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Chlorine 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:

Magnesium (Mg) 7 atoms
Sodium (Na) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 7 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5v7n

Go back to Chlorine Binding Sites List in 5v7n
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl405

b:27.6
occ:1.00
 O A:HOH779 2.9 37.7 1.0
ND2 A:ASN13 3.1 26.6 1.0
NH1 A:ARG286 3.1 21.5 1.0
O A:HOH734 3.2 27.3 1.0
O A:HOH783 3.5 27.1 1.0
CB A:ASN13 3.6 22.1 1.0
CD A:ARG286 3.8 20.5 1.0
CG A:ASN13 3.8 24.8 1.0
CD1 B:LEU135 3.8 25.9 1.0
CG A:ARG286 3.9 19.2 1.0
CB A:ARG286 4.1 21.6 1.0
CD2 B:LEU135 4.1 19.5 1.0
CA A:ASN13 4.1 22.7 1.0
CZ A:PHE70 4.2 17.6 1.0
CZ A:ARG286 4.2 22.9 1.0
N A:ASN13 4.4 23.7 1.0
CG B:LEU135 4.4 23.5 1.0
NE A:ARG286 4.4 19.3 1.0
CE1 A:PHE70 4.4 23.2 1.0
O A:HOH770 4.6 39.5 1.0
O A:HOH689 4.7 27.9 1.0
O A:HOH598 4.8 25.6 1.0
O A:HOH755 5.0 44.8 1.0
OD1 A:ASN13 5.0 21.4 1.0

Chlorine binding site 2 out of 7 in 5v7n

Go back to Chlorine Binding Sites List in 5v7n
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl406

b:41.6
occ:1.00
 N A:ALA34 3.2 28.4 1.0
CB A:ALA34 3.7 32.5 1.0
CB A:PRO54 3.7 23.9 1.0
CB A:PRO56 3.8 34.6 1.0
CA A:ASP33 3.8 26.4 1.0
OD1 A:ASP33 4.0 35.4 1.0
C A:ASP33 4.0 26.1 1.0
CA A:ALA34 4.0 29.4 1.0
N A:LEU57 4.1 29.6 1.0
CG A:PRO56 4.2 41.5 1.0
CG A:PRO54 4.3 26.5 1.0
O A:ALA32 4.3 29.7 1.0
CB A:LEU57 4.3 28.8 1.0
CD A:PRO56 4.4 35.5 1.0
O A:HOH519 4.4 42.8 1.0
C A:PRO56 4.6 26.1 1.0
CA A:LEU57 4.6 29.3 1.0
N A:ASP33 4.7 24.8 1.0
CA A:PRO56 4.7 29.1 1.0
CG A:ASP33 4.7 42.9 1.0
CB A:ASP33 4.8 30.0 1.0
C A:ALA32 4.9 26.2 1.0
N A:PRO56 4.9 29.2 1.0

Chlorine binding site 3 out of 7 in 5v7n

Go back to Chlorine Binding Sites List in 5v7n
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl404

b:26.2
occ:1.00
 O B:HOH763 2.9 30.8 1.0
O B:HOH773 3.0 44.8 1.0
NH1 B:ARG286 3.1 21.5 1.0
ND2 B:ASN13 3.2 22.1 1.0
O B:HOH775 3.4 30.1 1.0
CD B:ARG286 3.7 19.3 1.0
CB B:ASN13 3.8 20.9 1.0
CG B:ARG286 3.8 18.8 1.0
CD1 A:LEU135 4.0 28.1 1.0
CG B:ASN13 4.0 25.9 1.0
CB B:ARG286 4.0 21.1 1.0
CD2 A:LEU135 4.1 20.2 1.0
CZ B:PHE70 4.2 19.8 1.0
CZ B:ARG286 4.2 23.4 1.0
CA B:ASN13 4.3 19.4 1.0
CE1 B:PHE70 4.4 20.0 1.0
NE B:ARG286 4.4 23.1 1.0
CG A:LEU135 4.5 23.3 1.0
N B:ASN13 4.5 22.8 1.0
O B:HOH769 4.6 47.7 1.0
O B:HOH721 4.8 34.5 1.0
O B:HOH598 4.8 28.5 1.0
O A:HOH859 4.9 51.1 1.0

Chlorine binding site 4 out of 7 in 5v7n

Go back to Chlorine Binding Sites List in 5v7n
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl405

b:41.3
occ:1.00
 N B:ALA34 3.2 32.2 1.0
O B:HOH809 3.3 50.1 1.0
CB B:ALA34 3.7 38.8 1.0
CB B:PRO54 3.7 32.5 1.0
CB B:PRO56 3.9 34.9 1.0
CA B:ASP33 3.9 36.0 1.0
OD1 B:ASP33 4.0 41.1 1.0
C B:ASP33 4.0 42.6 1.0
CA B:ALA34 4.1 42.6 1.0
N B:LEU57 4.1 30.8 1.0
CG B:PRO54 4.1 31.7 1.0
CG B:PRO56 4.2 51.6 1.0
CB B:LEU57 4.4 24.9 1.0
CD B:PRO56 4.4 35.4 1.0
O B:ALA32 4.5 34.6 1.0
C B:PRO56 4.6 29.8 1.0
CA B:LEU57 4.7 29.0 1.0
CA B:PRO56 4.7 46.9 1.0
CG B:ASP33 4.8 40.1 1.0
N B:ASP33 4.8 32.8 1.0
CB B:ASP33 4.9 36.5 1.0
N B:PRO56 4.9 34.5 1.0
C B:ALA32 5.0 31.2 1.0

Chlorine binding site 5 out of 7 in 5v7n

Go back to Chlorine Binding Sites List in 5v7n
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl404

b:34.0
occ:1.00
 NH1 C:ARG286 3.1 32.5 1.0
O C:HOH721 3.2 33.4 1.0
ND2 C:ASN13 3.2 29.3 1.0
O C:HOH757 3.3 44.9 1.0
O C:HOH741 3.6 35.9 1.0
CD C:ARG286 3.7 27.7 1.0
CB C:ASN13 3.7 30.2 1.0
CD1 D:LEU135 3.8 29.7 1.0
CG C:ARG286 3.8 23.1 1.0
CG C:ASN13 3.9 36.5 1.0
CD2 D:LEU135 3.9 29.4 1.0
CB C:ARG286 4.0 26.7 1.0
CZ C:PHE70 4.1 25.3 1.0
CZ C:ARG286 4.2 27.4 1.0
CA C:ASN13 4.2 32.7 1.0
CG D:LEU135 4.3 23.3 1.0
CE1 C:PHE70 4.4 29.3 1.0
NE C:ARG286 4.4 24.1 1.0
N C:ASN13 4.4 29.2 1.0
O C:HOH745 4.8 45.2 1.0
O C:HOH703 4.9 38.2 1.0
O C:HOH602 4.9 31.6 1.0

Chlorine binding site 6 out of 7 in 5v7n

Go back to Chlorine Binding Sites List in 5v7n
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl405

b:35.1
occ:1.00
 O D:HOH724 2.8 44.2 1.0
O D:HOH707 3.0 30.7 1.0
ND2 D:ASN13 3.1 34.8 1.0
NH1 D:ARG286 3.1 28.2 1.0
CB D:ASN13 3.6 28.6 1.0
O D:HOH756 3.7 28.4 1.0
CD D:ARG286 3.7 26.1 1.0
CG D:ASN13 3.8 33.7 1.0
CG D:ARG286 3.9 24.3 1.0
CD1 C:LEU135 4.0 27.0 1.0
CB D:ARG286 4.0 24.2 1.0
CZ D:PHE70 4.1 26.1 1.0
CA D:ASN13 4.1 27.7 1.0
CD2 C:LEU135 4.2 28.2 1.0
CZ D:ARG286 4.2 24.3 1.0
CE1 D:PHE70 4.3 22.3 1.0
N D:ASN13 4.4 28.6 1.0
NE D:ARG286 4.4 25.3 1.0
O D:HOH729 4.5 40.3 1.0
CG C:LEU135 4.6 27.1 1.0
O D:HOH606 4.6 33.5 1.0
O D:HOH565 4.8 29.7 1.0
O D:HOH734 4.8 49.3 1.0
O D:HOH785 5.0 47.9 1.0

Chlorine binding site 7 out of 7 in 5v7n

Go back to Chlorine Binding Sites List in 5v7n
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl406

b:51.1
occ:1.00
 N D:ALA34 3.1 37.6 1.0
O D:HOH696 3.2 62.0 1.0
CB D:ALA34 3.6 38.2 1.0
CB D:PRO54 3.8 37.9 1.0
CA D:ASP33 3.8 41.3 1.0
CB D:PRO56 3.8 50.2 1.0
C D:ASP33 3.9 36.6 1.0
CA D:ALA34 3.9 40.9 1.0
OD1 D:ASP33 4.0 46.5 1.0
N D:LEU57 4.0 36.9 1.0
CG D:PRO54 4.2 39.0 1.0
CB D:LEU57 4.3 38.9 1.0
CG D:PRO56 4.3 48.5 1.0
O D:ALA32 4.4 39.1 1.0
CD D:PRO56 4.4 39.8 1.0
C D:PRO56 4.5 40.0 1.0
CA D:LEU57 4.6 38.0 1.0
N D:ASP33 4.7 32.2 1.0
CA D:PRO56 4.7 44.4 1.0
CG D:ASP33 4.7 47.1 1.0
CB D:ASP33 4.8 39.1 1.0
C D:ALA32 4.9 35.6 1.0
N D:PRO56 4.9 34.7 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: Fri Jul 26 18:39:43 2024

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