Atomistry » Magnesium » PDB 1z6n-1zk2 » 1zem
Atomistry »
  Magnesium »
    PDB 1z6n-1zk2 »
      1zem »

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

Go back to Magnesium Binding Sites List in 1zem
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

Go back to Magnesium Binding Sites List in 1zem
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

Go back to Magnesium Binding Sites List in 1zem
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

Go back to Magnesium Binding Sites List in 1zem
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

Go back to Magnesium Binding Sites List in 1zem
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: Tue Aug 13 20:09:24 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy