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Sodium in PDB 1h16: Pyruvate Formate-Lyase (E.Coli) in Complex with Pyruvate and Coa

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

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

Protein crystallography data

The structure of Pyruvate Formate-Lyase (E.Coli) in Complex with Pyruvate and Coa, PDB code: 1h16 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) 15.00 / 1.53
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 54.900, 153.050, 205.950, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 16.3

Other elements in 1h16:

The structure of Pyruvate Formate-Lyase (E.Coli) in Complex with Pyruvate and Coa 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 Pyruvate and Coa (pdb code 1h16). 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 and Coa, PDB code: 1h16:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 1h16

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


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

b:18.2
occ:1.00
OE1 A:GLU700 2.3 17.7 1.0
O A:HOH3160 2.3 17.7 1.0
O A:LEU654 2.4 12.7 1.0
O A:ALA652 2.4 13.3 1.0
O A:HOH3157 2.4 19.1 1.0
O A:GLY701 2.9 14.1 1.0
CD A:GLU700 3.4 18.2 1.0
C A:LEU654 3.5 12.1 1.0
C A:ALA652 3.5 11.5 1.0
O A:HOH3161 3.8 18.2 1.0
CB A:GLU700 3.8 17.2 1.0
C A:GLY701 3.9 13.2 1.0
O A:HOH3089 3.9 14.8 1.0
CG A:GLU700 3.9 18.6 1.0
N A:PHE656 4.1 11.5 1.0
C A:LYS653 4.1 12.9 1.0
CA A:PRO655 4.1 12.3 1.0
N A:LEU654 4.2 12.6 1.0
N A:PRO655 4.2 12.8 1.0
O A:LYS653 4.2 14.1 1.0
N A:GLY701 4.3 13.7 1.0
CA A:ALA652 4.4 11.8 1.0
N A:LYS653 4.4 13.1 1.0
CA A:LEU654 4.5 11.4 1.0
OE2 A:GLU700 4.5 18.0 1.0
CA A:LYS653 4.5 13.6 1.0
C A:PRO655 4.6 12.2 1.0
CA A:GLY702 4.7 10.8 1.0
N A:GLY702 4.7 11.3 1.0
O A:HOH2639 4.7 28.5 1.0
CA A:GLY701 4.8 13.1 1.0
C A:GLU700 4.8 14.5 1.0
O A:VAL651 4.9 11.4 1.0
CA A:GLU700 4.9 13.9 1.0
CB A:PHE656 4.9 12.9 1.0

Sodium binding site 2 out of 7 in 1h16

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


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

b:48.3
occ:1.00
O A:HOH2595 2.1 28.6 1.0
O A:HOH2920 2.1 20.3 1.0
O A:HOH2591 3.9 36.8 1.0
OE1 A:GLU214 4.0 26.9 1.0
OH A:TYR499 4.1 13.6 1.0
CE1 A:TYR499 4.5 10.0 1.0
O A:HOH2594 4.8 37.1 0.5
CZ A:TYR499 4.8 10.4 1.0
CD A:GLU214 5.0 20.6 1.0

Sodium binding site 3 out of 7 in 1h16

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


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 and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9003

b:48.4
occ:1.00
O A:HOH2330 2.0 19.6 1.0
O A:HOH2138 2.1 25.6 1.0
O A:HOH2327 2.9 14.7 1.0
N A:ILE81 3.0 8.7 1.0
CB A:SER268 3.0 7.9 1.0
O A:HOH2140 3.0 38.1 1.0
CA A:THR80 3.0 7.9 1.0
O A:HOH2139 3.3 16.9 1.0
C A:THR80 3.4 8.3 1.0
CB A:THR80 3.4 10.4 1.0
CG1 A:ILE81 3.7 8.2 1.0
CA A:SER268 3.8 7.6 1.0
O A:HOH3257 3.9 40.4 1.0
CA A:ILE81 4.1 8.3 1.0
O A:HOH2689 4.1 26.8 0.5
CG2 A:THR80 4.2 11.8 1.0
OG A:SER268 4.2 8.9 1.0
CB A:ILE81 4.3 7.9 1.0
N A:THR80 4.3 8.3 1.0
CD1 A:ILE81 4.4 8.8 1.0
O A:SER79 4.5 9.4 1.0
O A:HOH2637 4.5 17.5 1.0
O A:THR80 4.5 9.4 1.0
O A:HOH2334 4.5 20.0 1.0
OG1 A:THR80 4.6 11.5 1.0
O A:SER268 4.7 9.5 1.0
N A:SER268 4.7 8.3 1.0
C A:SER268 4.7 8.2 1.0
OE1 A:GLN232 4.8 12.4 1.0
C A:SER79 4.8 8.6 1.0
O A:LYS267 4.9 9.2 1.0
O A:HOH2687 4.9 9.8 1.0
O A:HOH3254 4.9 19.0 1.0

