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Calcium in PDB 1w3h: The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus

Enzymatic activity of The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus

All present enzymatic activity of The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus:
3.2.1.8;

Protein crystallography data

The structure of The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus, PDB code: 1w3h was solved by S.Andrews, E.J.Taylor, G.N.Pell, F.Vincent, V.M.A.Ducros, G.J.Davies, J.H.Lakey, H.J.Glbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.80 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.232, 95.232, 151.784, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 25.1

Calcium Binding Sites:

The binding sites of Calcium atom in the The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus (pdb code 1w3h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus, PDB code: 1w3h:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1w3h

Go back to Calcium Binding Sites List in 1w3h
Calcium binding site 1 out of 3 in the The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1347

b:28.6
occ:0.50
 CA A:CA1347 0.0 28.6 0.5
CA A:CA1347 0.6 19.7 0.5
OD1 A:ASP256 2.0 22.4 0.5
O A:ASN258 2.1 22.9 0.5
O A:ASN258 2.2 24.5 0.5
OD1 A:ASN261 2.3 25.5 0.5
OD1 A:ASP256 2.3 23.5 0.5
OD2 A:ASP256 2.4 21.4 0.5
ND2 A:ASN262 2.5 25.2 0.5
O A:HOH2252 2.5 22.9 1.0
OD1 A:ASN261 2.5 20.6 0.5
CG A:ASP256 2.5 22.8 0.5
OD2 A:ASP256 2.5 21.6 0.5
O A:ASN253 2.5 20.6 0.5
CG A:ASP256 2.7 24.9 0.5
O A:HOH2251 2.9 25.5 1.0
O A:ASN253 2.9 18.6 0.5
C A:ASN258 3.2 23.3 0.5
ND2 A:ASN262 3.4 20.9 0.5
CG A:ASN261 3.4 25.0 0.5
C A:ASN258 3.4 24.6 0.5
CG A:ASN261 3.5 24.0 0.5
CG A:ASN262 3.6 22.4 0.5
C A:ASN253 3.7 20.9 0.5
ND2 A:ASN261 3.7 22.6 0.5
ND2 A:ASN261 3.8 27.0 0.5
CA A:ASN258 3.9 23.1 0.5
N A:ASN258 3.9 23.5 0.5
CB A:ASN258 3.9 22.8 0.5
OD1 A:ASN262 4.0 22.6 0.5
CB A:ASP256 4.0 23.0 0.5
C A:ASN253 4.1 17.7 0.5
CB A:ASP256 4.2 25.0 0.5
CG A:ASN262 4.2 21.5 0.5
CA A:ASN258 4.2 24.7 0.5
CB A:ASN258 4.3 24.8 0.5
N A:SER259 4.3 23.4 0.5
OD1 A:ASN262 4.3 19.9 0.5
N A:ASN258 4.3 25.2 0.5
N A:ASN253 4.4 18.9 0.5
N A:SER259 4.4 23.8 0.5
CA A:ASN253 4.4 19.8 0.5
CB A:ASN253 4.4 19.8 0.5
CA A:SER259 4.5 22.8 0.5
N A:ASN262 4.5 22.8 0.5
C A:ASN261 4.5 23.3 0.5
N A:ASP256 4.6 23.0 0.5
CA A:SER259 4.6 23.2 0.5
CG A:ASN258 4.6 23.0 0.5
O A:ASN261 4.7 24.4 0.5
N A:PRO254 4.7 21.7 0.5
CA A:ASP256 4.7 23.2 0.5
CB A:ASN261 4.7 24.1 0.5
CB A:ASN262 4.8 22.3 0.5
CB A:ASN261 4.9 23.4 0.5
N A:ASP256 4.9 25.6 0.5
N A:ASN261 4.9 23.9 0.5
C A:ASP256 4.9 23.5 0.5
CA A:ASN262 4.9 22.0 0.5
CA A:PRO254 4.9 22.2 0.5
C A:SER259 4.9 22.9 0.5
N A:ASN253 4.9 16.3 0.5
O A:PRO254 4.9 23.3 0.5
CA A:ASN261 5.0 23.6 0.5
CA A:ASN253 5.0 16.9 0.5
CA A:ASP256 5.0 25.3 0.5
C A:PRO254 5.0 23.2 0.5
N A:GLY257 5.0 23.8 0.5

Calcium binding site 2 out of 3 in 1w3h

Go back to Calcium Binding Sites List in 1w3h
Calcium binding site 2 out of 3 in the The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1347

b:19.7
occ:0.50
 CA A:CA1347 0.0 19.7 0.5
CA A:CA1347 0.6 28.6 0.5
ND2 A:ASN262 2.0 25.2 0.5
O A:ASN253 2.3 20.6 0.5
OD1 A:ASP256 2.4 22.4 0.5
O A:ASN258 2.5 22.9 0.5
O A:HOH2251 2.5 25.5 1.0
OD1 A:ASN261 2.5 20.6 0.5
O A:HOH2252 2.5 22.9 1.0
OD1 A:ASN261 2.5 25.5 0.5
O A:ASN253 2.6 18.6 0.5
OD2 A:ASP256 2.6 21.4 0.5
OD1 A:ASP256 2.7 23.5 0.5
O A:ASN258 2.7 24.5 0.5
ND2 A:ASN262 2.8 20.9 0.5
CG A:ASP256 2.9 22.8 0.5
OD2 A:ASP256 3.1 21.6 0.5
CG A:ASP256 3.1 24.9 0.5
CG A:ASN262 3.2 22.4 0.5
C A:ASN253 3.4 20.9 0.5
CG A:ASN261 3.5 24.0 0.5
CG A:ASN261 3.6 25.0 0.5
C A:ASN258 3.6 23.3 0.5
OD1 A:ASN262 3.7 22.6 0.5
CG A:ASN262 3.7 21.5 0.5
ND2 A:ASN261 3.8 22.6 0.5
C A:ASN253 3.8 17.7 0.5
N A:ASN253 3.9 18.9 0.5
C A:ASN258 3.9 24.6 0.5
OD1 A:ASN262 3.9 19.9 0.5
ND2 A:ASN261 4.0 27.0 0.5
CA A:ASN253 4.0 19.8 0.5
CB A:ASN253 4.2 19.8 0.5
N A:ASN262 4.3 22.8 0.5
C A:ASN261 4.4 23.3 0.5
N A:PRO254 4.4 21.7 0.5
N A:ASN253 4.4 16.3 0.5
CB A:ASP256 4.4 23.0 0.5
CA A:ASN258 4.4 23.1 0.5
O A:ASN261 4.4 24.4 0.5
CB A:ASN262 4.5 22.3 0.5
CB A:ASN258 4.5 22.8 0.5
CB A:ASP256 4.5 25.0 0.5
CA A:ASN262 4.5 22.0 0.5
N A:ASN258 4.5 23.5 0.5
CA A:ASN253 4.6 16.9 0.5
N A:SER259 4.6 23.4 0.5
CA A:PRO254 4.7 22.2 0.5
N A:PRO254 4.7 18.4 0.5
CA A:SER259 4.7 23.2 0.5
CA A:SER259 4.7 22.8 0.5
CA A:ASN258 4.8 24.7 0.5
N A:SER259 4.8 23.8 0.5
CB A:ASN261 4.9 24.1 0.5
N A:ASN262 4.9 22.4 0.5
CA A:PRO254 4.9 19.0 0.5
N A:ASP256 4.9 23.0 0.5
CB A:ASN261 4.9 23.4 0.5
CB A:ASN258 4.9 24.8 0.5
CB A:ASN253 4.9 16.7 0.5
C A:ASN261 4.9 22.8 0.5
N A:ASN258 4.9 25.2 0.5
C A:PRO254 4.9 23.2 0.5
CA A:ASN261 5.0 23.6 0.5

Calcium binding site 3 out of 3 in 1w3h

Go back to Calcium Binding Sites List in 1w3h
Calcium binding site 3 out of 3 in the The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The 3-Dimensional Structure of A Thermostable Mutant of A Xylanase (XYN10A) From Cellvibrio Japonicus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1348

b:17.9
occ:1.00
 OD1 B:ASN262 2.3 19.3 1.0
OD1 B:ASP256 2.4 17.9 1.0
OD1 B:ASN261 2.4 19.6 1.0
O B:HOH2248 2.4 17.9 1.0
O B:ASN258 2.4 17.4 1.0
O B:HOH2239 2.5 18.0 1.0
OD2 B:ASP256 2.6 18.3 1.0
O B:ASN253 2.6 18.5 1.0
CG B:ASP256 2.8 19.9 1.0
CG B:ASN261 3.4 23.1 1.0
CG B:ASN262 3.4 20.2 1.0
C B:ASN258 3.6 18.9 1.0
C B:ASN253 3.7 18.9 1.0
ND2 B:ASN261 3.7 23.4 1.0
ND2 B:ASN262 3.9 17.4 1.0
CB B:ASP256 4.3 18.7 1.0
N B:ASN253 4.3 18.4 1.0
CA B:ASN253 4.4 18.8 1.0
CA B:ASN258 4.4 18.4 1.0
N B:SER259 4.5 18.4 1.0
N B:ASN258 4.5 17.6 1.0
CB B:ASN253 4.5 20.3 1.0
CA B:SER259 4.5 19.8 1.0
CB B:ASN258 4.6 19.2 1.0
C B:ASN261 4.6 21.2 1.0
N B:ASN262 4.6 19.7 1.0
O B:HOH2246 4.7 23.9 1.0
CB B:ASN262 4.7 19.9 1.0
CB B:ASN261 4.7 21.9 1.0
O B:ASN261 4.7 24.6 1.0
N B:PRO254 4.8 18.1 0.5
N B:PRO254 4.8 19.6 0.5
N B:ASP256 4.9 18.6 1.0
O B:HOH2237 4.9 33.0 1.0
CA B:ASN262 4.9 19.1 1.0
N B:ASN261 5.0 22.0 1.0
CA B:PRO254 5.0 20.0 0.5
CA B:ASN261 5.0 22.1 1.0
C B:PRO254 5.0 17.6 0.5

Reference:

S.Andrews, E.J.Taylor, G.N.Pell, F.Vincent, V.M.A.Ducros, G.J.Davies, J.H.Lakey, H.J.Gilbert. The Use of Forced Protein Evolution to Investigate and Improve Stability of Family 10 Xylanases: the Production of CA2+-Independent Stable Xylanases J.Biol.Chem. V. 279 54369 2004.
ISSN: ISSN 0021-9258
PubMed: 15452124
DOI: 10.1074/JBC.M409044200
Page generated: Tue Jul 8 03:06:49 2025

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