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Sodium in PDB 1h17: Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate

Enzymatic activity of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate

All present enzymatic activity of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate:
2.3.1.54;

Protein crystallography data

The structure of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate, PDB code: 1h17 was solved by A.Becker, W.Kabsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 54.938, 153.169, 205.909, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 17.3

Other elements in 1h17:

The structure of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate (pdb code 1h17). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate, PDB code: 1h17:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 1h17

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Sodium binding site 1 out of 7 in the Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9001

b:20.3
occ:1.00
O A:HOH3157 2.3 16.2 1.0
OE1 A:GLU700 2.4 19.1 1.0
O A:ALA652 2.4 14.4 1.0
O A:HOH3085 2.4 20.0 1.0
O A:LEU654 2.4 13.6 1.0
O A:GLY701 3.0 15.5 1.0
CD A:GLU700 3.4 19.2 1.0
C A:LEU654 3.5 13.1 1.0
C A:ALA652 3.5 14.1 1.0
O A:HOH3158 3.7 18.9 1.0
CB A:GLU700 3.8 19.1 1.0
CG A:GLU700 3.9 19.2 1.0
C A:GLY701 4.0 15.3 1.0
C A:LYS653 4.0 16.7 1.0
O A:HOH3083 4.1 14.9 1.0
N A:PHE656 4.1 13.1 1.0
CA A:PRO655 4.1 13.6 1.0
N A:LEU654 4.2 15.8 1.0
N A:PRO655 4.2 13.7 1.0
O A:LYS653 4.2 16.7 1.0
CA A:ALA652 4.3 14.0 1.0
N A:GLY701 4.4 15.6 1.0
N A:LYS653 4.4 16.0 1.0
CA A:LYS653 4.5 16.9 1.0
OE2 A:GLU700 4.5 18.4 1.0
CA A:LEU654 4.5 13.8 1.0
C A:PRO655 4.7 13.5 1.0
O A:HOH2603 4.7 31.1 1.0
C A:GLU700 4.8 16.1 1.0
CA A:GLY702 4.8 11.7 1.0
N A:GLY702 4.8 13.7 1.0
CA A:GLY701 4.8 15.5 1.0
O A:VAL651 4.9 14.4 1.0
CA A:GLU700 4.9 16.4 1.0
CB A:PHE656 5.0 13.6 1.0

Sodium binding site 2 out of 7 in 1h17

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Sodium binding site 2 out of 7 in the Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9002

b:67.3
occ:1.00
O A:HOH2912 2.1 22.6 1.0
O A:HOH2588 2.2 27.5 1.0
O A:HOH2590 3.8 38.6 1.0
OH A:TYR499 3.9 13.9 1.0
OE1 A:GLU214 4.0 25.1 1.0
CE1 A:TYR499 4.4 11.6 1.0
O A:HOH2587 4.6 68.1 0.5
CZ A:TYR499 4.7 11.8 1.0
CD A:GLU214 5.0 19.3 1.0

Sodium binding site 3 out of 7 in 1h17

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Sodium binding site 3 out of 7 in the Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9003

b:79.0
occ:1.00
N A:ILE81 2.2 8.8 1.0
O A:HOH2313 2.3 20.6 1.0
CB A:SER268 2.5 9.1 1.0
CG1 A:ILE81 2.6 10.1 1.0
C A:THR80 2.9 8.9 1.0
CA A:ILE81 2.9 8.7 1.0
O A:HOH2138 3.1 35.1 1.0
CB A:ILE81 3.2 9.5 1.0
CA A:THR80 3.2 8.8 1.0
CA A:SER268 3.4 8.9 1.0
CD1 A:ILE81 3.5 11.2 1.0
OG A:SER268 3.6 9.0 1.0
O A:THR80 3.8 8.7 1.0
O A:HOH2136 3.8 17.2 1.0
O A:HOH2681 3.8 16.6 1.0
N A:SER268 3.9 9.0 1.0
CB A:THR80 3.9 9.2 1.0
C A:LYS267 4.3 9.7 1.0
O A:ALA264 4.4 9.2 1.0
O A:LYS267 4.4 10.8 1.0
C A:ILE81 4.4 10.3 1.0
O A:HOH2137 4.4 36.5 1.0
N A:THR80 4.5 9.7 1.0
O A:HOH2315 4.6 20.5 1.0
CG2 A:ILE81 4.6 9.7 1.0
C A:SER268 4.7 8.6 1.0
OG1 A:THR80 4.8 10.9 1.0
OE1 A:GLN232 4.8 11.4 1.0
N A:THR82 4.9 11.2 1.0
O A:HOH2680 4.9 10.2 1.0
CB A:LYS267 5.0 9.0 1.0
O A:HOH2631 5.0 18.4 1.0
O A:HOH3254 5.0 48.7 1.0
O A:SER268 5.0 10.4 1.0

Sodium binding site 4 out of 7 in 1h17

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Sodium binding site 4 out of 7 in the Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9004

b:68.5
occ:1.00
O A:HOH2298 2.4 52.2 1.0
O A:HOH3133 2.5 42.3 1.0
O4 A:PG49013 3.1 60.4 1.0
C5 A:PG49013 3.3 55.3 1.0
C6 A:PG49013 3.5 57.3 1.0
CD2 A:LEU688 3.5 19.4 1.0
CG A:LEU688 4.1 18.3 1.0
CA A:LEU688 4.2 15.8 1.0
N A:LEU688 4.2 15.6 1.0
O A:HOH2619 4.3 65.0 1.0
C7 A:PG49013 4.4 60.9 1.0
C A:GLY687 4.4 17.0 1.0
O A:GLY687 4.5 17.7 1.0
O3 A:PG49013 4.5 52.9 1.0
C8 A:PG49013 4.6 61.3 1.0
CB A:LEU688 4.7 16.1 1.0
CG2 A:VAL645 4.7 19.7 1.0
O5 A:PG49013 4.9 60.8 1.0
O A:ASN684 4.9 18.4 1.0

Sodium binding site 5 out of 7 in 1h17

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Sodium binding site 5 out of 7 in the Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9005

b:63.1
occ:1.00
O A:HOH2550 2.3 29.9 1.0
O A:HOH3021 2.4 33.6 1.0
O A:GLN589 2.4 24.4 1.0
C A:GLN589 3.4 22.4 1.0
CD A:PRO599 3.6 14.5 1.0
CA A:GLN589 3.7 23.2 1.0
CG A:GLN589 3.7 31.5 1.0
O A:HOH3036 3.9 25.9 1.0
CG A:PRO599 4.0 16.3 1.0
CB A:GLN589 4.3 25.5 1.0
O A:HOH3025 4.3 40.4 1.0
N A:LYS590 4.6 22.1 1.0
O A:HOH3034 4.7 45.3 1.0
O A:LEU591 4.8 14.9 1.0
CB A:PRO599 4.8 16.0 1.0
O A:ILE588 4.9 18.4 1.0
N A:PRO599 4.9 13.6 1.0

Sodium binding site 6 out of 7 in 1h17

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Sodium binding site 6 out of 7 in the Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9006

b:59.2
occ:1.00
O A:HOH3191 2.3 42.2 1.0
O A:HOH2088 2.4 51.5 1.0
O A:HOH2243 2.8 49.6 1.0
CE A:LYS62 2.8 24.0 1.0
NZ A:LYS62 3.2 25.7 1.0
O A:HOH2233 3.3 22.6 1.0
CB A:MET58 3.6 15.1 1.0
CE A:MET58 3.7 16.4 1.0
CB A:PRO726 3.9 16.0 1.0
CG A:MET58 4.0 16.2 1.0
CG A:PRO726 4.1 17.5 1.0
CD A:LYS62 4.1 20.1 1.0
O A:HOH2089 4.4 34.7 1.0
OE2 A:GLU59 4.4 18.6 1.0
CG A:LYS62 4.6 18.5 1.0
SD A:MET58 4.7 16.0 1.0
O A:MET58 4.8 15.7 1.0
CA A:MET58 4.9 14.6 1.0
C A:MET58 4.9 15.8 1.0
CG A:GLN727 5.0 18.1 1.0

Sodium binding site 7 out of 7 in 1h17

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Sodium binding site 7 out of 7 in the Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate within 5.0Å range:

Reference:

A.Becker, W.Kabsch. X-Ray Structure of Pyruvate Formate-Lyase in Complex with Pyruvate and Coa.How the Enzyme Uses the Cys-418 Thiyl Radical For Pyruvate Cleavage J.Biol.Chem. V. 277 40036 2002.
ISSN: ISSN 0021-9258
PubMed: 12163496
DOI: 10.1074/JBC.M205821200
Page generated: Thu Oct 29 03:47:43 2020

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