Atomistry » Calcium » PDB 3atj-3b1t » 3axd
Atomistry »
  Calcium »
    PDB 3atj-3b1t »
      3axd »

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

Go back to Calcium Binding Sites List in 3axd
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

Go back to Calcium Binding Sites List in 3axd
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

Go back to Calcium Binding Sites List in 3axd
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

Go back to Calcium Binding Sites List in 3axd
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

Go back to Calcium Binding Sites List in 3axd
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

Go back to Calcium Binding Sites List in 3axd
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

Go back to Calcium Binding Sites List in 3axd
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

Go back to Calcium Binding Sites List in 3axd
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: Tue Jul 8 10:57:33 2025

Last articles

Mg in 6XLC
Mg in 6XL9
Mg in 6XIM
Mg in 6XL5
Mg in 6XL4
Mg in 6XKI
Mg in 6XJU
Mg in 6XJT
Mg in 6XJS
Mg in 6XJR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy