Calcium in PDB 7zei: Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A

Protein crystallography data

The structure of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A, PDB code: 7zei was solved by M.Baudrexl, T.Fida, B.Berk, W.Schwarz, V.V.Zverlov, M.Groll, W.Liebl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.09, 108.74, 251.27, 90, 90, 90
R / Rfree (%) 12.6 / 15.3

Other elements in 7zei:

The structure of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A (pdb code 7zei). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A, PDB code: 7zei:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7zei

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Calcium binding site 1 out of 6 in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:29.0
occ:1.00
 O A:HOH1220 2.2 26.6 1.0
NE2 A:HIS244 2.4 26.0 1.0
O A:HOH1071 2.4 31.9 1.0
O A:HOH1248 2.5 31.3 1.0
O A:HOH1043 2.5 18.9 1.0
O A:HOH1020 2.5 19.2 1.0
O A:HOH1157 3.1 23.7 1.0
CD2 A:HIS244 3.2 25.8 1.0
CE1 A:HIS244 3.5 25.0 1.0
O A:ALA143 3.9 18.2 1.0
O A:PRO192 4.2 18.4 1.0
CG A:HIS244 4.4 22.0 1.0
O A:HOH1123 4.5 26.5 1.0
O A:ALA245 4.5 19.1 1.0
ND1 A:HIS244 4.5 22.3 1.0
CA A:GLY191 4.7 18.0 1.0
ND2 A:ASN193 4.7 24.6 1.0
O A:ALA86 4.8 18.1 1.0
O A:PRO87 4.8 19.7 1.0
C A:GLY191 4.9 17.9 1.0
O A:ASP142 4.9 19.1 1.0
C A:ALA143 5.0 18.1 1.0

Calcium binding site 2 out of 6 in 7zei

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Calcium binding site 2 out of 6 in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:22.7
occ:1.00
 O B:HOH1249 2.3 22.9 1.0
O B:HOH1281 2.3 26.9 1.0
O B:HOH1103 2.4 22.8 1.0
NE2 B:HIS244 2.4 23.0 1.0
O B:HOH1146 2.4 17.7 1.0
O B:HOH1053 2.4 18.2 1.0
O B:HOH1211 3.0 25.1 1.0
CD2 B:HIS244 3.2 23.1 1.0
CE1 B:HIS244 3.5 22.1 1.0
O B:ALA143 4.0 17.8 1.0
O B:PRO192 4.2 17.2 1.0
CG B:HIS244 4.4 20.3 1.0
O B:HOH1142 4.4 27.0 1.0
O B:ALA245 4.5 19.3 1.0
ND2 B:ASN193 4.5 21.2 1.0
ND1 B:HIS244 4.5 20.7 1.0
CA B:GLY191 4.6 16.5 1.0
O B:ALA86 4.8 16.8 1.0
C B:GLY191 4.8 16.6 1.0
O B:PRO87 4.8 18.8 1.0
O B:GLY191 4.9 17.5 1.0
O B:ASP142 4.9 17.8 1.0
CB B:ALA86 4.9 17.5 1.0
C B:ALA143 5.0 17.4 1.0
C B:ASP142 5.0 17.2 1.0

Calcium binding site 3 out of 6 in 7zei

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Calcium binding site 3 out of 6 in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca902

b:24.1
occ:1.00
 O C:HOH1223 2.3 23.5 1.0
O C:HOH1228 2.4 29.2 1.0
NE2 C:HIS244 2.4 21.2 1.0
O C:HOH1054 2.5 20.7 1.0
O C:HOH1069 2.5 20.0 1.0
O C:HOH1021 2.5 24.5 1.0
O C:HOH1148 2.8 21.9 1.0
CD2 C:HIS244 3.2 22.1 1.0
CE1 C:HIS244 3.5 22.4 1.0
O C:ALA143 4.0 18.0 1.0
O C:PRO192 4.3 19.3 1.0
O C:ALA245 4.4 19.7 1.0
CG C:HIS244 4.4 21.0 1.0
ND1 C:HIS244 4.5 21.4 1.0
ND2 C:ASN193 4.6 22.6 1.0
O C:PRO87 4.6 18.9 1.0
O C:HOH1088 4.6 27.6 1.0
O C:ALA86 4.7 17.9 1.0
CA C:GLY191 4.8 18.6 1.0
CB C:ALA86 4.9 17.1 1.0
C C:GLY191 4.9 18.8 1.0
O C:ASP142 5.0 18.3 1.0

Calcium binding site 4 out of 6 in 7zei

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Calcium binding site 4 out of 6 in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca902

b:30.5
occ:1.00
 O D:HOH1252 2.3 27.7 1.0
O D:HOH1056 2.4 20.7 1.0
NE2 D:HIS244 2.4 28.0 1.0
O D:HOH1041 2.4 30.6 1.0
O D:HOH1129 2.5 18.6 1.0
O D:HOH1269 2.5 38.3 1.0
CD2 D:HIS244 3.2 27.2 1.0
O D:HOH1179 3.4 28.3 1.0
CE1 D:HIS244 3.5 27.2 1.0
O D:HOH1009 3.8 28.9 1.0
O D:ALA143 4.0 16.9 1.0
O D:PRO192 4.2 17.7 1.0
CG D:HIS244 4.4 24.1 1.0
O D:ALA245 4.5 19.8 1.0
ND1 D:HIS244 4.5 23.4 1.0
O D:HOH1184 4.5 29.2 1.0
CA D:GLY191 4.6 16.8 1.0
ND2 D:ASN193 4.6 24.4 1.0
C D:GLY191 4.8 16.1 1.0
O D:ALA86 4.8 18.4 1.0
O D:GLY191 4.9 16.1 1.0
O D:ASP142 4.9 17.5 1.0
C D:ALA143 5.0 16.8 1.0
O D:PRO87 5.0 20.5 1.0

Calcium binding site 5 out of 6 in 7zei

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Calcium binding site 5 out of 6 in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca902

b:28.9
occ:1.00
 O E:HOH1511 2.2 28.1 1.0
O E:HOH1328 2.4 30.7 1.0
NE2 E:HIS244 2.4 27.5 1.0
O E:HOH1341 2.4 20.5 1.0
O E:HOH1416 2.4 18.7 1.0
O E:HOH1573 2.5 34.6 1.0
CD2 E:HIS244 3.2 27.1 1.0
O E:HOH1451 3.4 25.1 1.0
CE1 E:HIS244 3.5 26.2 1.0
O E:ALA143 3.9 18.6 1.0
O E:HOH1304 4.0 30.0 1.0
O E:PRO192 4.2 19.6 1.0
CG E:HIS244 4.4 23.6 1.0
O E:HOH1422 4.5 30.4 1.0
ND1 E:HIS244 4.5 22.8 1.0
O E:ALA245 4.5 19.8 1.0
CA E:GLY191 4.6 19.3 1.0
ND2 E:ASN193 4.6 25.1 1.0
C E:GLY191 4.8 19.2 1.0
O E:ALA86 4.8 16.6 1.0
O E:ASP142 4.9 18.8 1.0
O E:GLY191 4.9 18.9 1.0
C E:ALA143 4.9 18.4 1.0
O E:PRO87 4.9 19.0 1.0
C E:ASP142 5.0 18.1 1.0
CB E:ALA86 5.0 17.4 1.0

Calcium binding site 6 out of 6 in 7zei

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Calcium binding site 6 out of 6 in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca902

b:25.8
occ:1.00
 O F:HOH1180 2.3 25.1 1.0
O F:HOH1218 2.4 31.0 1.0
O F:HOH1027 2.4 27.2 1.0
O F:HOH1112 2.4 19.2 1.0
O F:HOH1035 2.4 19.8 1.0
NE2 F:HIS244 2.4 22.6 1.0
O F:HOH1151 3.0 27.6 1.0
CD2 F:HIS244 3.3 24.2 1.0
CE1 F:HIS244 3.5 22.7 1.0
O F:ALA143 4.0 19.2 1.0
O F:PRO192 4.3 19.1 1.0
CG F:HIS244 4.5 22.3 1.0
O F:ALA245 4.5 23.1 1.0
O F:HOH1109 4.5 32.7 1.0
ND2 F:ASN193 4.6 24.4 1.0
ND1 F:HIS244 4.6 22.1 1.0
CA F:GLY191 4.7 19.8 1.0
O F:ALA86 4.8 17.7 1.0
O F:PRO87 4.8 21.8 1.0
C F:GLY191 4.9 19.2 1.0
O F:ASP142 4.9 19.0 1.0
O F:GLY191 4.9 20.1 1.0
C F:ALA143 4.9 19.3 1.0
C F:ASP142 5.0 18.4 1.0
CB F:ALA86 5.0 17.8 1.0

Reference:

M.Baudrexl, T.Fida, B.Berk, W.H.Schwarz, V.V.Zverlov, M.Groll, W.Liebl. Biochemical and Structural Characterization of Thermostable GH159 Glycoside Hydrolases Exhibiting Alpha-L-Arabinofuranosidase Activity. Front Mol Biosci V. 9 07439 2022.
ISSN: ESSN 2296-889X
PubMed: 35847984
DOI: 10.3389/FMOLB.2022.907439
Page generated: Fri Jul 19 06:31:32 2024

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