Atomistry » Sodium » PDB 4mfc-4mzx » 4mkk
Atomistry »
  Sodium »
    PDB 4mfc-4mzx »
      4mkk »

Sodium in PDB 4mkk: Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine

Enzymatic activity of Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine

All present enzymatic activity of Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine:
4.4.1.11;

Protein crystallography data

The structure of Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine, PDB code: 4mkk was solved by S.V.Revtovich, A.D.Nikulin, E.A.Morozova, L.N.Zakomirdina, T.V.Demidkina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 1.45
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 56.690, 122.860, 128.600, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 17.3

Other elements in 4mkk:

The structure of Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine (pdb code 4mkk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine, PDB code: 4mkk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4mkk

Go back to Sodium Binding Sites List in 4mkk
Sodium binding site 1 out of 5 in the Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:26.2
occ:1.00
 OD1 A:ASP342 2.7 19.3 1.0
OG A:SER339 2.9 12.3 0.5
O A:THR209 2.9 11.8 1.0
O A:HOH514 3.4 13.2 1.0
CG A:ASP342 3.6 18.0 1.0
OD2 A:ASP342 3.7 21.1 1.0
CB A:SER339 3.8 20.7 0.5
CG2 A:THR209 3.8 12.9 1.0
CA A:GLY216 3.9 11.7 1.0
CB A:SER339 3.9 13.3 0.5
O A:LEU340 3.9 14.7 1.0
C A:THR209 4.0 10.7 1.0
O A:HOH515 4.0 10.8 1.0
OG A:SER339 4.1 22.8 0.5
N A:GLY216 4.5 11.8 1.0
CD A:LLP210 4.6 16.5 1.0
C A:GLY216 4.7 11.1 1.0
CA A:LLP210 4.7 11.4 1.0
N A:LEU340 4.7 14.2 1.0
N A:LLP210 4.8 10.4 1.0
CA A:THR209 4.8 11.4 1.0
CB A:THR209 4.9 11.2 1.0
C A:LEU340 4.9 15.1 1.0
CA A:SER339 5.0 17.9 0.5
CB A:ASP342 5.0 14.5 1.0

Sodium binding site 2 out of 5 in 4mkk

Go back to Sodium Binding Sites List in 4mkk
Sodium binding site 2 out of 5 in the Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:24.5
occ:1.00
 O A:ALA84 2.7 11.6 1.0
N A:MET246 2.9 11.3 1.0
CA A:C1S245 3.3 15.4 0.5
CA A:C1S245 3.3 12.7 0.5
O A:HOH774 3.4 32.8 1.0
CB A:C1S245 3.5 18.4 0.5
CB A:C1S245 3.5 19.9 0.5
C A:C1S245 3.6 14.1 0.5
C A:ALA84 3.6 8.4 1.0
C A:C1S245 3.6 11.4 0.5
O A:HOH790 3.6 34.1 1.0
CB A:MET246 3.9 10.5 1.0
CA A:MET246 3.9 9.7 1.0
O A:MET246 4.0 12.8 1.0
SG A:C1S245 4.0 24.4 0.5
CD1 A:LEU238 4.1 17.2 1.0
O A:HOH789 4.3 17.5 1.0
CB A:ALA84 4.3 11.4 1.0
CG2 A:THR66 4.3 12.2 1.0
CA A:ALA84 4.4 10.0 1.0
N A:THR85 4.4 9.5 1.0
C A:MET246 4.4 10.9 1.0
CA A:THR85 4.5 10.7 1.0
OE2 A:GLU70 4.6 12.0 1.0
N A:ALA84 4.6 9.2 1.0
N A:C1S245 4.6 12.3 0.5
N A:C1S245 4.7 13.5 0.5
O A:GLY244 4.7 12.2 1.0
O A:C1S245 4.8 15.2 0.5
O A:C1S245 4.9 10.5 0.5

