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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

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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

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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

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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

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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

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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: Tue Dec 15 06:54:16 2020

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