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Magnesium in PDB 5ocm: Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate

Protein crystallography data

The structure of Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate, PDB code: 5ocm was solved by M.Sharma, B.Nestl, G.Grogan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 125.80 / 1.81
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 92.811, 152.434, 251.598, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 19.6

Other elements in 5ocm:

The structure of Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate also contains other interesting chemical elements:

Fluorine (F) 18 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate (pdb code 5ocm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate, PDB code: 5ocm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5ocm

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Magnesium binding site 1 out of 7 in the Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:39.1
occ:1.00
 O C:HOH536 2.1 30.7 1.0
O A:HOH471 2.3 26.3 1.0
CZ C:ARG2 3.7 47.6 1.0
NE2 A:GLN225 3.8 12.1 1.0
O C:HOH501 4.0 14.1 1.0
O A:GLN225 4.1 13.0 1.0
O A:ASP224 4.1 16.3 1.0
CB C:ALA28 4.2 17.0 1.0
CA A:GLN225 4.4 13.8 1.0
O C:HOH415 4.5 34.2 1.0
NE C:ARG2 4.5 50.2 1.0
CA C:ALA28 4.5 15.4 1.0
C A:GLN225 4.6 14.6 1.0
CD A:GLN225 4.8 14.2 1.0

Magnesium binding site 2 out of 7 in 5ocm

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Magnesium binding site 2 out of 7 in the Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:34.4
occ:1.00
 O C:HOH426 2.0 25.1 1.0
O C:HOH599 2.0 25.0 1.0
O C:HOH594 2.2 25.4 1.0
O C:HOH483 2.2 27.4 1.0
O C:HOH411 2.3 26.1 1.0
O C:HOH601 2.5 40.7 1.0
O E:HOH538 3.8 28.2 1.0
NE2 C:GLN225 3.9 12.5 1.0
O C:HOH485 4.0 11.8 1.0
O C:GLN225 4.1 14.8 1.0
O C:ASP224 4.1 15.6 1.0
CB E:ALA28 4.2 15.7 1.0
CA C:GLN225 4.4 15.1 1.0
C C:GLN225 4.6 15.7 1.0
CA E:ALA28 4.6 14.8 1.0

Magnesium binding site 3 out of 7 in 5ocm

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Magnesium binding site 3 out of 7 in the Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:41.8
occ:1.00
 O D:HOH584 2.0 39.2 1.0
O D:HOH565 2.0 35.4 1.0
O E:HOH484 2.1 36.9 1.0
O D:HOH504 2.2 28.9 1.0
O D:HOH420 2.5 29.7 1.0
O E:HOH430 2.5 34.7 1.0
O D:ASP224 4.0 18.0 1.0
OE2 E:GLU197 4.1 34.6 1.0
OE1 E:GLU197 4.1 33.8 1.0
O D:VAL223 4.4 15.5 1.0
O D:HOH475 4.4 31.8 1.0
CA D:ASP224 4.4 17.3 1.0
O D:HOH523 4.5 25.9 1.0
O D:HOH574 4.5 38.0 1.0
OD1 D:ASP224 4.5 26.2 1.0
CD E:GLU197 4.6 30.5 1.0
C D:ASP224 4.6 18.1 1.0

Magnesium binding site 4 out of 7 in 5ocm

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Magnesium binding site 4 out of 7 in the Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg304

b:46.6
occ:1.00
 O D:HOH483 2.1 33.2 1.0
O D:HOH583 2.1 31.2 1.0
O D:HOH484 2.1 28.4 1.0
O D:HOH592 2.2 39.7 1.0
O D:HOH475 2.2 31.8 1.0
O D:HOH590 2.3 35.9 1.0
O B:HOH495 4.0 32.9 1.0
NE2 D:GLN225 4.1 13.8 1.0
O B:HOH460 4.2 17.7 1.0
O D:GLN225 4.2 15.2 1.0
O B:HOH409 4.3 31.4 1.0
CB B:ALA28 4.3 18.5 1.0
O D:ASP224 4.4 18.0 1.0
CA D:GLN225 4.7 15.3 1.0
C D:GLN225 4.7 16.3 1.0
CA B:ALA28 4.8 18.8 1.0

Magnesium binding site 5 out of 7 in 5ocm

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Magnesium binding site 5 out of 7 in the Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg305

b:40.5
occ:1.00
 O D:HOH573 2.0 35.1 1.0
OD1 D:ASP3 2.1 28.9 1.0
O D:HOH497 2.2 29.7 1.0
CG D:ASP3 3.4 36.0 1.0
OD2 D:ASP3 4.2 34.6 1.0
O D:GLU58 4.3 22.2 1.0
O D:ARG2 4.3 28.2 1.0
CB D:ASP3 4.4 31.6 1.0
CA D:ASP3 4.4 30.5 1.0
O D:HOH435 4.5 23.0 1.0
CA D:ALA59 4.6 19.3 1.0
C D:ARG2 4.8 31.8 1.0
N D:ASP3 4.8 27.2 1.0
O D:ALA59 5.0 18.7 1.0

Magnesium binding site 6 out of 7 in 5ocm

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Magnesium binding site 6 out of 7 in the Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg303

b:32.2
occ:1.00
 O E:HOH533 2.0 22.1 1.0
O E:HOH536 2.0 30.7 1.0
O E:HOH498 2.1 27.0 1.0
O E:HOH612 2.1 36.0 1.0
O E:HOH613 2.2 29.9 1.0
O E:HOH611 2.2 29.6 1.0
O A:HOH517 3.8 26.1 1.0
NE2 E:GLN225 4.0 10.9 1.0
O A:HOH486 4.1 11.1 1.0
O E:GLN225 4.2 13.8 1.0
O A:HOH408 4.2 23.7 1.0
CB A:ALA28 4.3 30.0 1.0
O E:ASP224 4.3 16.1 1.0
CA E:GLN225 4.6 13.7 1.0
C E:GLN225 4.6 14.7 1.0
CA A:ALA28 4.7 15.6 1.0

Magnesium binding site 7 out of 7 in 5ocm

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Magnesium binding site 7 out of 7 in the Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Imine Reductase From Streptosporangium Roseum in Complex with Nadp+ and 2,2,2-Trifluoroacetophenone Hydrate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg303

b:43.3
occ:1.00
 O F:HOH443 2.1 36.5 1.0
O F:HOH556 2.4 25.2 1.0
O F:HOH406 4.2 26.7 1.0
O F:THR193 4.4 18.3 1.0
NZ F:LYS195 4.6 40.4 1.0

Reference:

M.Lenz, S.Fademrecht, M.Sharma, J.Pleiss, G.Grogan, B.M.Nestl. New Imine-Reducing Enzymes From Beta-Hydroxyacid Dehydrogenases By Single Amino Acid Substitutions. Protein Eng. Des. Sel. V. 31 109 2018.
ISSN: ESSN 1741-0134
PubMed: 29733377
DOI: 10.1093/PROTEIN/GZY006
Page generated: Mon Sep 30 00:15:43 2024

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