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

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

Sodium

(Na)

6 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cryo-Em Structure of the Methanogenic Na+ Translocating N5-Methyl- H4MPT:Com Methyltransferase Complex, PDB code: 8q3v:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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 B:Mg201 b:30.0 occ:1.00 O B:HOH303 1.8 30.0 1.0 O B:HOH301 1.8 30.0 1.0 O a:HOH303 1.9 30.0 1.0 OXT B:LEU100 2.2 67.4 1.0 O a:LEU235 2.3 61.8 1.0 O B:ALA97 2.4 59.1 1.0 C B:LEU100 3.3 70.4 1.0 O a:VAL238 3.5 81.0 1.0 C B:ALA97 3.5 43.6 1.0 C a:LEU235 3.5 61.2 1.0 O B:LEU100 3.7 67.0 1.0 C a:VAL238 4.0 80.9 1.0 CA B:ALA97 4.1 38.2 1.0 OXT a:VAL238 4.2 79.5 1.0 CA a:LEU235 4.3 56.9 1.0 N a:LEU236 4.5 61.9 1.0 N B:LEU98 4.6 48.2 1.0 CB B:ALA97 4.6 36.6 1.0 CA a:LEU236 4.6 57.2 1.0 CA B:LEU100 4.6 64.1 1.0 C a:LEU236 4.7 60.6 1.0 N B:LEU100 4.7 57.3 1.0 CB a:LEU235 4.7 55.7 1.0 O B:LEU98 4.8 57.0 1.0 O a:LEU236 4.8 65.9 1.0 CA a:VAL238 4.9 73.8 1.0 C B:LEU98 4.9 54.3 1.0 CA B:LEU98 4.9 49.2 1.0 N a:VAL238 4.9 71.6 1.0

Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg 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 b:Mg201 b:30.0 occ:1.00 O b:HOH301 1.9 30.0 1.0 O b:HOH304 2.1 30.0 1.0 O Q:HOH301 2.1 30.0 1.0 O b:ALA97 2.1 59.1 1.0 O Q:LEU235 2.4 61.8 1.0 OXT b:LEU100 2.4 67.4 1.0 C b:ALA97 3.3 43.6 1.0 O Q:VAL238 3.5 81.0 1.0 C b:LEU100 3.5 70.4 1.0 C Q:LEU235 3.5 61.2 1.0 CA b:ALA97 4.0 38.2 1.0 O b:LEU100 4.0 67.0 1.0 C Q:VAL238 4.0 80.9 1.0 OXT Q:VAL238 4.2 79.5 1.0 CA Q:LEU235 4.3 56.9 1.0 N b:LEU98 4.4 48.2 1.0 O b:LEU98 4.5 57.0 1.0 CB b:ALA97 4.5 36.6 1.0 N Q:LEU236 4.6 61.9 1.0 C b:LEU98 4.6 54.3 1.0 CA b:LEU98 4.6 49.2 1.0 CB Q:LEU235 4.6 55.7 1.0 N b:LEU100 4.7 57.3 1.0 CA b:LEU100 4.7 64.1 1.0 CA Q:LEU236 4.8 57.2 1.0 CY6 W:JCV101 4.9 61.2 0.0 C Q:LEU236 4.9 60.6 1.0 CA Q:VAL238 5.0 73.8 1.0 O b:PHE96 5.0 46.6 1.0 CD2 Q:LEU235 5.0 57.5 1.0

Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg 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 R:Mg201 b:30.0 occ:1.00 O R:HOH302 1.9 30.0 1.0 O A:HOH301 2.1 30.0 1.0 O R:HOH304 2.2 30.0 1.0 OXT R:LEU100 2.3 67.4 1.0 O R:ALA97 2.4 59.1 1.0 O A:LEU235 2.4 61.8 1.0 C R:LEU100 3.4 70.4 1.0 C R:ALA97 3.5 43.6 1.0 O A:VAL238 3.5 81.0 1.0 C A:LEU235 3.6 61.2 1.0 O R:LEU100 3.8 67.0 1.0 C A:VAL238 4.0 80.9 1.0 CA R:ALA97 4.1 38.2 1.0 OXT A:VAL238 4.3 79.5 1.0 CA A:LEU235 4.4 56.9 1.0 N A:LEU236 4.6 61.9 1.0 N R:LEU98 4.6 48.2 1.0 CA R:LEU100 4.6 64.1 1.0 N R:LEU100 4.6 57.3 1.0 CB R:ALA97 4.7 36.6 1.0 CA A:LEU236 4.7 57.2 1.0 O R:LEU98 4.7 57.0 1.0 C A:LEU236 4.8 60.6 1.0 O A:LEU236 4.8 65.9 1.0 CB A:LEU235 4.8 55.7 1.0 C R:LEU98 4.8 54.3 1.0 CA R:LEU98 4.9 49.2 1.0 CA A:VAL238 4.9 73.8 1.0 O R:PHE96 5.0 46.6 1.0 N A:VAL238 5.0 71.6 1.0

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