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Sodium in PDB 1h18: Pyruvate Formate-Lyase (E.Coli) in Complex with Pyruvate

Enzymatic activity of Pyruvate Formate-Lyase (E.Coli) in Complex with Pyruvate

All present enzymatic activity of Pyruvate Formate-Lyase (E.Coli) in Complex with Pyruvate:
2.3.1.54;

Protein crystallography data

The structure of Pyruvate Formate-Lyase (E.Coli) in Complex with Pyruvate, PDB code: 1h18 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 / 2.3
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 158.905, 158.905, 159.922, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Pyruvate Formate-Lyase (E.Coli) in Complex with Pyruvate (pdb code 1h18). 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 Pyruvate, PDB code: 1h18:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 1h18

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


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 Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9001

b:69.1
occ:1.00
 OE1 A:GLU700 2.3 57.6 1.0
O A:HOH2566 2.4 52.1 1.0
O A:ALA652 2.4 51.8 1.0
O A:LEU654 2.6 51.5 1.0
O A:HOH2564 2.7 73.8 1.0
O A:GLY701 2.8 50.0 1.0
CD A:GLU700 3.4 60.2 1.0
C A:ALA652 3.6 51.2 1.0
C A:GLY701 3.6 53.7 1.0
C A:LEU654 3.6 50.8 1.0
CB A:GLU700 3.6 61.0 1.0
CG A:GLU700 3.8 61.4 1.0
N A:GLY701 3.8 55.5 1.0
O A:HOH2588 3.8 60.1 1.0
C A:LYS653 4.1 54.7 1.0
O A:HOH2563 4.1 49.8 1.0
CA A:GLY701 4.2 54.2 1.0
N A:PHE656 4.2 48.4 1.0
N A:LEU654 4.2 52.5 1.0
O A:LYS653 4.3 54.6 1.0
N A:PRO655 4.3 50.7 1.0
C A:GLU700 4.3 57.5 1.0
CA A:PRO655 4.3 49.3 1.0
CA A:ALA652 4.4 50.2 1.0
OE2 A:GLU700 4.5 61.1 1.0
N A:GLY702 4.5 52.2 1.0
N A:LYS653 4.5 51.9 1.0
CA A:LYS653 4.6 54.9 1.0
CA A:LEU654 4.6 51.2 1.0
CA A:GLU700 4.6 60.5 1.0
CA A:GLY702 4.8 51.7 1.0
C A:PRO655 4.8 49.5 1.0
O A:HOH2280 4.9 58.7 1.0
CB A:PHE656 4.9 46.6 1.0

Sodium binding site 2 out of 7 in 1h18

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


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 Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9002

b:92.5
occ:1.00
 O A:HOH2467 2.2 47.0 1.0
O A:HOH2272 2.4 57.9 1.0
O B:GLU214 2.6 45.6 1.0
C B:GLU214 2.9 44.9 1.0
CB B:GLU214 3.4 46.2 1.0
O B:HOH2258 3.4 51.1 1.0
N B:GLN215 3.5 45.2 1.0
CA B:GLU214 3.7 45.0 1.0
CA B:GLN215 3.7 44.0 1.0
CB B:ARG218 3.7 36.2 1.0
NH1 B:ARG218 3.8 41.2 1.0
OH A:TYR499 3.8 36.3 1.0
CZ B:ARG218 3.9 40.9 1.0
NE B:ARG218 4.0 41.7 1.0
CE1 A:TYR499 4.0 33.8 1.0
O B:HOH2263 4.1 50.1 1.0
CD B:ARG218 4.1 38.3 1.0
OE1 A:GLU214 4.3 54.8 1.0
CZ A:TYR499 4.4 34.3 1.0
NH2 B:ARG218 4.5 41.3 1.0
CG B:ARG218 4.6 37.9 1.0
OE1 B:GLU214 4.6 54.5 1.0
CG B:GLU214 4.6 51.2 1.0
CG B:GLN215 4.7 55.8 1.0
C B:GLN215 4.8 42.7 1.0
CB B:GLN215 4.8 48.7 1.0
N B:ARG218 4.8 35.3 1.0
CA B:ARG218 4.9 36.2 1.0
N B:GLU214 5.0 43.6 1.0

Sodium binding site 3 out of 7 in 1h18

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


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 Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9004

b:95.4
occ:1.00
 N A:LEU688 3.8 60.0 1.0
CD2 A:LEU688 4.0 59.4 1.0
C A:GLY687 4.0 59.2 1.0
CA A:LEU688 4.1 60.3 1.0
CG A:LEU688 4.2 59.7 1.0
O A:ASN684 4.3 63.3 1.0
C5 A:PG49013 4.3 95.8 1.0
CE A:MET759 4.3 77.5 1.0
CA A:GLY687 4.4 59.0 1.0
O4 A:PG49013 4.4 0.2 1.0
O A:GLY687 4.4 59.7 1.0
CB A:LEU688 4.7 59.7 1.0
C6 A:PG49013 4.9 98.1 1.0

