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Chlorine in PDB 5v7g: Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadph and Oxalate

Enzymatic activity of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadph and Oxalate

All present enzymatic activity of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadph and Oxalate:
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 Nadph and Oxalate, PDB code: 5v7g was solved by I.G.Shabalin, D.V.Mason, K.B.Handing, J.Kutner, D.Matelska, D.R.Cooper, J.Bonanno, S.C.Almo, W.Minor, New York Structural Genomics Researchconsortium (Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.07 / 1.75
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 178.209, 178.209, 133.799, 90.00, 90.00, 120.00
R / Rfree (%) 15 / 18

Other elements in 5v7g:

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

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 Nadph and Oxalate (pdb code 5v7g). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadph and Oxalate, PDB code: 5v7g:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5v7g

Go back to Chlorine Binding Sites List in 5v7g
Chlorine binding site 1 out of 4 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadph and Oxalate


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 Nadph and Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:36.3
occ:1.00
 O A:HOH777 2.9 39.3 1.0
NH1 A:ARG286 3.1 24.8 1.0
O A:HOH658 3.1 37.5 1.0
ND2 A:ASN13 3.1 27.6 1.0
O A:HOH724 3.6 34.2 1.0
CB A:ASN13 3.7 22.7 1.0
CD A:ARG286 3.7 31.8 1.0
CG A:ASN13 3.9 22.1 1.0
CD1 B:LEU135 3.9 33.0 1.0
CG A:ARG286 3.9 22.0 1.0
CB A:ARG286 4.0 23.4 1.0
CZ A:PHE70 4.1 31.1 1.0
O A:HOH604 4.1 36.1 1.0
CZ A:ARG286 4.2 24.9 1.0
CD2 B:LEU135 4.2 24.0 1.0
CA A:ASN13 4.2 24.6 1.0
CE1 A:PHE70 4.3 31.3 1.0
NE A:ARG286 4.4 26.5 1.0
CG B:LEU135 4.5 23.9 1.0
N A:ASN13 4.5 24.9 1.0
O A:HOH824 4.7 43.9 1.0
O A:HOH722 4.8 48.9 1.0

Chlorine binding site 2 out of 4 in 5v7g

Go back to Chlorine Binding Sites List in 5v7g
Chlorine binding site 2 out of 4 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadph and Oxalate


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 Nadph and Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:38.5
occ:1.00
 O B:HOH766 2.9 41.5 1.0
O B:HOH713 2.9 32.7 1.0
ND2 B:ASN13 3.1 28.9 1.0
NH1 B:ARG286 3.2 26.4 1.0
CB B:ASN13 3.7 29.1 1.0
CD B:ARG286 3.7 25.2 1.0
O B:HOH750 3.8 41.2 1.0
CG B:ASN13 3.9 25.1 1.0
CZ B:PHE70 4.0 24.6 1.0
CG B:ARG286 4.0 22.4 1.0
CB B:ARG286 4.0 25.8 1.0
CD1 A:LEU135 4.1 32.4 1.0
CE1 B:PHE70 4.2 30.4 1.0
O B:HOH738 4.2 52.6 1.0
CZ B:ARG286 4.2 21.2 1.0
CA B:ASN13 4.2 23.9 1.0
CD2 A:LEU135 4.4 25.3 1.0
NE B:ARG286 4.4 30.4 1.0
N B:ASN13 4.5 26.4 1.0
O B:HOH715 4.6 57.3 1.0
CG A:LEU135 4.7 28.1 1.0
CE2 B:PHE70 5.0 32.1 1.0

Chlorine binding site 3 out of 4 in 5v7g

Go back to Chlorine Binding Sites List in 5v7g
Chlorine binding site 3 out of 4 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadph and Oxalate


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 Nadph and Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:27.1
occ:1.00
 NH1 C:ARG286 2.9 18.8 1.0
O C:HOH766 3.1 31.9 1.0
O C:HOH814 3.2 31.9 1.0
ND2 C:ASN13 3.3 21.2 1.0
O C:HOH783 3.5 23.4 1.0
CD C:ARG286 3.7 14.2 1.0
CB C:ASN13 3.8 22.8 1.0
CG C:ARG286 3.9 12.0 1.0
CZ C:ARG286 4.0 18.8 1.0
CG C:ASN13 4.0 22.4 1.0
CD1 D:LEU135 4.0 17.9 1.0
CB C:ARG286 4.0 16.3 1.0
CZ C:PHE70 4.1 24.5 1.0
CD2 D:LEU135 4.2 16.7 1.0
CE1 C:PHE70 4.2 17.7 1.0
NE C:ARG286 4.3 15.7 1.0
CA C:ASN13 4.3 23.9 1.0
CG D:LEU135 4.5 15.0 1.0
N C:ASN13 4.6 25.2 1.0
O C:HOH833 4.7 33.1 1.0

Chlorine binding site 4 out of 4 in 5v7g

Go back to Chlorine Binding Sites List in 5v7g
Chlorine binding site 4 out of 4 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadph and Oxalate


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 Nadph and Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl404

b:31.4
occ:1.00
 O D:HOH824 2.9 39.1 1.0
NH1 D:ARG286 3.1 24.4 1.0
ND2 D:ASN13 3.1 20.8 1.0
O D:HOH682 3.1 35.3 1.0
CD D:ARG286 3.6 22.2 1.0
CB D:ASN13 3.7 25.6 1.0
CZ D:PHE70 3.8 16.4 1.0
CG D:ARG286 3.9 15.8 1.0
CG D:ASN13 3.9 25.1 1.0
CB D:ARG286 3.9 16.6 1.0
O D:HOH741 4.0 34.2 1.0
CE1 D:PHE70 4.1 20.9 1.0
CZ D:ARG286 4.1 21.1 1.0
CD1 C:LEU135 4.1 23.5 1.0
CA D:ASN13 4.3 26.0 1.0
NE D:ARG286 4.3 15.1 1.0
CD2 C:LEU135 4.4 18.8 1.0
O D:HOH548 4.4 42.8 1.0
N D:ASN13 4.6 26.2 1.0
O D:HOH735 4.7 40.3 1.0
O D:HOH784 4.7 53.9 1.0
CG C:LEU135 4.8 18.2 1.0
CE2 D:PHE70 4.8 21.9 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 18:39:42 2024

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