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Chlorine in PDB 5v72: Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Citrate

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

All present enzymatic activity of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Citrate:
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 Citrate, PDB code: 5v72 was solved by I.G.Shabalin, K.B.Handing, O.A.Gasiorowska, D.R.Cooper, D.Matelska, 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) 50.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.188, 157.926, 64.719, 90.00, 110.74, 90.00
R / Rfree (%) 16.4 / 20.4

Other elements in 5v72:

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

Sodium (Na) 5 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 Citrate (pdb code 5v72). 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 Citrate, PDB code: 5v72:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5v72

Go back to Chlorine Binding Sites List in 5v72
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 Citrate


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 Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:32.8
occ:1.00
 O A:HOH774 2.6 38.6 1.0
ND2 A:ASN13 2.9 22.4 1.0
O A:HOH776 3.0 32.7 1.0
NH2 A:ARG286 3.2 18.8 1.0
CD A:ARG286 3.7 19.6 1.0
CG A:ASN13 3.8 22.3 1.0
CB A:ASN13 3.9 21.9 1.0
CG A:ARG286 3.9 20.2 1.0
CB A:ARG286 4.0 20.3 1.0
CZ A:PHE70 4.0 22.0 1.0
CZ A:ARG286 4.2 19.8 1.0
CD1 C:LEU135 4.3 20.3 1.0
CE1 A:PHE70 4.3 22.8 1.0
O A:HOH669 4.4 22.4 1.0
NE A:ARG286 4.4 19.4 1.0
O A:HOH731 4.4 39.0 1.0
CA A:ASN13 4.6 21.9 1.0
O A:HOH761 4.7 42.1 1.0
CD2 C:LEU135 4.8 20.5 1.0
O A:HOH757 4.8 36.7 1.0
O A:HOH612 5.0 19.9 1.0
CE2 A:PHE70 5.0 21.6 1.0
CG C:LEU135 5.0 20.6 1.0

Chlorine binding site 2 out of 4 in 5v72

Go back to Chlorine Binding Sites List in 5v72
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 Citrate


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 Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:35.3
occ:1.00
 O B:HOH699 2.8 36.6 1.0
NH2 B:ARG286 3.1 27.0 1.0
ND2 B:ASN13 3.2 35.8 1.0
CB B:ASN13 3.7 35.5 1.0
CD B:ARG286 3.8 26.6 1.0
CD1 D:LEU135 3.8 25.5 1.0
CG B:ARG286 3.9 27.1 1.0
O B:HOH635 3.9 36.4 1.0
CG B:ASN13 3.9 35.1 1.0
CZ B:PHE70 4.0 35.2 1.0
CB B:ARG286 4.0 27.4 1.0
O B:HOH631 4.0 34.7 1.0
CE1 B:PHE70 4.1 36.3 1.0
CD2 D:LEU135 4.1 24.6 1.0
CZ B:ARG286 4.2 26.9 1.0
CA B:ASN13 4.3 37.4 1.0
NE B:ARG286 4.5 26.1 1.0
CG D:LEU135 4.5 24.5 1.0
O B:HOH639 4.5 47.0 1.0
N B:ASN13 4.6 38.2 1.0
CE2 B:PHE70 4.9 33.7 1.0

Chlorine binding site 3 out of 4 in 5v72

Go back to Chlorine Binding Sites List in 5v72
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 Citrate


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 Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:29.5
occ:1.00
 O C:HOH776 2.9 34.4 1.0
ND2 C:ASN13 2.9 20.9 1.0
NH2 C:ARG286 3.2 20.6 1.0
CB C:ASN13 3.5 21.4 1.0
O C:HOH675 3.6 25.4 1.0
CD C:ARG286 3.7 18.3 1.0
CG C:ASN13 3.7 21.6 1.0
CG C:ARG286 3.7 18.4 1.0
CB C:ARG286 3.8 18.1 1.0
CZ C:PHE70 3.8 22.4 1.0
CD1 A:LEU135 3.9 23.3 1.0
CE1 C:PHE70 4.1 23.0 1.0
CA C:ASN13 4.2 22.3 1.0
CZ C:ARG286 4.2 20.3 1.0
CD2 A:LEU135 4.3 23.4 1.0
NE C:ARG286 4.4 18.8 1.0
O C:HOH756 4.4 44.9 1.0
O C:HOH703 4.6 45.6 1.0
N C:ASN13 4.6 22.2 1.0
CG A:LEU135 4.6 23.1 1.0
CE2 C:PHE70 4.7 22.5 1.0
OD1 C:ASN13 4.9 20.9 1.0
O C:HOH808 5.0 50.0 1.0

Chlorine binding site 4 out of 4 in 5v72

Go back to Chlorine Binding Sites List in 5v72
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 Citrate


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 Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:41.1
occ:1.00
 O D:HOH679 2.9 42.3 1.0
ND2 D:ASN13 2.9 39.2 1.0
NH2 D:ARG286 3.1 26.8 1.0
CB D:ASN13 3.5 40.4 1.0
CD D:ARG286 3.6 27.1 1.0
CG D:ASN13 3.7 40.3 1.0
CG D:ARG286 3.7 27.3 1.0
CB D:ARG286 3.8 27.3 1.0
CZ D:PHE70 3.9 33.1 1.0
CD1 B:LEU135 4.0 30.9 1.0
O D:HOH570 4.0 43.0 1.0
CE1 D:PHE70 4.2 33.2 1.0
CZ D:ARG286 4.2 26.9 1.0
CA D:ASN13 4.2 42.8 1.0
NE D:ARG286 4.3 27.0 1.0
O D:HOH607 4.4 34.2 1.0
CD2 B:LEU135 4.5 29.2 1.0
N D:ASN13 4.6 42.6 1.0
CG B:LEU135 4.7 29.6 1.0
CE2 D:PHE70 4.8 34.1 1.0
OD1 D:ASN13 4.9 40.0 1.0
O D:HOH694 4.9 52.8 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 18:39:10 2024

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