Atomistry » Sodium » PDB 1ghy-1hn1 » 1h16
Atomistry »
  Sodium »
    PDB 1ghy-1hn1 »
      1h16 »

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

Go back to Sodium Binding Sites List in 1h16
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

Go back to Sodium Binding Sites List in 1h16
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

Go back to Sodium Binding Sites List in 1h16
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

Go back to Sodium Binding Sites List in 1h16
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

Go back to Sodium Binding Sites List in 1h16
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

Go back to Sodium Binding Sites List in 1h16
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

Go back to Sodium Binding Sites List in 1h16
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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy