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Magnesium in PDB 1zk3: Triclinic Crystal Structure of the Apo-Form of R-Specific Alcohol Dehydrogenase (Mutant G37D) From Lactobacillus Brevis

Enzymatic activity of Triclinic Crystal Structure of the Apo-Form of R-Specific Alcohol Dehydrogenase (Mutant G37D) From Lactobacillus Brevis

All present enzymatic activity of Triclinic Crystal Structure of the Apo-Form of R-Specific Alcohol Dehydrogenase (Mutant G37D) From Lactobacillus Brevis:
1.1.1.2;

Protein crystallography data

The structure of Triclinic Crystal Structure of the Apo-Form of R-Specific Alcohol Dehydrogenase (Mutant G37D) From Lactobacillus Brevis, PDB code: 1zk3 was solved by N.H.Schlieben, K.Niefind, J.Muller, B.Riebel, W.Hummel, D.Schomburg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.80 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 62.632, 72.234, 118.092, 101.41, 92.78, 114.48
R / Rfree (%) 21.4 / 24.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Triclinic Crystal Structure of the Apo-Form of R-Specific Alcohol Dehydrogenase (Mutant G37D) From Lactobacillus Brevis (pdb code 1zk3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Triclinic Crystal Structure of the Apo-Form of R-Specific Alcohol Dehydrogenase (Mutant G37D) From Lactobacillus Brevis, PDB code: 1zk3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1zk3

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Magnesium binding site 1 out of 4 in the Triclinic Crystal Structure of the Apo-Form of R-Specific Alcohol Dehydrogenase (Mutant G37D) From Lactobacillus Brevis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Triclinic Crystal Structure of the Apo-Form of R-Specific Alcohol Dehydrogenase (Mutant G37D) From Lactobacillus Brevis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3252

b:4.6
occ:1.00
 O C:HOH683 2.1 19.5 1.0
O A:HOH329 2.3 23.5 1.0
O A:HOH656 2.5 5.5 1.0
O C:HOH256 2.5 1.8 1.0
C A:GLN251 3.2 12.0 1.0
C C:GLN251 3.4 12.0 1.0
O A:GLN251 3.4 14.3 1.0
O A:HOH283 3.4 18.3 1.0
O C:GLN251 3.6 15.3 1.0
CG1 C:VAL147 4.3 4.9 1.0
O C:TYR248 4.4 10.3 1.0
CG1 A:VAL147 4.4 6.7 1.0
O C:THR249 4.5 14.2 1.0
O A:THR249 4.5 12.0 1.0
O A:TYR248 4.5 8.3 1.0
CA A:GLN251 4.6 11.6 1.0
CA C:THR249 4.6 11.4 1.0
CA C:GLN251 4.7 12.4 1.0
C C:THR249 4.7 11.9 1.0
CA A:THR249 4.7 9.1 1.0
C A:THR249 4.8 10.0 1.0
N A:GLN251 4.8 10.8 1.0
N C:GLN251 4.9 11.2 1.0

Magnesium binding site 2 out of 4 in 1zk3

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Magnesium binding site 2 out of 4 in the Triclinic Crystal Structure of the Apo-Form of R-Specific Alcohol Dehydrogenase (Mutant G37D) From Lactobacillus Brevis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Triclinic Crystal Structure of the Apo-Form of R-Specific Alcohol Dehydrogenase (Mutant G37D) From Lactobacillus Brevis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3253

b:9.1
occ:1.00
 O D:HOH529 2.1 3.8 1.0
O B:HOH483 2.2 17.5 1.0
O D:HOH456 2.4 1.8 1.0
O B:HOH856 2.8 8.0 1.0
O D:HOH883 3.1 31.0 1.0
C D:GLN251 3.2 11.0 1.0
C B:GLN251 3.3 12.8 1.0
O D:GLN251 3.5 13.0 1.0
O B:GLN251 3.5 14.7 1.0
O D:HOH2012 4.2 32.7 1.0
O D:TYR248 4.4 8.6 1.0
O B:TYR248 4.4 9.4 1.0
CG1 B:VAL147 4.5 8.9 1.0
O B:HOH1912 4.5 15.9 1.0
CA D:GLN251 4.6 11.7 1.0
CG1 D:VAL147 4.6 9.2 1.0
CA B:GLN251 4.7 13.3 1.0
O B:THR249 4.7 12.8 1.0
O D:THR249 4.7 13.3 1.0
N D:GLN251 4.8 10.9 1.0
CA B:THR249 4.9 11.2 1.0
CA D:THR249 4.9 9.6 1.0
N B:GLN251 4.9 11.9 1.0
C B:THR249 5.0 11.4 1.0
C D:THR249 5.0 10.9 1.0

Magnesium binding site 3 out of 4 in 1zk3

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Magnesium binding site 3 out of 4 in the Triclinic Crystal Structure of the Apo-Form of R-Specific Alcohol Dehydrogenase (Mutant G37D) From Lactobacillus Brevis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Triclinic Crystal Structure of the Apo-Form of R-Specific Alcohol Dehydrogenase (Mutant G37D) From Lactobacillus Brevis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3254

b:6.9
occ:1.00
 O E:HOH1083 1.9 22.5 1.0
O G:HOH1129 2.1 16.8 1.0
O G:HOH1456 2.4 4.1 1.0
O E:HOH1056 2.4 3.7 1.0
O G:HOH1483 2.7 21.4 1.0
C G:GLN251 3.2 11.3 1.0
C E:GLN251 3.3 10.9 1.0
O G:GLN251 3.4 13.1 1.0
O E:GLN251 3.6 12.2 1.0
CG1 E:VAL147 4.3 8.5 1.0
CG1 G:VAL147 4.3 9.5 1.0
O E:THR249 4.4 12.1 1.0
O G:THR249 4.4 11.3 1.0
O E:TYR248 4.5 7.0 1.0
O G:TYR248 4.6 9.7 1.0
O G:HOH1970 4.6 27.8 1.0
CA G:GLN251 4.6 10.9 1.0
O E:HOH1971 4.7 26.0 1.0
CA E:GLN251 4.7 11.2 1.0
CA E:THR249 4.7 9.3 1.0
CA G:THR249 4.7 9.6 1.0
C E:THR249 4.8 10.2 1.0
C G:THR249 4.8 10.3 1.0
N G:GLN251 4.8 9.8 1.0
N E:GLN251 4.9 10.8 1.0

Magnesium binding site 4 out of 4 in 1zk3

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Magnesium binding site 4 out of 4 in the Triclinic Crystal Structure of the Apo-Form of R-Specific Alcohol Dehydrogenase (Mutant G37D) From Lactobacillus Brevis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Triclinic Crystal Structure of the Apo-Form of R-Specific Alcohol Dehydrogenase (Mutant G37D) From Lactobacillus Brevis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg3255

b:6.6
occ:1.00
 O H:HOH1683 1.9 16.5 1.0
O H:HOH1656 2.0 1.8 1.0
O H:HOH1329 2.1 11.5 1.0
O F:HOH1256 2.3 7.7 1.0
O F:HOH1283 2.6 14.8 1.0
C F:GLN251 3.3 12.7 1.0
C H:GLN251 3.3 12.4 1.0
O H:GLN251 3.5 13.9 1.0
O F:GLN251 3.6 13.1 1.0
CG1 H:VAL147 4.3 7.4 1.0
CG1 F:VAL147 4.4 8.4 1.0
O H:HOH1853 4.4 17.8 1.0
O F:TYR248 4.5 10.3 1.0
O F:THR249 4.5 14.0 1.0
O H:TYR248 4.6 8.8 1.0
O H:THR249 4.6 12.9 1.0
CA F:GLN251 4.6 12.5 1.0
CA F:THR249 4.7 10.1 1.0
CA H:GLN251 4.7 12.7 1.0
C F:THR249 4.8 12.4 1.0
N F:GLN251 4.8 12.8 1.0
CA H:THR249 4.8 10.7 1.0
C H:THR249 4.9 11.3 1.0
N H:GLN251 5.0 11.8 1.0

Reference:

N.H.Schlieben, K.Niefind, J.Muller, B.Riebel, W.Hummel, D.Schomburg. Atomic Resolution Structures of R-Specific Alcohol Dehydrogenase From Lactobacillus Brevis Provide the Structural Bases of Its Substrate and Cosubstrate Specificity J.Mol.Biol. V. 349 801 2005.
ISSN: ISSN 0022-2836
PubMed: 15896805
DOI: 10.1016/J.JMB.2005.04.029
Page generated: Mon Dec 14 07:12:06 2020

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