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Sodium in PDB 8q3v: Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex

Other elements in 8q3v:

The structure of Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex (pdb code 8q3v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex, PDB code: 8q3v:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 8q3v

Go back to Sodium Binding Sites List in 8q3v
Sodium binding site 1 out of 6 in the Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:57.4
occ:1.00
 OD1 E:ASP187 2.1 61.1 1.0
O E:HOH408 2.1 47.9 1.0
O E:HOH404 2.2 48.6 1.0
OG E:SER29 2.2 54.1 1.0
O E:HOH405 2.3 50.7 1.0
OE2 E:GLU61 2.3 53.0 1.0
CB E:SER29 3.0 45.9 1.0
CG E:ASP187 3.1 55.4 1.0
CD E:GLU61 3.3 54.4 1.0
OE1 E:GLU61 3.6 55.1 1.0
OD2 E:ASP187 3.7 56.2 1.0
O E:SER29 3.8 57.8 1.0
OD2 E:ASP26 3.9 56.0 1.0
OD1 E:ASP30 4.1 58.1 1.0
C E:SER29 4.1 48.4 1.0
O E:ASP26 4.1 45.8 1.0
CA E:SER29 4.1 47.3 1.0
CA E:ASP187 4.3 46.3 1.0
CB E:ASP187 4.3 45.8 1.0
O E:GLY182 4.3 53.0 1.0
OG E:SER35 4.4 51.4 1.0
O E:GLN34 4.4 53.9 1.0
N E:ASP187 4.4 50.1 1.0
CG E:GLU61 4.6 45.4 1.0
CG E:ASP26 4.6 53.1 1.0
CA E:ASP26 4.8 43.6 1.0
CG E:PRO37 4.8 42.5 1.0
C E:GLY186 4.9 50.2 1.0
C E:GLY182 4.9 50.7 1.0
C E:ASP26 4.9 41.9 1.0
N E:ASP30 4.9 44.6 1.0
CD E:PRO37 4.9 42.2 1.0
N E:SER29 5.0 46.4 1.0

Sodium binding site 2 out of 6 in 8q3v

Go back to Sodium Binding Sites List in 8q3v
Sodium binding site 2 out of 6 in the Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:57.5
occ:1.00
 OD1 E:ASP26 2.4 62.9 1.0
OD2 E:ASP30 2.5 55.0 1.0
O E:GLY186 2.7 51.5 1.0
CG E:ASP26 3.1 53.1 1.0
OD2 E:ASP26 3.2 56.0 1.0
CG E:ASP30 3.4 58.1 1.0
O E:HOH405 3.4 50.7 1.0
CB E:CYS231 3.5 42.1 1.0
OD1 E:ASP30 3.6 58.1 1.0
C E:GLY186 3.7 50.2 1.0
SG E:CYS231 3.7 65.7 1.0
CA E:GLY186 4.1 44.2 1.0
C E:GLY235 4.1 40.0 1.0
O E:ASP26 4.3 45.8 1.0
N E:GLY236 4.3 49.4 1.0
O E:GLY235 4.3 46.2 1.0
CA E:GLY235 4.4 34.3 1.0
N E:TYR190 4.4 40.0 1.0
CB E:HIS189 4.4 37.1 1.0
CB E:TYR190 4.5 35.0 1.0
CB E:ASP26 4.6 40.1 1.0
CA E:CYS231 4.6 39.9 1.0
O E:CYS231 4.7 49.6 1.0
C E:ASP26 4.7 41.9 1.0
N E:ASP187 4.8 50.1 1.0
CD2 E:LEU27 4.8 44.6 1.0
CB E:ASP30 4.8 51.4 1.0
CA E:GLY236 4.9 34.7 1.0
C E:CYS231 5.0 44.8 1.0

Sodium binding site 3 out of 6 in 8q3v

Go back to Sodium Binding Sites List in 8q3v
Sodium binding site 3 out of 6 in the Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Na301

b:57.4
occ:1.00
 OD1 e:ASP187 2.0 61.1 1.0
O e:HOH402 2.1 47.5 1.0
O e:HOH404 2.1 49.0 1.0
OE2 e:GLU61 2.2 53.0 1.0
O e:HOH403 2.2 48.1 1.0
OG e:SER29 2.4 54.1 1.0
CB e:SER29 2.9 45.9 1.0
CG e:ASP187 3.1 55.4 1.0
CD e:GLU61 3.2 54.4 1.0
OE1 e:GLU61 3.6 55.1 1.0
OD2 e:ASP187 3.7 56.2 1.0
O e:SER29 3.8 57.8 1.0
OD2 e:ASP26 3.9 56.0 1.0
OD1 e:ASP30 4.0 58.1 1.0
C e:SER29 4.1 48.4 1.0
CA e:SER29 4.1 47.3 1.0
O e:ASP26 4.2 45.8 1.0
CB e:ASP187 4.3 45.8 1.0
O e:GLN34 4.3 53.9 1.0
CA e:ASP187 4.3 46.3 1.0
O e:GLY182 4.3 53.0 1.0
OG e:SER35 4.4 51.4 1.0
CG e:GLU61 4.5 45.4 1.0
N e:ASP187 4.5 50.1 1.0
CG e:ASP26 4.7 53.1 1.0
CA e:ASP26 4.8 43.6 1.0
N e:ASP30 4.9 44.6 1.0
C e:GLY182 4.9 50.7 1.0
CD e:PRO37 5.0 42.2 1.0
N e:SER29 5.0 46.4 1.0
C e:GLY186 5.0 50.2 1.0
C e:ASP26 5.0 41.9 1.0

