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Magnesium 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:

Calcium (Ca) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A, PDB code: 7zei:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7zei

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg901

b:25.8
occ:1.00
 O A:HOH1001 2.2 42.2 1.0
O A:HOH1050 2.3 43.0 1.0
OD1 A:ASP246 2.3 22.3 1.0
O A:HOH1107 2.3 24.9 1.0
O A:HOH1349 2.4 43.1 1.0
O A:HOH1263 2.6 36.7 1.0
O A:HOH1055 2.6 23.6 1.0
O A:HOH1123 3.0 26.5 1.0
CG A:ASP246 3.1 20.8 1.0
OD2 A:ASP246 3.3 23.3 1.0
ND2 A:ASN193 3.9 24.6 1.0
OE2 A:GLU88 4.0 27.0 1.0
O A:VAL247 4.1 19.5 1.0
OE1 A:GLU88 4.3 22.8 1.0
O A:HOH1151 4.3 34.5 1.0
OG1 A:THR21 4.4 25.5 1.0
O A:HOH1112 4.4 25.3 1.0
O A:HOH1256 4.4 29.3 1.0
OD1 A:ASN193 4.5 25.9 1.0
CB A:ASP246 4.6 20.0 1.0
CD A:GLU88 4.6 24.8 1.0
CG A:ASN193 4.7 21.8 1.0
O A:HOH1022 4.7 35.3 1.0
O A:HOH1074 4.8 26.1 1.0
N A:VAL247 4.9 18.6 1.0
O A:HOH1070 4.9 22.4 1.0
O A:ILE22 5.0 18.1 1.0

Magnesium binding site 2 out of 6 in 7zei

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg901

b:25.9
occ:1.00
 O B:HOH1147 2.3 26.6 1.0
O B:HOH1038 2.3 41.7 1.0
O B:HOH1247 2.4 37.8 1.0
OD1 B:ASP246 2.4 21.2 1.0
O B:HOH1042 2.4 24.4 1.0
O B:HOH1142 3.1 27.0 1.0
CG B:ASP246 3.2 19.7 1.0
OD2 B:ASP246 3.4 20.6 1.0
ND2 B:ASN193 4.0 21.2 1.0
OE2 B:GLU88 4.0 21.5 1.0
O B:VAL247 4.0 19.1 1.0
O B:HOH1120 4.2 24.1 1.0
O B:HOH1214 4.2 68.1 1.0
OD1 B:ASN193 4.3 21.6 1.0
OE1 B:GLU88 4.4 19.6 1.0
OG1 B:THR21 4.4 26.5 1.0
O B:HOH1229 4.5 31.9 1.0
CG B:ASN193 4.6 19.4 1.0
CD B:GLU88 4.6 20.0 1.0
CB B:ASP246 4.7 19.1 1.0
O B:HOH1016 4.8 33.1 1.0
O B:HOH1043 4.8 21.1 1.0
O B:HOH1125 4.8 28.2 1.0
N B:VAL247 4.8 18.1 1.0

Magnesium binding site 3 out of 6 in 7zei

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg901

b:26.6
occ:1.00
 O C:HOH1304 2.2 48.9 1.0
O C:HOH1128 2.3 28.7 1.0
O C:HOH1016 2.3 41.3 1.0
OD1 C:ASP246 2.3 22.7 1.0
O C:HOH1008 2.4 39.3 1.0
O C:HOH1099 2.5 24.1 1.0
O C:HOH1088 2.9 27.6 1.0
CG C:ASP246 3.2 20.9 1.0
OD2 C:ASP246 3.4 21.1 1.0
ND2 C:ASN193 3.9 22.6 1.0
O C:HOH1275 3.9 56.6 1.0
OE2 C:GLU88 4.0 24.0 1.0
O C:VAL247 4.1 18.6 1.0
O C:HOH1106 4.2 34.4 1.0
O C:HOH1066 4.2 26.6 1.0
OD1 C:ASN193 4.3 25.0 1.0
OE1 C:GLU88 4.3 21.0 1.0
OG1 C:THR21 4.4 24.9 1.0
CG C:ASN193 4.5 21.6 1.0
CD C:GLU88 4.6 21.4 1.0
CB C:ASP246 4.6 19.5 1.0
O C:HOH1216 4.7 32.7 1.0
O C:HOH1030 4.7 33.5 1.0
O C:HOH1036 4.8 22.4 1.0
N C:VAL247 4.8 18.5 1.0

Magnesium binding site 4 out of 6 in 7zei

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg901

b:25.7
occ:1.00
 O D:HOH1343 2.1 50.1 1.0
O D:HOH1178 2.3 27.1 1.0
O D:HOH1010 2.3 43.1 1.0
OD1 D:ASP246 2.3 22.7 1.0
O D:HOH1007 2.3 34.0 1.0
O D:HOH1050 2.5 25.0 1.0
O D:HOH1219 2.6 46.9 1.0
O D:HOH1184 3.1 29.2 1.0
CG D:ASP246 3.2 22.1 1.0
OD2 D:ASP246 3.3 25.0 1.0
ND2 D:ASN193 3.9 24.4 1.0
OE2 D:GLU88 4.0 23.0 1.0
O D:VAL247 4.1 20.9 1.0
O D:HOH1088 4.2 36.0 1.0
O D:HOH1125 4.2 25.0 1.0
OE1 D:GLU88 4.4 19.6 1.0
OD1 D:ASN193 4.4 25.1 1.0
O D:HOH1226 4.5 31.5 1.0
OG1 D:THR21 4.5 27.2 1.0
CB D:ASP246 4.6 20.6 1.0
CD D:GLU88 4.6 21.0 1.0
CG D:ASN193 4.6 20.9 1.0
O D:HOH1085 4.9 32.4 1.0
O D:HOH1053 4.9 21.5 1.0
N D:VAL247 4.9 18.1 1.0

Magnesium binding site 5 out of 6 in 7zei

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg901

b:27.4
occ:1.00
 O E:HOH1301 2.1 47.1 1.0
OD1 E:ASP246 2.3 23.7 1.0
O E:HOH1406 2.3 25.0 1.0
O E:HOH1534 2.3 34.9 1.0
O E:HOH1644 2.4 39.0 1.0
O E:HOH1347 2.6 26.2 1.0
CG E:ASP246 3.1 22.0 1.0
O E:HOH1422 3.1 30.4 1.0
OD2 E:ASP246 3.2 24.0 1.0
OE2 E:GLU88 4.0 25.4 1.0
ND2 E:ASN193 4.1 25.1 1.0
O E:VAL247 4.1 20.4 1.0
O E:HOH1429 4.2 26.3 1.0
O E:HOH1433 4.3 37.1 1.0
O E:HOH1544 4.3 29.5 1.0
OE1 E:GLU88 4.4 21.3 1.0
OG1 E:THR21 4.5 25.5 1.0
OD1 E:ASN193 4.5 27.2 1.0
CB E:ASP246 4.6 20.5 1.0
O E:HOH1316 4.6 39.2 1.0
CD E:GLU88 4.6 22.8 1.0
O E:HOH1413 4.7 26.5 1.0
CG E:ASN193 4.7 23.2 1.0
N E:VAL247 4.9 19.1 1.0
O E:ILE22 5.0 18.4 1.0
O E:HOH1386 5.0 22.8 1.0

Magnesium binding site 6 out of 6 in 7zei

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg901

b:34.4
occ:1.00
 O F:HOH1153 2.2 26.3 1.0
O F:HOH1166 2.3 44.1 1.0
O F:HOH1001 2.3 42.3 1.0
OD1 F:ASP246 2.4 25.2 1.0
O F:HOH1295 2.5 41.8 1.0
O F:HOH1022 2.5 29.6 1.0
O F:HOH1109 3.1 32.7 1.0
CG F:ASP246 3.2 24.1 1.0
OD2 F:ASP246 3.3 25.0 1.0
O F:VAL247 3.9 23.2 1.0
ND2 F:ASN193 4.0 24.4 1.0
OE2 F:GLU88 4.1 24.6 1.0
O F:HOH1130 4.1 29.7 1.0
O F:HOH1058 4.2 44.3 1.0
OD1 F:ASN193 4.3 27.2 1.0
OE1 F:GLU88 4.3 22.5 1.0
O F:HOH1203 4.4 40.6 1.0
OG1 F:THR21 4.6 28.2 1.0
CG F:ASN193 4.6 24.2 1.0
CB F:ASP246 4.6 22.7 1.0
CD F:GLU88 4.7 22.5 1.0
O F:HOH1063 4.8 23.3 1.0
O F:HOH1002 4.8 36.5 1.0
O F:HOH1076 4.8 31.9 1.0
N F:VAL247 4.9 22.7 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: Thu Oct 3 16:45:07 2024

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