Sodium binding site 4 out of 7 in 1h18

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


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 Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na9001

b:70.3
occ:1.00
 OE1 B:GLU700 2.2 70.0 1.0
O B:HOH2532 2.4 61.9 1.0
O B:LEU654 2.4 60.7 1.0
O B:GLY701 2.5 63.8 1.0
O B:ALA652 2.8 64.9 1.0
O B:HOH2514 3.1 63.6 1.0
CD B:GLU700 3.4 70.5 1.0
C B:LEU654 3.5 60.5 1.0
O B:HOH2512 3.5 60.3 1.0
C B:GLY701 3.6 65.2 1.0
C B:ALA652 3.8 62.0 1.0
CG B:GLU700 3.9 70.8 1.0
N B:PHE656 3.9 60.9 1.0
CB B:GLU700 4.0 71.2 1.0
N B:GLY701 4.1 66.7 1.0
C B:LYS653 4.1 62.5 1.0
O B:LYS653 4.2 61.5 1.0
CA B:PRO655 4.2 60.0 1.0
N B:PRO655 4.2 59.8 1.0
N B:LEU654 4.3 60.8 1.0
CA B:GLY701 4.4 65.4 1.0
OE2 B:GLU700 4.4 71.0 1.0
N B:LYS653 4.5 63.1 1.0
C B:PRO655 4.5 60.8 1.0
CA B:LYS653 4.5 62.9 1.0
CA B:LEU654 4.6 61.0 1.0
CA B:ALA652 4.6 61.5 1.0
N B:GLY702 4.6 63.9 1.0
CB B:PHE656 4.7 60.8 1.0
C B:GLU700 4.7 68.2 1.0
CA B:GLY702 4.7 62.9 1.0
CA B:PHE656 4.9 61.3 1.0
O B:VAL651 4.9 64.1 1.0
CA B:GLU700 5.0 70.3 1.0

Sodium binding site 5 out of 7 in 1h18

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


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 Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na9003

b:77.8
occ:1.00
 O B:HOH2116 3.0 46.1 1.0
O B:HOH2279 3.3 36.6 1.0
N B:ILE81 3.5 39.7 1.0
CB B:THR80 3.6 40.8 1.0
O B:HOH2570 3.6 71.7 1.0
CA B:THR80 3.8 40.1 1.0
O B:HOH2277 3.8 61.7 1.0
OE1 B:GLN232 3.9 46.1 1.0
O B:HOH2123 3.9 49.5 1.0
O B:HOH2135 4.0 83.5 1.0
CG1 B:ILE81 4.1 34.1 1.0
C B:THR80 4.2 39.9 1.0
CG2 B:THR80 4.2 37.0 1.0
CB B:SER268 4.2 35.1 1.0
CD1 B:ILE81 4.3 34.5 1.0
CB B:ILE81 4.4 36.1 1.0
CA B:ILE81 4.6 37.6 1.0
OG1 B:THR80 4.7 39.7 1.0
O A:HOH2193 4.7 59.9 1.0
C4 B:DTL9009 4.8 70.1 1.0
CD B:GLN232 4.8 45.2 1.0
O4 B:DTL9009 5.0 69.7 1.0

Sodium binding site 6 out of 7 in 1h18

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


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 Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na9006

b:77.9
occ:1.00
 CE B:LYS62 3.3 61.4 1.0
O B:HOH2081 3.4 63.8 1.0
NZ B:LYS62 3.5 62.7 1.0
CB B:MET58 4.0 54.6 1.0
CE B:MET58 4.2 56.4 1.0
CG B:MET58 4.3 52.6 1.0
CG B:PRO726 4.5 61.2 1.0
CB B:PRO726 4.6 60.5 1.0
CD B:LYS62 4.7 59.2 1.0
NE2 B:GLN727 4.8 58.8 1.0

Sodium binding site 7 out of 7 in 1h18

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Sodium binding site 7 out of 7 in the Pyruvate Formate-Lyase (E.Coli) in Complex with Pyruvate


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 Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na9007

b:97.4
occ:1.00
 O A:HOH2477 1.8 43.3 1.0
O A:HOH2198 2.2 68.2 1.0
O A:HOH2070 2.4 70.4 1.0
CD2 A:PHE112 2.6 35.5 0.4
CE2 A:PHE112 2.8 35.0 0.4
CG A:PHE112 3.6 34.1 0.4
CG A:PHE112 3.7 33.3 0.3
CD1 A:PHE112 3.8 33.3 0.3
CD2 A:PHE112 3.8 31.3 0.3
CZ A:PHE112 3.9 33.2 0.4
CE1 A:PHE112 4.0 32.2 0.3
CE2 A:PHE112 4.1 30.3 0.3
NH2 A:ARG141 4.1 41.8 1.0
O A:HOH2630 4.2 68.7 1.0
CZ A:PHE112 4.2 31.9 0.3
CB A:PHE112 4.2 35.5 1.0
O A:HOH2324 4.4 37.8 1.0
NE2 A:GLN269 4.4 33.8 1.0
O A:TYR506 4.5 34.6 1.0
CD1 A:PHE112 4.5 32.9 0.4
O A:HOH2326 4.5 41.6 1.0
CE1 A:PHE112 4.6 31.9 0.4
O A:HOH2475 4.6 47.2 1.0
CA A:SER505 4.6 35.8 1.0
O B:HOH2179 4.6 75.7 1.0
O A:HOH2285 4.7 52.4 1.0
O A:HOH2037 4.7 38.3 1.0
O A:TYR504 4.8 33.5 1.0
OG A:SER505 5.0 40.4 1.0
O3 A:DTL9009 5.0 77.5 1.0
C A:SER505 5.0 35.6 1.0

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: Sun Oct 6 18:39:59 2024

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