Sodium in PDB 6ymz: Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043

Enzymatic activity of Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043

All present enzymatic activity of Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043:
3.1.1.61; 3.5.1.44;

Protein crystallography data

The structure of Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043, PDB code: 6ymz was solved by J.A.Gavira, T.Krell, F.Velando-Soriano, M.A.Matilla, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.31 / 2.30
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 148.741, 148.741, 206.34, 90, 90, 90
R / Rfree (%) 19.2 / 22.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043 (pdb code 6ymz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043, PDB code: 6ymz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 6ymz

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Sodium binding site 1 out of 8 in the Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:38.9
occ:1.00
 O A:ILE210 2.4 27.1 1.0
O A:ASN205 2.4 30.2 1.0
O A:CYS208 2.5 27.7 1.0
OD1 A:ASN205 2.7 23.4 1.0
C A:ASN205 3.4 31.4 1.0
C A:CYS208 3.5 24.2 1.0
CG A:ASN205 3.5 24.2 1.0
C A:ILE210 3.5 22.0 1.0
CA A:ASN205 3.7 29.5 1.0
O A:GLN209 4.0 25.3 1.0
C A:GLN209 4.1 30.8 1.0
CA A:THR211 4.1 21.8 1.0
CA A:CYS208 4.2 25.1 1.0
CB A:ASN205 4.2 26.1 1.0
CB A:CYS208 4.2 26.6 1.0
N A:THR211 4.2 22.5 1.0
N A:CYS208 4.3 29.4 1.0
O A:HOH573 4.3 57.9 1.0
ND2 A:ASN205 4.3 23.8 1.0
N A:ILE210 4.4 25.3 1.0
N A:GLN209 4.4 23.3 1.0
N A:VAL212 4.5 23.8 1.0
CA A:GLN209 4.5 28.3 1.0
N A:LYS206 4.6 34.5 0.5
N A:LYS206 4.6 34.5 0.5
CA A:ILE210 4.6 21.2 1.0
C A:THR211 4.8 24.2 1.0
O A:LEU204 4.9 22.4 1.0

Sodium binding site 2 out of 8 in 6ymz

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Sodium binding site 2 out of 8 in the Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:57.3
occ:1.00
 O A:HIS26 2.4 40.6 1.0
O A:ASN24 2.5 42.0 1.0
NZ A:LYS3 2.6 68.4 1.0
O A:MET29 2.6 39.0 1.0
C A:ASN24 3.3 41.2 1.0
C A:HIS26 3.5 42.8 1.0
CA A:ASN24 3.6 47.4 1.0
C A:MET29 3.8 36.8 1.0
CE A:LYS3 3.8 68.5 1.0
O A:ILE23 4.0 47.2 1.0
CA A:PRO27 4.1 47.4 1.0
CD A:LYS3 4.2 68.2 1.0
N A:HIS26 4.2 42.9 1.0
N A:PRO27 4.3 45.6 1.0
C A:PRO27 4.4 48.1 1.0
CB A:ASN24 4.4 47.4 1.0
N A:SER25 4.5 34.0 1.0
N A:MET29 4.5 42.6 1.0
CA A:HIS26 4.5 41.1 1.0
O A:PRO27 4.6 54.1 1.0
CA A:GLU30 4.6 39.8 1.0
CB A:GLU30 4.6 50.1 1.0
C A:SER25 4.7 44.3 1.0
N A:GLU30 4.7 38.2 1.0
N A:ASN24 4.7 44.1 1.0
C A:ILE23 4.8 44.7 1.0
CA A:MET29 4.8 37.6 1.0
OD1 A:ASN24 4.9 43.0 1.0
N A:ASP28 4.9 43.2 1.0
CA A:SER25 5.0 38.6 1.0

