.0
C A:GLY201 4.4 13.2 1.0
N A:GLY201 4.4 12.2 1.0
CB A:LYS200 4.4 13.0 1.0
CA A:GLY201 4.4 13.0 1.0
OH A:TYR13 4.5 15.9 1.0
OD2 A:ASP214 4.6 23.5 1.0
OD2 A:ASP202 4.6 21.4 1.0
CA A:ASP202 4.8 13.8 1.0
O A:HOH407 4.8 34.9 1.0
CB A:ASP214 4.9 16.1 1.0
O A:GLY201 5.0 15.0 1.0

Calcium binding site 4 out of 4 in 3axe

Go back to Calcium Binding Sites List in 3axe
Calcium binding site 4 out of 4 in the The Truncated Fibrobacter Succinogenes 1,3-1,4-Beta-D-Glucanase V18Y/W203Y in Complex with Cellotetraose (Cellobiose Density Was Observed)


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 Complex with Cellotetraose (Cellobiose Density Was Observed) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3004

b:28.2
occ:1.00
 O A:HOH386 2.1 31.2 1.0
O A:HOH601 2.2 29.8 1.0
OD1 A:ASP185 2.3 24.4 1.0
O A:HOH600 2.4 40.4 1.0
O A:HOH436 2.5 31.2 1.0
O A:ASP185 2.5 17.6 1.0
C A:ASP185 3.5 17.1 1.0
CG A:ASP185 3.5 22.4 1.0
O A:HOH490 3.8 33.8 1.0
CA A:ASP185 3.9 17.0 1.0
O A:HOH450 4.2 41.5 1.0
CB A:ASP185 4.3 18.0 1.0
OD2 A:ASP185 4.5 26.2 1.0
O A:HOH530 4.6 39.0 1.0
N A:TRP186 4.6 15.2 1.0
NZ A:LYS170 4.6 37.3 1.0
CB A:TRP186 4.8 16.5 1.0
CA A:TRP186 5.0 14.2 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 08:02:37 2024

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