Sodium binding site 4 out of 6 in 8q3v

Go back to Sodium Binding Sites List in 8q3v
Sodium binding site 4 out of 6 in the Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Na302

b:57.5
occ:1.00
 OD1 e:ASP26 2.3 62.9 1.0
OD2 e:ASP30 2.5 55.0 1.0
O e:GLY186 2.6 51.5 1.0
CG e:ASP26 3.1 53.1 1.0
OD2 e:ASP26 3.2 56.0 1.0
CG e:ASP30 3.5 58.1 1.0
O e:HOH403 3.5 48.1 1.0
C e:GLY186 3.5 50.2 1.0
CB e:CYS231 3.6 42.1 1.0
OD1 e:ASP30 3.6 58.1 1.0
SG e:CYS231 3.8 65.7 1.0
CA e:GLY186 3.9 44.2 1.0
C e:GLY235 4.1 40.0 1.0
O e:GLY235 4.3 46.2 1.0
O e:ASP26 4.3 45.8 1.0
N e:GLY236 4.3 49.4 1.0
CA e:GLY235 4.3 34.3 1.0
N e:TYR190 4.3 40.0 1.0
CB e:HIS189 4.4 37.1 1.0
CB e:TYR190 4.5 35.0 1.0
CB e:ASP26 4.5 40.1 1.0
N e:ASP187 4.6 50.1 1.0
C e:ASP26 4.7 41.9 1.0
O e:CYS231 4.7 49.6 1.0
CA e:CYS231 4.7 39.9 1.0
CB e:ASP30 4.9 51.4 1.0
CD2 e:LEU27 4.9 44.6 1.0
CA e:GLY236 4.9 34.7 1.0

Sodium binding site 5 out of 6 in 8q3v

Go back to Sodium Binding Sites List in 8q3v
Sodium binding site 5 out of 6 in the Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Na301

b:57.4
occ:1.00
 O U:HOH407 2.1 48.1 1.0
OD1 U:ASP187 2.1 61.1 1.0
O U:HOH402 2.3 50.6 1.0
OE2 U:GLU61 2.3 53.0 1.0
O U:HOH401 2.3 47.9 1.0
OG U:SER29 2.4 54.1 1.0
CB U:SER29 3.0 45.9 1.0
CG U:ASP187 3.2 55.4 1.0
CD U:GLU61 3.3 54.4 1.0
OD2 U:ASP26 3.6 56.0 1.0
OE1 U:GLU61 3.6 55.1 1.0
OD2 U:ASP187 3.9 56.2 1.0
O U:SER29 3.9 57.8 1.0
OD1 U:ASP30 4.1 58.1 1.0
O U:ASP26 4.1 45.8 1.0
C U:SER29 4.2 48.4 1.0
CA U:SER29 4.2 47.3 1.0
CA U:ASP187 4.2 46.3 1.0
O U:GLY182 4.2 53.0 1.0
CB U:ASP187 4.3 45.8 1.0
N U:ASP187 4.4 50.1 1.0
OG U:SER35 4.4 51.4 1.0
O U:GLN34 4.5 53.9 1.0
CG U:ASP26 4.6 53.1 1.0
CG U:GLU61 4.6 45.4 1.0
CA U:ASP26 4.7 43.6 1.0
C U:GLY186 4.8 50.2 1.0
C U:GLY182 4.8 50.7 1.0
C U:ASP26 4.9 41.9 1.0
N U:ASP30 5.0 44.6 1.0
O U:GLY186 5.0 51.5 1.0

Sodium binding site 6 out of 6 in 8q3v

Go back to Sodium Binding Sites List in 8q3v
Sodium binding site 6 out of 6 in the Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Na302

b:57.5
occ:1.00
 OD1 U:ASP26 2.4 62.9 1.0
OD2 U:ASP30 2.5 55.0 1.0
O U:GLY186 2.6 51.5 1.0
CG U:ASP26 3.1 53.1 1.0
OD2 U:ASP26 3.2 56.0 1.0
O U:HOH402 3.3 50.6 1.0
CG U:ASP30 3.4 58.1 1.0
OD1 U:ASP30 3.5 58.1 1.0
CB U:CYS231 3.5 42.1 1.0
C U:GLY186 3.6 50.2 1.0
SG U:CYS231 3.7 65.7 1.0
CA U:GLY186 4.0 44.2 1.0
C U:GLY235 4.2 40.0 1.0
O U:ASP26 4.3 45.8 1.0
N U:TYR190 4.3 40.0 1.0
CB U:HIS189 4.4 37.1 1.0
O U:GLY235 4.4 46.2 1.0
CB U:TYR190 4.4 35.0 1.0
N U:GLY236 4.4 49.4 1.0
CA U:GLY235 4.4 34.3 1.0
N U:ASP187 4.5 50.1 1.0
CB U:ASP26 4.6 40.1 1.0
C U:ASP26 4.7 41.9 1.0
CA U:CYS231 4.7 39.9 1.0
O U:CYS231 4.8 49.6 1.0
CB U:ASP30 4.8 51.4 1.0
CD2 U:LEU27 4.9 44.6 1.0
CA U:TYR190 5.0 37.9 1.0
CA U:GLY236 5.0 34.7 1.0

Reference:

I.Aziz, K.Kayastha, S.Kaltwasser, J.Vonck, S.Welsch, B.J.Murphy, J.Kahnt, D.Wu, T.Wagner, S.Shima, U.Ermler. Structural and Mechanistic Basis of the Central Energy-Converting Methyltransferase Complex of Methanogenesis. Proc.Natl.Acad.Sci.Usa V. 121 68121 2024.
ISSN: ESSN 1091-6490
PubMed: 38530900
DOI: 10.1073/PNAS.2315568121
Page generated: Mon Aug 18 15:09:26 2025

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