Sodium binding site 3 out of 5 in 4mkk

Go back to Sodium Binding Sites List in 4mkk
Sodium binding site 3 out of 5 in the Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:33.8
occ:1.00
 O A:ILE317 2.6 17.4 1.0
O A:HOH582 2.7 36.5 1.0
O A:HOH627 2.8 25.9 1.0
N A:GLY320 2.9 22.8 1.0
CA A:GLY320 3.3 22.2 1.0
N A:GLY319 3.5 21.1 1.0
C A:ILE317 3.8 15.6 1.0
CG A:GLU316 3.9 13.3 0.6
C A:ALA318 3.9 19.7 1.0
C A:GLY319 4.0 23.7 1.0
O A:HOH671 4.0 42.6 1.0
CA A:GLY371 4.0 15.3 1.0
CD A:GLU316 4.0 16.7 0.6
CA A:ALA318 4.1 16.2 1.0
OE2 A:GLU316 4.2 16.6 0.6
CA A:GLY319 4.3 22.3 1.0
N A:GLY371 4.3 16.9 1.0
N A:ALA318 4.4 15.4 1.0
O A:HOH773 4.4 32.3 1.0
C A:GLY320 4.5 20.6 1.0
OE1 A:GLU316 4.6 19.0 0.6
O A:ALA318 4.8 21.1 1.0
O A:GLY320 4.9 19.5 1.0
N A:ILE317 4.9 14.8 1.0
CA A:ILE317 5.0 15.2 1.0

Sodium binding site 4 out of 5 in 4mkk

Go back to Sodium Binding Sites List in 4mkk
Sodium binding site 4 out of 5 in the Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:36.6
occ:1.00
 O A:HOH598 2.8 22.9 1.0
O A:HOH672 2.8 37.8 1.0
CL A:CL406 2.8 43.9 1.0
O A:HOH537 2.9 23.1 1.0
CD A:PRO382 3.3 15.0 1.0
NH1 A:ARG267 3.7 19.4 1.0
CZ A:ARG267 4.0 19.0 1.0
CG A:PRO382 4.1 16.0 1.0
OD1 A:ASP381 4.2 16.3 1.0
CD A:ARG267 4.3 16.3 1.0
NE A:ARG267 4.3 18.4 1.0
OD1 A:ASN271 4.3 14.3 1.0
O3 A:PGE402 4.4 43.8 1.0
O A:HOH661 4.5 37.3 1.0
C6 A:PGE402 4.5 40.8 1.0
CA A:ASP381 4.5 10.9 1.0
N A:PRO382 4.6 13.4 1.0
C5 A:PGE402 4.6 43.0 1.0
OE2 A:GLU270 4.6 21.6 1.0
O A:HOH640 4.7 36.3 1.0
NH2 A:ARG267 4.7 21.3 1.0
O A:GLU380 4.8 12.9 1.0
OE1 A:GLU383 4.9 15.7 0.5
CG A:ASP381 5.0 14.7 1.0

Sodium binding site 5 out of 5 in 4mkk

Go back to Sodium Binding Sites List in 4mkk
Sodium binding site 5 out of 5 in the Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of C115A Mutant L-Methionine Gamma-Lyase From Citrobacter Freundii Modified By Allicine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:41.9
occ:1.00
 O A:PRO64 2.7 12.2 1.0
O A:HOH759 2.7 31.8 1.0
OD2 A:ASP67 3.3 20.8 1.0
C A:PRO64 3.6 11.3 1.0
O A:HOH754 3.7 76.3 1.0
N A:ALA68 3.8 10.3 1.0
CA A:PRO64 3.9 11.9 1.0
CB A:ASP67 3.9 11.7 1.0
O A:HOH809 3.9 45.4 1.0
CB A:ALA68 4.0 9.4 1.0
CG A:ASP67 4.1 16.5 1.0
OH A:TYR58 4.1 61.0 0.9
CA A:ALA68 4.2 10.6 1.0
CB A:PRO64 4.3 14.8 1.0
C A:ASP67 4.4 9.6 1.0
CA A:ASP67 4.7 11.5 1.0
NE2 A:GLN19 4.7 27.7 0.6
N A:THR65 4.8 10.5 1.0
O A:GLY17 4.9 16.2 1.0

Reference:

E.A.Morozova, S.V.Revtovich, N.V.Anufrieva, V.V.Kulikova, A.D.Nikulin, T.V.Demidkina. Alliin Is A Suicide Substrate of Citrobacter Freundii Methionine [Gamma]-Lyase: Structural Bases of Inactivation of the Enzyme Acta Crystallogr.,Sect.D V. 70 3034 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004714020938
Page generated: Mon Oct 7 17:00:22 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy