Magnesium in PDB 5v7n: Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid

Enzymatic activity of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid

All present enzymatic activity of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid:
1.1.1.81;

Protein crystallography data

The structure of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid, PDB code: 5v7n was solved by I.G.Shabalin, K.B.Handing, C.D.Miks, J.Kutner, D.Matelska, J.Bonanno, S.C.Almo, W.Minor, New York Structural Genomics Research Consortium(Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.11 / 1.75
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 175.902, 175.902, 135.336, 90.00, 90.00, 120.00
R / Rfree (%) 14.4 / 16.7

Other elements in 5v7n:

The structure of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms
Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid (pdb code 5v7n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid, PDB code: 5v7n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5v7n

Go back to Magnesium Binding Sites List in 5v7n
Magnesium binding site 1 out of 7 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid


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 Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:56.4
occ:1.00
 O A:HOH746 2.1 46.6 1.0
O A:HOH738 2.1 48.4 1.0
O3X A:NAP401 2.1 28.4 1.0
O A:HOH763 2.1 61.0 1.0
O A:HOH724 2.1 55.6 1.0
O A:HOH812 2.1 54.4 1.0
P2B A:NAP401 3.4 31.5 1.0
O1X A:NAP401 3.8 34.7 1.0
NH2 A:ARG173 3.8 32.6 1.0
O A:HOH508 3.9 40.8 1.0
O2B A:NAP401 4.0 30.3 1.0
C2B A:NAP401 4.3 37.0 1.0
O A:HOH837 4.4 44.5 1.0
O2X A:NAP401 4.6 31.6 1.0
CZ A:ARG173 4.9 42.3 1.0

Magnesium binding site 2 out of 7 in 5v7n

Go back to Magnesium Binding Sites List in 5v7n
Magnesium binding site 2 out of 7 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid


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 Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:50.6
occ:1.00
 O A:HOH802 2.1 34.2 1.0
O A:HOH595 2.1 26.5 1.0
O A:HOH800 2.1 43.7 1.0
O A:HOH830 2.1 51.2 1.0
O A:HOH527 2.1 41.3 1.0
O A:HOH860 2.1 48.4 1.0
O A:SER50 3.8 22.6 1.0
O A:HOH807 4.0 30.4 1.0
O A:HOH637 4.1 33.5 1.0
OG A:SER50 4.1 23.8 1.0
O A:HOH676 4.2 41.3 1.0
O B:HOH811 4.3 42.3 1.0
O A:LYS11 4.4 22.8 1.0
C A:SER50 4.5 19.8 1.0
CB A:SER50 4.5 24.0 1.0
O A:HOH797 4.6 44.2 1.0
O A:HOH515 4.8 32.6 1.0
CB A:LYS11 4.9 34.3 1.0
O A:HOH770 4.9 39.5 1.0
O A:HOH664 5.0 29.5 1.0

Magnesium binding site 3 out of 7 in 5v7n

Go back to Magnesium Binding Sites List in 5v7n
Magnesium binding site 3 out of 7 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid


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 Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg407

b:44.8
occ:1.00
 O B:HOH725 2.1 76.3 1.0
O B:HOH681 2.1 41.7 1.0
O B:ALA319 2.1 48.8 1.0
C B:ALA319 3.3 40.0 1.0
N B:ALA319 3.9 30.7 1.0
CA B:ALA319 4.1 33.4 1.0
N B:ILE320 4.2 48.5 1.0
CB B:ALA319 4.4 50.1 1.0
CA B:ILE320 4.4 53.3 1.0
C B:ILE320 4.6 68.3 1.0
C B:ARG318 5.0 30.8 1.0

Magnesium binding site 4 out of 7 in 5v7n

Go back to Magnesium Binding Sites List in 5v7n
Magnesium binding site 4 out of 7 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid


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 Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg408

b:55.3
occ:1.00
 O B:HOH739 2.1 38.0 1.0
O B:HOH710 2.1 55.2 1.0
O3X B:NAP401 2.1 26.9 1.0
O B:HOH616 2.1 49.5 1.0
O B:HOH723 2.1 49.8 1.0
O B:HOH808 2.1 53.2 1.0
P2B B:NAP401 3.3 27.1 1.0
O1X B:NAP401 3.7 33.4 1.0
NH2 B:ARG173 3.8 34.6 1.0
O B:HOH765 3.9 39.0 1.0
O2B B:NAP401 4.0 28.4 1.0
C2B B:NAP401 4.2 22.8 1.0
O B:HOH791 4.4 39.1 1.0
O B:HOH518 4.5 41.4 1.0
O2X B:NAP401 4.5 30.1 1.0
CZ B:ARG173 4.9 31.8 1.0
C3B B:NAP401 4.9 26.4 1.0

Magnesium binding site 5 out of 7 in 5v7n

Go back to Magnesium Binding Sites List in 5v7n
Magnesium binding site 5 out of 7 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid


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 Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg405

b:50.3
occ:1.00
 O C:HOH628 2.1 46.2 1.0
O C:HOH716 2.1 61.3 1.0
O C:HOH618 2.1 59.3 1.0
O C:HOH533 2.1 76.3 1.0
O C:HOH770 2.1 51.3 1.0
O3X C:NAP401 2.1 35.6 1.0
P2B C:NAP401 3.2 39.8 1.0
O1X C:NAP401 3.4 42.5 1.0
O2B C:NAP401 3.9 34.5 1.0
O C:HOH565 3.9 51.9 1.0
NH2 C:ARG173 4.2 42.1 1.0
C2B C:NAP401 4.3 36.7 1.0
O C:HOH505 4.4 52.3 1.0
O2X C:NAP401 4.5 32.1 1.0
O C:HOH776 4.7 47.2 1.0
O C:HOH529 4.8 42.1 1.0
C3B C:NAP401 5.0 35.0 1.0

Magnesium binding site 6 out of 7 in 5v7n

Go back to Magnesium Binding Sites List in 5v7n
Magnesium binding site 6 out of 7 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg408

b:60.5
occ:1.00
 O3X D:NAP401 2.1 40.8 1.0
O D:HOH519 2.1 50.7 1.0
O D:HOH620 2.1 57.9 1.0
O D:HOH770 2.1 65.2 1.0
O D:HOH692 2.1 69.6 1.0
O D:HOH684 2.1 44.8 1.0
P2B D:NAP401 3.3 41.3 1.0
O D:HOH562 3.7 52.3 1.0
O1X D:NAP401 3.7 39.3 1.0
O2B D:NAP401 3.9 41.5 1.0
NH2 D:ARG173 4.1 55.0 1.0
C2B D:NAP401 4.3 36.7 1.0
O D:HOH759 4.5 43.1 1.0
O2X D:NAP401 4.5 30.5 1.0
O D:HOH535 4.6 43.6 1.0
C3B D:NAP401 5.0 43.4 1.0

Magnesium binding site 7 out of 7 in 5v7n

Go back to Magnesium Binding Sites List in 5v7n
Magnesium binding site 7 out of 7 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg409

b:68.1
occ:1.00
 O D:HOH771 2.1 56.9 1.0
O D:HOH597 2.1 40.7 1.0
O D:HOH633 2.1 38.8 1.0
O D:HOH804 2.1 87.7 1.0
O D:HOH761 2.1 42.4 1.0
O D:SER50 3.8 35.4 1.0
O D:HOH669 4.0 48.2 1.0
O D:HOH581 4.0 40.8 1.0
OG D:SER50 4.1 29.0 1.0
O D:HOH768 4.2 34.4 1.0
O D:HOH609 4.4 35.6 1.0
O C:HOH788 4.4 46.5 1.0
C D:SER50 4.5 40.7 1.0
O D:LYS11 4.6 29.6 1.0
CB D:SER50 4.6 31.2 1.0
O D:HOH613 4.8 38.7 1.0
O D:HOH749 5.0 38.7 1.0
CA D:GLY51 5.0 38.8 1.0
CB D:LYS11 5.0 35.4 1.0

Reference:

J.Kutner, I.G.Shabalin, D.Matelska, K.B.Handing, O.Gasiorowska, P.Sroka, M.W.Gorna, K.Ginalski, K.Wozniak, W.Minor. Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division Into Two Distinct Subfamilies. Biochemistry V. 57 963 2018.
ISSN: ISSN 1520-4995
PubMed: 29309127
DOI: 10.1021/ACS.BIOCHEM.7B01137
Page generated: Mon Dec 14 21:17:50 2020

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