Sodium binding site 4 out of 7 in 1h16

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


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

b:52.1
occ:1.00
O A:HOH2624 2.3 50.2 1.0
O A:HOH3136 2.4 43.8 1.0
O4 A:PG49013 2.5 50.6 1.0
C6 A:PG49013 3.4 49.0 1.0
C7 A:PG49013 3.6 51.5 1.0
C5 A:PG49013 3.7 48.1 1.0
CD2 A:LEU688 3.8 16.6 1.0
N A:LEU688 3.9 13.4 1.0
C8 A:PG49013 4.0 51.7 1.0
C A:GLY687 4.0 14.9 1.0
O A:GLY687 4.1 15.1 1.0
CA A:LEU688 4.1 13.1 1.0
CG A:LEU688 4.3 15.6 1.0
O A:HOH2625 4.6 57.6 1.0
CA A:GLY687 4.7 14.4 1.0
CB A:LEU688 4.7 13.9 1.0
O A:ASN684 4.8 15.2 1.0
O A:HOH3137 5.0 32.8 1.0

Sodium binding site 5 out of 7 in 1h16

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


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 and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9005

b:51.1
occ:1.00
O A:HOH2558 2.2 39.0 1.0
O A:HOH3027 2.5 31.9 1.0
O A:GLN589 2.6 19.9 1.0
CD A:PRO599 3.5 14.9 1.0
C A:GLN589 3.5 17.7 1.0
CG A:GLN589 3.7 27.4 1.0
CA A:GLN589 3.7 18.2 1.0
O A:HOH3042 3.8 27.2 1.0
CG A:PRO599 4.0 15.2 1.0
CB A:GLN589 4.3 20.7 1.0
O A:HOH3031 4.4 39.5 1.0
N A:PRO599 4.7 12.6 1.0
N A:LYS590 4.7 17.5 1.0
O A:HOH3040 4.8 46.3 1.0
CB A:PRO599 4.8 16.0 1.0
O A:LEU591 4.8 14.8 1.0
O A:ILE588 4.9 14.1 1.0
O A:HOH3025 5.0 40.3 1.0

Sodium binding site 6 out of 7 in 1h16

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


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 and Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9006

b:47.5
occ:1.00
O A:HOH2101 2.3 46.9 1.0
O A:HOH3192 2.3 36.8 1.0
O A:HOH2258 2.5 45.1 1.0
CE A:LYS62 2.8 20.1 1.0
NZ A:LYS62 3.0 22.5 1.0
O A:HOH2253 3.2 20.7 1.0
CB A:MET58 3.8 13.1 1.0
CE A:MET58 4.0 14.9 1.0
CG A:PRO726 4.1 15.3 1.0
CB A:PRO726 4.2 14.2 1.0
CD A:LYS62 4.2 16.6 1.0
O A:HOH2093 4.2 39.8 1.0
CG A:MET58 4.2 14.0 1.0
OE2 A:GLU59 4.4 16.6 1.0
CG A:LYS62 4.8 14.7 1.0
SD A:MET58 5.0 14.2 1.0

Sodium binding site 7 out of 7 in 1h16

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


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 and Coa 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: Tue Dec 15 05:25:09 2020

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