Sodium binding site 3 out of 8 in 6ymz

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Sodium binding site 3 out of 8 in the Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:55.0
occ:1.00
 O B:HOH579 2.0 44.5 1.0
O B:HIS26 2.4 41.5 1.0
O B:ASN24 2.6 38.3 1.0
O B:MET29 2.6 36.4 1.0
C B:ASN24 3.4 33.3 1.0
C B:HIS26 3.5 39.3 1.0
CA B:ASN24 3.6 32.4 1.0
NZ B:LYS3 3.7 56.3 1.0
C B:MET29 3.8 37.7 1.0
O B:ILE23 4.0 30.6 1.0
CE B:LYS3 4.0 50.7 1.0
CA B:PRO27 4.1 41.5 1.0
CD B:LYS3 4.3 44.9 1.0
N B:HIS26 4.3 35.5 1.0
C B:PRO27 4.3 38.9 1.0
N B:PRO27 4.3 41.3 1.0
N B:MET29 4.4 29.8 1.0
O B:PRO27 4.4 42.2 1.0
N B:SER25 4.5 32.1 1.0
CB B:ASN24 4.5 35.5 1.0
CA B:HIS26 4.5 37.3 1.0
C B:SER25 4.7 33.0 1.0
N B:ASN24 4.7 28.7 1.0
CA B:GLU30 4.7 31.1 1.0
N B:GLU30 4.7 32.4 1.0
C B:ILE23 4.8 28.4 1.0
CA B:MET29 4.8 33.9 1.0
CB B:GLU30 4.8 38.3 1.0
OD1 B:ASN24 4.8 38.7 1.0
N B:ASP28 4.8 38.6 1.0
CA B:SER25 5.0 33.5 1.0

Sodium binding site 4 out of 8 in 6ymz

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Sodium binding site 4 out of 8 in the Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:54.5
occ:1.00
 O B:HOH589 2.1 48.7 1.0
O B:ILE210 2.5 35.5 1.0
O B:CYS208 2.5 39.4 1.0
O B:ASN205 2.5 41.0 1.0
OD1 B:ASN205 2.6 33.2 1.0
C B:ASN205 3.5 38.0 1.0
C B:ILE210 3.5 29.5 1.0
CG B:ASN205 3.6 34.0 1.0
C B:CYS208 3.6 41.5 1.0
CA B:ASN205 3.9 32.4 1.0
O B:GLN209 3.9 37.1 1.0
CA B:THR211 4.0 30.7 1.0
C B:GLN209 4.0 35.4 1.0
N B:THR211 4.2 26.8 1.0
CB B:ASN205 4.3 29.2 1.0
ND2 B:ASN205 4.4 29.2 1.0
N B:ILE210 4.4 31.8 1.0
CA B:CYS208 4.5 42.1 1.0
N B:CYS208 4.5 47.6 1.0
N B:GLN209 4.5 40.7 1.0
CA B:GLN209 4.5 38.8 1.0
N B:VAL212 4.6 27.4 1.0
CA B:ILE210 4.6 33.1 1.0
CB B:CYS208 4.7 39.9 1.0
N B:LYS206 4.7 40.6 1.0
C B:THR211 4.8 29.3 1.0
OG1 B:THR211 4.9 31.8 1.0
O B:LEU204 5.0 31.1 1.0

Sodium binding site 5 out of 8 in 6ymz

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Sodium binding site 5 out of 8 in the Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:42.1
occ:1.00
 O C:GLY231 2.3 35.8 1.0
O C:ARG258 2.5 29.0 1.0
O C:MET192 2.5 33.3 1.0
C C:GLY231 3.4 34.4 1.0
C C:MET192 3.5 29.6 1.0
C C:ARG258 3.6 31.5 1.0
CD C:PRO259 3.6 23.9 1.0
CA C:GLY231 3.8 26.5 1.0
CA C:PRO193 3.9 28.5 1.0
N C:PRO259 4.0 28.4 1.0
N C:PRO193 4.1 31.1 1.0
N C:MET192 4.2 20.7 1.0
CD C:PRO194 4.4 32.3 1.0
C C:PRO193 4.5 32.8 1.0
CA C:MET192 4.5 28.3 1.0
N C:ALA232 4.6 31.1 1.0
N C:PRO194 4.7 37.7 1.0
CA C:ARG258 4.8 27.1 1.0
N C:ARG258 5.0 26.2 1.0
CG C:PRO259 5.0 27.7 1.0
CA C:ALA232 5.0 39.2 1.0

Sodium binding site 6 out of 8 in 6ymz

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Sodium binding site 6 out of 8 in the Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:34.3
occ:1.00
 O C:ILE210 2.4 25.7 1.0
O C:ASN205 2.5 32.4 1.0
O C:CYS208 2.5 26.1 1.0
OD1 C:ASN205 2.7 19.3 1.0
O C:HOH609 2.7 43.4 1.0
CG C:ASN205 3.5 18.6 1.0
C C:ILE210 3.5 20.1 1.0
C C:CYS208 3.5 22.4 1.0
C C:ASN205 3.5 30.4 1.0
CA C:ASN205 3.9 25.8 1.0
O C:GLN209 4.0 27.1 1.0
C C:GLN209 4.0 24.1 1.0
O C:HOH613 4.1 60.0 1.0
CA C:THR211 4.1 15.8 1.0
N C:THR211 4.2 21.1 1.0
ND2 C:ASN205 4.2 26.8 1.0
CA C:CYS208 4.3 20.9 1.0
CB C:ASN205 4.3 18.2 1.0
N C:CYS208 4.4 26.3 1.0
CB C:CYS208 4.4 21.3 1.0
N C:ILE210 4.4 21.8 1.0
N C:GLN209 4.4 24.5 1.0
CA C:GLN209 4.5 25.5 1.0
N C:VAL212 4.6 20.6 1.0
CA C:ILE210 4.6 19.6 1.0
N C:LYS206 4.7 31.7 0.4
N C:LYS206 4.7 31.4 0.6
C C:THR211 4.8 22.8 1.0

Sodium binding site 7 out of 8 in 6ymz

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Sodium binding site 7 out of 8 in the Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:44.8
occ:1.00
 O D:ASN205 2.5 29.9 1.0
O D:ILE210 2.5 29.4 1.0
OD1 D:ASN205 2.5 28.4 1.0
O D:CYS208 2.7 44.0 1.0
C D:ASN205 3.4 30.8 1.0
CG D:ASN205 3.4 31.2 1.0
C D:ILE210 3.5 26.5 1.0
C D:CYS208 3.7 40.4 1.0
CA D:ASN205 3.7 24.5 1.0
O D:GLN209 3.9 32.8 1.0
CA D:THR211 4.0 29.1 1.0
C D:GLN209 4.1 33.2 1.0
N D:THR211 4.1 25.5 1.0
CB D:ASN205 4.2 20.4 1.0
ND2 D:ASN205 4.2 29.4 1.0
CA D:CYS208 4.4 35.5 1.0
N D:CYS208 4.5 35.4 1.0
N D:ILE210 4.5 28.6 1.0
CB D:CYS208 4.5 35.7 1.0
N D:VAL212 4.5 33.0 1.0
N D:GLN209 4.6 37.9 1.0
N D:LYS206 4.6 37.8 1.0
CA D:GLN209 4.6 37.9 1.0
CA D:ILE210 4.6 22.3 1.0
C D:THR211 4.8 31.2 1.0
O D:LEU204 4.9 29.0 1.0
OG1 D:THR211 5.0 37.3 1.0

Sodium binding site 8 out of 8 in 6ymz

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Sodium binding site 8 out of 8 in the Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na401

b:46.4
occ:1.00
 O E:ILE210 2.5 40.6 1.0
O E:CYS208 2.5 58.1 1.0
O E:ASN205 2.6 60.4 1.0
OD1 E:ASN205 2.6 42.1 1.0
C E:ILE210 3.5 46.3 1.0
CG E:ASN205 3.5 41.6 1.0
C E:ASN205 3.6 56.8 1.0
C E:CYS208 3.6 57.5 1.0
O E:GLN209 3.7 56.4 1.0
CA E:ASN205 3.8 48.8 1.0
C E:GLN209 3.9 58.2 1.0
CA E:THR211 4.1 48.0 1.0
N E:THR211 4.1 47.1 1.0
CB E:ASN205 4.3 40.1 1.0
ND2 E:ASN205 4.3 40.5 1.0
N E:ILE210 4.4 53.6 1.0
CA E:CYS208 4.4 58.2 1.0
N E:GLN209 4.5 61.7 1.0
CB E:CYS208 4.5 61.4 1.0
CA E:GLN209 4.5 63.4 1.0
N E:CYS208 4.5 54.8 1.0
CA E:ILE210 4.6 52.0 1.0
N E:VAL212 4.6 42.4 1.0
N E:LYS206 4.8 59.6 0.6
N E:LYS206 4.8 59.6 0.4
C E:THR211 4.8 45.8 1.0
O E:LEU204 5.0 40.4 1.0

Reference:

F.Velando, J.A.Gavira, M.Rico-Jimenez, M.A.Matilla, T.Krell. Evidence For Pentapeptide-Dependent and Independent Cheb Methylesterases. Int J Mol Sci V. 21 2020.
ISSN: ESSN 1422-0067
PubMed: 33187094
DOI: 10.3390/IJMS21228459
Page generated: Wed Mar 3 15:30:49 2021

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