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Calcium in PDB 4rhh: Crystal Structure of the Catalytic Mutant XYN52B2-E335G, A GH52 Beta- D-Xylosidase From Geobacillus Stearothermophilus T6

Protein crystallography data

The structure of Crystal Structure of the Catalytic Mutant XYN52B2-E335G, A GH52 Beta- D-Xylosidase From Geobacillus Stearothermophilus T6, PDB code: 4rhh was solved by R.Dann, S.Lansky, N.Lavid, A.Zehavi, V.Belakhov, T.Baasov, B.Manjasetty, H.Belrhali, Y.Shoham, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.43 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.450, 119.080, 243.020, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 20.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Mutant XYN52B2-E335G, A GH52 Beta- D-Xylosidase From Geobacillus Stearothermophilus T6 (pdb code 4rhh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Mutant XYN52B2-E335G, A GH52 Beta- D-Xylosidase From Geobacillus Stearothermophilus T6, PDB code: 4rhh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4rhh

Go back to Calcium Binding Sites List in 4rhh
Calcium binding site 1 out of 5 in the Crystal Structure of the Catalytic Mutant XYN52B2-E335G, A GH52 Beta- D-Xylosidase From Geobacillus Stearothermophilus T6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Catalytic Mutant XYN52B2-E335G, A GH52 Beta- D-Xylosidase From Geobacillus Stearothermophilus T6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:22.6
occ:1.00
 O A:HOH1279 2.2 23.3 1.0
OD1 A:ASN475 2.3 24.4 1.0
O A:HOH1011 2.3 20.6 1.0
O A:ASP467 2.3 19.9 1.0
O A:VAL477 2.3 24.5 1.0
OD1 A:ASP467 2.3 21.6 1.0
O A:HOH982 2.4 20.0 1.0
C A:ASP467 3.2 23.0 1.0
CG A:ASN475 3.3 25.9 1.0
C A:VAL477 3.5 27.6 1.0
CG A:ASP467 3.5 23.9 1.0
CA A:ASP467 3.6 24.4 1.0
ND2 A:ASN475 3.9 24.3 1.0
N A:GLY479 4.0 25.7 1.0
N A:VAL477 4.0 30.3 1.0
N A:ASN475 4.1 25.4 1.0
CB A:ASP467 4.2 24.4 1.0
CA A:VAL477 4.2 27.7 1.0
C A:MET478 4.3 24.2 1.0
N A:HIS468 4.3 23.7 1.0
CA A:GLY479 4.3 27.9 1.0
CB A:ASN475 4.5 25.8 1.0
OD2 A:ASP467 4.5 23.1 1.0
CB A:HIS468 4.5 24.5 1.0
N A:MET478 4.6 26.1 1.0
CB A:VAL477 4.6 29.2 1.0
O A:MET478 4.6 20.6 1.0
CA A:ASN475 4.7 24.6 1.0
CA A:MET478 4.8 24.3 1.0
CA A:HIS468 4.9 25.1 1.0
N A:GLY476 4.9 25.5 1.0
C A:ASN475 4.9 25.7 1.0
O A:LYS473 4.9 28.0 1.0
ND1 A:HIS468 5.0 26.1 1.0
N A:ASP467 5.0 23.9 1.0

Calcium binding site 2 out of 5 in 4rhh

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Calcium binding site 2 out of 5 in the Crystal Structure of the Catalytic Mutant XYN52B2-E335G, A GH52 Beta- D-Xylosidase From Geobacillus Stearothermophilus T6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Catalytic Mutant XYN52B2-E335G, A GH52 Beta- D-Xylosidase From Geobacillus Stearothermophilus T6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:13.2
occ:1.00
 O B:VAL477 2.3 12.6 1.0
OD1 B:ASP467 2.4 12.2 1.0
O B:ASP467 2.4 12.1 1.0
OD1 B:ASN475 2.5 13.1 1.0
O B:HOH988 2.5 14.4 1.0
O B:HOH1016 2.5 19.8 1.0
O B:HOH987 2.5 22.6 1.0
C B:ASP467 3.2 12.7 1.0
CG B:ASN475 3.4 12.8 1.0
C B:VAL477 3.5 13.2 1.0
CG B:ASP467 3.5 12.1 1.0
CA B:ASP467 3.6 11.8 1.0
ND2 B:ASN475 3.8 11.8 1.0
N B:GLY479 3.9 15.6 1.0
O B:HOH1129 4.0 26.9 1.0
N B:VAL477 4.1 13.0 1.0
CB B:ASP467 4.1 11.4 1.0
N B:ASN475 4.2 15.1 1.0
C B:MET478 4.2 14.4 1.0
CA B:VAL477 4.2 13.0 1.0
CA B:GLY479 4.2 16.0 1.0
N B:HIS468 4.3 13.5 1.0
OD2 B:ASP467 4.5 12.7 1.0
N B:MET478 4.5 14.4 1.0
CB B:ASN475 4.5 13.2 1.0
CB B:VAL477 4.5 12.7 1.0
CB B:HIS468 4.7 14.7 1.0
CA B:MET478 4.7 14.2 1.0
O B:MET478 4.7 14.7 1.0
CA B:ASN475 4.8 13.4 1.0
O B:HOH1009 4.8 13.9 1.0
CA B:HIS468 4.9 13.9 1.0
O B:LYS473 4.9 17.9 1.0
N B:ASP467 5.0 12.5 1.0
O B:ARG466 5.0 11.8 1.0

Calcium binding site 3 out of 5 in 4rhh

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Calcium binding site 3 out of 5 in the Crystal Structure of the Catalytic Mutant XYN52B2-E335G, A GH52 Beta- D-Xylosidase From Geobacillus Stearothermophilus T6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Catalytic Mutant XYN52B2-E335G, A GH52 Beta- D-Xylosidase From Geobacillus Stearothermophilus T6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca801

b:19.7
occ:1.00
 OD1 C:ASP467 2.2 15.2 1.0
OD1 C:ASN475 2.3 18.6 1.0
O C:ASP467 2.4 22.4 1.0
O C:HOH1030 2.4 14.2 1.0
O C:VAL477 2.4 22.2 1.0
O C:HOH995 2.5 20.6 1.0
O C:HOH994 2.5 24.7 1.0
C C:ASP467 3.3 20.2 1.0
CG C:ASN475 3.3 20.1 1.0
CG C:ASP467 3.4 16.0 1.0
C C:VAL477 3.6 21.4 1.0
CA C:ASP467 3.8 20.2 1.0
ND2 C:ASN475 3.8 17.5 1.0
N C:GLY479 4.0 19.6 1.0
N C:ASN475 4.1 22.1 1.0
CA C:GLY479 4.2 19.5 1.0
CB C:ASP467 4.2 19.2 1.0
N C:VAL477 4.3 19.7 1.0
C C:MET478 4.3 19.8 1.0
N C:HIS468 4.3 23.2 1.0
OD2 C:ASP467 4.3 16.0 1.0
CA C:VAL477 4.4 20.6 1.0
CB C:ASN475 4.5 19.6 1.0
O C:HOH1066 4.5 29.9 1.0
CB C:VAL477 4.5 21.8 1.0
N C:MET478 4.6 20.8 1.0
O C:HOH1135 4.7 27.7 1.0
CB C:HIS468 4.7 23.4 1.0
CA C:ASN475 4.7 20.5 1.0
O C:MET478 4.8 21.3 1.0
CA C:MET478 4.8 20.6 1.0
ND1 C:HIS468 4.8 25.0 1.0
O C:HOH1188 4.9 38.3 1.0
CA C:HIS468 4.9 22.0 1.0
O C:LYS473 4.9 22.6 1.0

Calcium binding site 4 out of 5 in 4rhh

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Calcium binding site 4 out of 5 in the Crystal Structure of the Catalytic Mutant XYN52B2-E335G, A GH52 Beta- D-Xylosidase From Geobacillus Stearothermophilus T6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Catalytic Mutant XYN52B2-E335G, A GH52 Beta- D-Xylosidase From Geobacillus Stearothermophilus T6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca804

b:53.3
occ:1.00
 O C:HOH1198 2.5 35.0 1.0
SG C:CYS420 3.2 27.0 1.0
O C:HOH1348 3.7 46.2 1.0
CB C:CYS420 4.2 23.1 1.0
N C:CYS420 4.3 18.8 1.0
O C:ASP495 4.4 25.3 1.0
CA C:SER496 4.5 20.9 1.0
O C:SER496 4.6 19.6 1.0
C C:SER496 4.7 20.5 1.0
CA C:CYS420 4.9 19.5 1.0

Calcium binding site 5 out of 5 in 4rhh

Go back to Calcium Binding Sites List in 4rhh
Calcium binding site 5 out of 5 in the Crystal Structure of the Catalytic Mutant XYN52B2-E335G, A GH52 Beta- D-Xylosidase From Geobacillus Stearothermophilus T6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Catalytic Mutant XYN52B2-E335G, A GH52 Beta- D-Xylosidase From Geobacillus Stearothermophilus T6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca801

b:17.9
occ:1.00
 O D:VAL477 2.2 12.9 1.0
OD1 D:ASP467 2.2 15.6 1.0
O D:HOH983 2.4 7.9 1.0
OD1 D:ASN475 2.5 19.8 1.0
O D:HOH1048 2.5 21.7 1.0
O D:HOH982 2.6 22.0 1.0
O D:ASP467 2.7 17.4 1.0
CG D:ASN475 3.3 16.9 1.0
C D:ASP467 3.3 16.2 1.0
CG D:ASP467 3.4 14.8 1.0
C D:VAL477 3.4 15.2 1.0
ND2 D:ASN475 3.6 17.6 1.0
CA D:ASP467 3.7 16.3 1.0
N D:GLY479 3.8 14.7 1.0
N D:VAL477 4.1 16.6 1.0
N D:ASN475 4.1 18.0 1.0
CB D:ASP467 4.1 15.8 1.0
CA D:VAL477 4.2 16.7 1.0
CA D:GLY479 4.2 15.1 1.0
C D:MET478 4.3 13.9 1.0
OD2 D:ASP467 4.3 15.6 1.0
N D:HIS468 4.4 16.7 1.0
CB D:ASN475 4.5 15.8 1.0
N D:MET478 4.5 14.8 1.0
CB D:VAL477 4.5 16.8 1.0
CB D:HIS468 4.6 16.1 1.0
CA D:ASN475 4.7 16.0 1.0
CA D:MET478 4.8 14.5 1.0
O D:MET478 4.8 13.5 1.0
O D:LYS473 4.9 19.4 1.0
O D:HOH1082 4.9 25.3 1.0
N D:GLY476 4.9 16.0 1.0
CA D:HIS468 4.9 16.6 1.0

Reference:

R.Dann, S.Lansky, N.Lavid, A.Zehavi, V.Belakhov, T.Baasov, B.Manjasetty, H.Belrhali, Y.Shoham, G.Shoham. To Be Published To Be Published.
Page generated: Wed Jul 9 01:53:44 2025

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