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Magnesium in PDB 1zem: Crystal Structure of Nad+-Bound Xylitol Dehydrogenase

Enzymatic activity of Crystal Structure of Nad+-Bound Xylitol Dehydrogenase

All present enzymatic activity of Crystal Structure of Nad+-Bound Xylitol Dehydrogenase:
1.1.1.9;

Protein crystallography data

The structure of Crystal Structure of Nad+-Bound Xylitol Dehydrogenase, PDB code: 1zem was solved by A.H.Ehrensberger, R.A.Elling, D.K.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.959, 64.717, 168.239, 90.00, 93.06, 90.00
R / Rfree (%) 16.7 / 21.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nad+-Bound Xylitol Dehydrogenase (pdb code 1zem). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Nad+-Bound Xylitol Dehydrogenase, PDB code: 1zem:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1zem

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Magnesium binding site 1 out of 5 in the Crystal Structure of Nad+-Bound Xylitol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Nad+-Bound Xylitol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3265

b:13.8
occ:1.00
 O C:HOH4265 2.1 10.1 1.0
O C:HOH4446 2.1 8.1 1.0
O A:HOH2270 2.1 14.1 1.0
O A:HOH2338 2.2 10.0 1.0
O C:HOH4279 2.2 14.6 1.0
O A:HOH2275 2.2 10.1 1.0
O C:HOH4299 3.8 9.2 1.0
O A:HOH2296 3.9 14.7 1.0
O C:HOH4302 4.0 11.8 1.0
O A:HOH2276 4.0 8.9 1.0
O C:GLY147 4.2 7.6 1.0
O C:GLY162 4.3 9.3 1.0
O A:GLY147 4.3 10.4 1.0
O A:GLY162 4.4 10.1 1.0
CG2 C:ILE165 4.6 9.8 1.0
CA A:GLY162 4.7 11.1 1.0
CA C:GLY162 4.7 10.1 1.0
CG2 A:ILE165 4.8 5.6 1.0
CB C:ILE165 4.8 8.2 1.0
O C:HOH4380 4.9 23.1 1.0
C C:GLY162 4.9 9.9 1.0

Magnesium binding site 2 out of 5 in 1zem

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Magnesium binding site 2 out of 5 in the Crystal Structure of Nad+-Bound Xylitol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Nad+-Bound Xylitol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3268

b:18.0
occ:1.00
 O C:HOH4428 2.2 20.8 1.0
O C:HOH4376 2.2 14.4 1.0
O C:HOH4362 2.2 13.0 1.0
O C:HOH4429 2.2 15.4 1.0
O C:HOH4430 2.2 21.1 1.0
O C:HOH4392 2.3 17.4 1.0
O C:HOH4361 3.9 14.5 1.0
O C:HOH4433 4.0 21.7 1.0
OD1 C:ASN18 4.1 17.0 1.0
ND2 C:ASN18 4.2 14.1 1.0
O C:HOH4486 4.2 32.5 1.0
O C:HOH4431 4.3 13.5 1.0
O C:HOH4340 4.3 24.6 1.0
CG C:ASN18 4.6 14.9 1.0
CE1 C:PHE194 4.8 14.7 1.0
CD1 C:PHE194 4.9 13.8 1.0
O C:HOH4382 4.9 28.2 1.0

Magnesium binding site 3 out of 5 in 1zem

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Magnesium binding site 3 out of 5 in the Crystal Structure of Nad+-Bound Xylitol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Nad+-Bound Xylitol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3264

b:11.8
occ:1.00
 O D:HOH5264 2.1 7.3 1.0
O D:HOH5273 2.1 14.5 1.0
O D:HOH5288 2.1 7.7 1.0
O D:HOH5271 2.2 10.4 1.0
O B:HOH3277 2.2 7.5 1.0
O B:HOH3267 2.2 10.8 1.0
O B:HOH3281 3.8 6.9 1.0
O B:HOH3266 3.9 10.3 1.0
O D:HOH5316 4.1 12.0 1.0
O B:HOH3293 4.1 14.7 1.0
O B:GLY147 4.2 8.9 1.0
O D:GLY147 4.2 9.8 1.0
O D:GLY162 4.4 7.9 1.0
O B:GLY162 4.5 10.3 1.0
CG2 D:ILE165 4.6 9.7 1.0
O D:HOH5421 4.7 32.1 1.0
O D:HOH5402 4.7 26.9 1.0
CA D:GLY162 4.7 8.7 1.0
CA B:GLY162 4.7 6.9 1.0
CG2 B:ILE165 4.7 3.8 1.0
CB D:ILE165 4.8 8.1 1.0
O B:HOH3407 4.8 29.8 1.0
CB B:ILE165 4.9 5.8 1.0
C D:GLY162 4.9 8.9 1.0

Magnesium binding site 4 out of 5 in 1zem

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Magnesium binding site 4 out of 5 in the Crystal Structure of Nad+-Bound Xylitol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Nad+-Bound Xylitol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg3266

b:13.0
occ:1.00
 O E:HOH6285 2.1 8.5 1.0
O E:HOH6266 2.1 9.8 1.0
O G:HOH8267 2.2 8.3 1.0
O G:HOH8274 2.2 12.9 1.0
O E:HOH6272 2.3 13.5 1.0
O G:HOH8269 2.3 10.2 1.0
O G:HOH8279 3.9 9.5 1.0
O E:HOH6277 3.9 5.8 1.0
O E:HOH6297 3.9 8.2 1.0
O G:HOH8275 4.1 9.9 1.0
O E:GLY147 4.2 8.4 1.0
O G:GLY147 4.3 9.2 1.0
O E:GLY162 4.5 13.5 1.0
O G:GLY162 4.5 10.9 1.0
O E:HOH6372 4.5 32.2 1.0
O E:HOH6397 4.6 27.5 1.0
O G:HOH8315 4.7 18.6 1.0
CG2 G:ILE165 4.7 6.1 1.0
CA E:GLY162 4.7 12.3 1.0
CG2 E:ILE165 4.7 10.5 1.0
CA G:GLY162 4.8 10.5 1.0
O G:HOH8406 4.8 29.7 1.0
O E:HOH6401 4.8 25.6 1.0
CB E:ILE165 4.9 13.7 1.0
CB G:ILE165 5.0 9.4 1.0

Magnesium binding site 5 out of 5 in 1zem

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Magnesium binding site 5 out of 5 in the Crystal Structure of Nad+-Bound Xylitol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Nad+-Bound Xylitol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg3267

b:12.7
occ:1.00
 O H:HOH9275 2.1 6.6 1.0
O H:HOH9277 2.1 9.7 1.0
O F:HOH7265 2.2 7.0 1.0
O H:HOH9266 2.2 5.5 1.0
O F:HOH7264 2.2 7.4 1.0
O F:HOH7276 2.2 10.4 1.0
O H:HOH9270 3.8 8.1 1.0
O H:HOH9292 3.9 9.1 1.0
O F:HOH7290 3.9 6.4 1.0
O F:HOH7295 4.0 7.4 1.0
O F:GLY147 4.2 9.0 1.0
O H:GLY147 4.4 9.1 1.0
O H:GLY162 4.4 6.3 1.0
O F:GLY162 4.5 7.3 1.0
CG2 H:ILE165 4.7 8.3 1.0
CA H:GLY162 4.8 5.8 1.0
CG2 F:ILE165 4.8 6.5 1.0
CA F:GLY162 4.8 4.9 1.0
O H:HOH9477 4.8 29.1 1.0
O H:HOH9279 4.9 14.8 1.0
CB H:ILE165 4.9 8.9 1.0
CB F:ILE165 5.0 6.7 1.0
O F:HOH7317 5.0 22.8 1.0

Reference:

A.H.Ehrensberger, R.A.Elling, D.K.Wilson. Structure-Guided Engineering of Xylitol Dehydrogenase Cosubstrate Specificity. Structure V. 14 567 2006.
ISSN: ISSN 0969-2126
PubMed: 16531240
DOI: 10.1016/J.STR.2005.11.016
Page generated: Mon Dec 14 07:11:55 2020

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