Magnesium in PDB 9h3f: Cryo-Em Structure of Yham

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Yham (pdb code 9h3f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Cryo-Em Structure of Yham, PDB code: 9h3f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Cryo-Em Structure of Yham


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 Yham within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:36.5 occ:1.00 NE2 A:HIS250 2.1 53.8 1.0 NE2 A:HIS218 2.1 53.0 1.0 CE1 A:HIS251 2.4 48.1 1.0 NE2 A:HIS251 2.4 49.6 1.0 CD2 A:HIS218 3.0 55.4 1.0 CE1 A:HIS250 3.1 55.2 1.0 CD2 A:HIS250 3.1 51.3 1.0 CE1 A:HIS218 3.2 56.6 1.0 OD1 A:ASP194 3.4 61.1 1.0 ND1 A:HIS251 3.4 53.0 1.0 CD2 A:HIS251 3.5 53.6 1.0 CG A:HIS251 4.1 54.6 1.0 CG A:HIS218 4.2 54.2 1.0 CG A:ASP194 4.2 60.3 1.0 ND1 A:HIS250 4.2 49.6 1.0 ND1 A:HIS218 4.2 56.5 1.0 CG A:HIS250 4.2 45.6 1.0 OD2 A:ASP194 4.4 58.6 1.0 O A:HIS193 4.6 52.4 1.0 CD2 A:HIS193 4.9 52.4 1.0

Magnesium binding site 2 out of 12 in the Cryo-Em Structure of Yham


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 Yham within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:48.4 occ:1.00 OD2 A:ASP194 2.0 58.6 1.0 OD1 A:ASP274 2.0 64.1 1.0 NE2 A:HIS193 2.1 51.3 1.0 NE2 A:HIS163 2.4 52.8 1.0 CE1 A:HIS193 2.8 47.5 1.0 CD2 A:HIS163 3.0 48.6 1.0 CD2 A:HIS193 3.1 52.4 1.0 CG A:ASP194 3.2 60.3 1.0 CG A:ASP274 3.3 64.8 1.0 CE1 A:HIS163 3.5 60.5 1.0 SD A:MET167 3.9 69.9 1.0 ND1 A:HIS193 3.9 47.1 1.0 OD1 A:ASP194 4.0 61.1 1.0 CG A:HIS193 4.1 48.5 1.0 OD2 A:ASP274 4.1 68.8 1.0 CB A:ASP274 4.2 55.1 1.0 CG A:HIS163 4.2 49.1 1.0 CB A:ASP194 4.3 54.1 1.0 ND1 A:HIS163 4.4 57.1 1.0 CE A:MET167 4.5 55.4 1.0 CA A:ASP274 4.8 54.1 1.0

Magnesium binding site 3 out of 12 in the Cryo-Em Structure of Yham


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 Yham within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:43.4 occ:1.00 NE2 B:HIS218 2.1 62.2 1.0 CE1 B:HIS251 2.3 59.5 1.0 NE2 B:HIS251 2.4 52.2 1.0 NE2 B:HIS250 2.5 60.6 1.0 OD1 B:ASP194 3.0 66.8 1.0 CE1 B:HIS218 3.0 63.0 1.0 CD2 B:HIS250 3.2 56.2 1.0 CD2 B:HIS218 3.2 65.2 1.0 ND1 B:HIS251 3.4 67.3 1.0 CE1 B:HIS250 3.6 62.1 1.0 CD2 B:HIS251 3.6 53.8 1.0 CG B:HIS251 4.1 60.2 1.0 CG B:ASP194 4.2 68.1 1.0 ND1 B:HIS218 4.2 60.7 1.0 CG B:HIS218 4.3 60.8 1.0 CG B:HIS250 4.5 53.3 1.0 ND1 B:HIS250 4.6 60.7 1.0 CE B:LYS197 4.7 75.0 1.0 OD2 B:ASP194 4.7 67.3 1.0 O B:HIS193 4.7 59.6 1.0 CD2 B:HIS193 4.8 59.4 1.0

Magnesium binding site 4 out of 12 in the Cryo-Em Structure of Yham


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Yham within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:43.3 occ:1.00 OD2 B:ASP194 2.1 67.3 1.0 NE2 B:HIS193 2.1 55.9 1.0 OD1 B:ASP274 2.2 70.3 1.0 NE2 B:HIS163 2.3 56.9 1.0 CD2 B:HIS163 2.9 54.5 1.0 CD2 B:HIS193 3.1 59.4 1.0 CE1 B:HIS193 3.1 57.2 1.0 CG B:ASP194 3.2 68.1 1.0 CG B:ASP274 3.4 73.6 1.0 CE1 B:HIS163 3.4 66.7 1.0 OD1 B:ASP194 3.8 66.8 1.0 SD B:MET167 3.8 73.5 1.0 CG B:HIS163 4.1 54.9 1.0 OD2 B:ASP274 4.2 83.0 1.0 CB B:ASP194 4.2 62.6 1.0 ND1 B:HIS193 4.2 57.6 1.0 CG B:HIS193 4.3 56.2 1.0 ND1 B:HIS163 4.3 65.5 1.0 CB B:ASP274 4.4 62.4 1.0 CE B:MET167 4.7 58.9 1.0 CA B:ASP274 4.8 61.4 1.0

Magnesium binding site 5 out of 12 in the Cryo-Em Structure of Yham


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Yham within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1001 b:50.0 occ:1.00 NE2 C:HIS218 2.1 60.0 1.0 NE2 C:HIS250 2.2 55.9 1.0 CE1 C:HIS251 2.4 58.0 1.0 OD1 C:ASP194 2.9 63.0 1.0 CD2 C:HIS218 3.0 61.0 1.0 ND1 C:HIS251 3.0 63.9 1.0 CD2 C:HIS250 3.0 52.6 1.0 CE1 C:HIS218 3.1 61.2 1.0 CE1 C:HIS250 3.3 57.0 1.0 NE2 C:HIS251 3.5 59.3 1.0 NZ C:LYS197 4.1 72.1 1.0 CG C:HIS218 4.1 58.8 1.0 ND1 C:HIS218 4.1 60.3 1.0 CG C:ASP194 4.1 64.9 1.0 CG C:HIS250 4.3 51.4 1.0 CG C:HIS251 4.3 62.7 1.0 ND1 C:HIS250 4.4 58.0 1.0 CD2 C:HIS193 4.5 56.4 1.0 CD2 C:HIS251 4.5 63.0 1.0 O C:HIS193 4.6 57.5 1.0 OD2 C:ASP194 4.7 64.6 1.0

Magnesium binding site 6 out of 12 in the Cryo-Em Structure of Yham


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Yham within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:52.3 occ:1.00 OD2 C:ASP194 2.1 64.6 1.0 NE2 C:HIS193 2.1 53.8 1.0 OD1 C:ASP274 2.4 63.1 1.0 CE1 C:HIS163 2.4 57.9 1.0 CE C:MET167 2.6 62.4 1.0 CE1 C:HIS193 2.7 52.6 1.0 CG C:ASP194 3.1 64.9 1.0 ND1 C:HIS163 3.1 52.7 1.0 NE2 C:HIS163 3.2 62.9 1.0 CD2 C:HIS193 3.3 56.4 1.0 CG C:ASP274 3.6 59.6 1.0 OD1 C:ASP194 3.8 63.0 1.0 SD C:MET167 3.8 77.1 1.0 ND1 C:HIS193 3.9 51.0 1.0 CG C:HIS163 4.1 52.9 1.0 CD2 C:HIS163 4.1 58.8 1.0 CB C:ASP194 4.2 61.9 1.0 CG C:HIS193 4.3 53.9 1.0 CB C:ASP274 4.4 51.6 1.0 OD2 C:ASP274 4.5 62.5 1.0 CA C:ASP274 4.8 54.7 1.0

Magnesium binding site 7 out of 12 in the Cryo-Em Structure of Yham


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of Yham within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1001 b:47.8 occ:1.00 NE2 D:HIS251 2.1 59.4 1.0 NE2 D:HIS218 2.2 65.3 1.0 CE1 D:HIS251 2.4 56.6 1.0 NE2 D:HIS250 2.5 58.1 1.0 OD1 D:ASP194 3.0 64.8 1.0 CE1 D:HIS218 3.0 65.0 1.0 CD2 D:HIS250 3.2 53.9 1.0 CD2 D:HIS218 3.2 67.3 1.0 CD2 D:HIS251 3.2 61.9 1.0 ND1 D:HIS251 3.5 58.0 1.0 CE1 D:HIS250 3.6 59.2 1.0 CG D:HIS251 3.9 59.5 1.0 CG D:ASP194 4.1 67.8 1.0 ND1 D:HIS218 4.1 65.9 1.0 CG D:HIS218 4.2 64.7 1.0 CG D:HIS250 4.3 52.4 1.0 ND1 D:HIS250 4.5 58.0 1.0 OD2 D:ASP194 4.6 68.8 1.0 CE D:LYS197 4.8 81.4 1.0 CD2 D:HIS193 4.8 57.6 1.0 O D:HIS193 4.8 60.7 1.0

Magnesium binding site 8 out of 12 in the Cryo-Em Structure of Yham


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of Yham within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:58.2 occ:1.00 OD2 D:ASP194 2.0 68.8 1.0 NE2 D:HIS163 2.1 64.5 1.0 OD1 D:ASP274 2.1 64.2 1.0 NE2 D:HIS193 2.1 56.3 1.0 CD2 D:HIS163 2.6 56.0 1.0 CE1 D:HIS193 3.1 57.6 1.0 CD2 D:HIS193 3.1 57.6 1.0 CG D:ASP194 3.1 67.8 1.0 CE1 D:HIS163 3.3 67.7 1.0 CG D:ASP274 3.3 63.8 1.0 SD D:MET167 3.8 71.9 1.0 CG D:HIS163 3.8 54.0 1.0 OD1 D:ASP194 3.9 64.8 1.0 OD2 D:ASP274 4.1 68.1 1.0 CB D:ASP194 4.1 62.2 1.0 ND1 D:HIS163 4.1 62.3 1.0 ND1 D:HIS193 4.2 55.2 1.0 CG D:HIS193 4.2 55.8 1.0 CB D:ASP274 4.4 56.1 1.0 CE D:MET167 4.5 59.8 1.0 CA D:ASP274 4.9 58.6 1.0

Magnesium binding site 9 out of 12 in the Cryo-Em Structure of Yham


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of Yham within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1001 b:41.3 occ:1.00 NE2 E:HIS218 2.1 53.2 1.0 NE2 E:HIS251 2.1 51.5 1.0 NE2 E:HIS250 2.2 51.7 1.0 CE1 E:HIS251 2.4 51.9 1.0 CE1 E:HIS218 3.0 54.9 1.0 CD2 E:HIS250 3.1 49.7 1.0 OD1 E:ASP194 3.1 60.4 1.0 CD2 E:HIS218 3.2 56.9 1.0 CE1 E:HIS250 3.2 52.3 1.0 CD2 E:HIS251 3.2 55.1 1.0 ND1 E:HIS251 3.5 54.5 1.0 CG E:HIS251 3.9 54.5 1.0 ND1 E:HIS218 4.1 55.6 1.0 CG E:HIS250 4.2 45.8 1.0 CG E:HIS218 4.2 54.9 1.0 ND1 E:HIS250 4.3 48.8 1.0 CG E:ASP194 4.3 62.6 1.0 OD2 E:ASP194 4.7 63.7 1.0 NZ E:LYS197 4.8 72.8 1.0 O E:HIS193 5.0 54.7 1.0 CD2 E:HIS193 5.0 48.8 1.0

Magnesium binding site 10 out of 12 in the Cryo-Em Structure of Yham


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of Yham within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1002 b:58.7 occ:1.00 OD2 E:ASP194 2.1 63.7 1.0 OD1 E:ASP274 2.1 63.9 1.0 NE2 E:HIS163 2.1 60.2 1.0 NE2 E:HIS193 2.3 47.9 1.0 CE1 E:HIS163 2.6 61.1 1.0 CD2 E:HIS163 3.1 55.8 1.0 CD2 E:HIS193 3.2 48.8 1.0 CG E:ASP194 3.2 62.6 1.0 CG E:ASP274 3.3 61.7 1.0 CE1 E:HIS193 3.3 50.0 1.0 ND1 E:HIS163 3.7 59.5 1.0 SD E:MET167 3.7 69.3 1.0 OD2 E:ASP274 3.8 66.2 1.0 CG E:HIS163 3.9 52.1 1.0 OD1 E:ASP194 3.9 60.4 1.0 CB E:ASP194 4.2 56.8 1.0 CG E:HIS193 4.4 49.1 1.0 ND1 E:HIS193 4.4 51.7 1.0 CB E:ASP274 4.5 51.9 1.0 CE E:MET167 4.7 59.6 1.0 CA E:ASP274 4.9 55.8 1.0

J.Hanssmann, J.Pane-Farre, M.Meiser, M.Girbig, L.Fu, M.G.Madej, F.L.Sendker, C.Tholken, M.Lechner, C.Ziegler, G.K.A.Hochberg, G.Bange, M.Thanbichler, R.Hinrichs. A Conserved Nuclease Facilitates Environmental Dna Uptake. Nucleic Acids Res. V. 53 2025.
ISSN: ESSN 1362-4962
PubMed: 40421801
DOI: 10.1093/NAR/GKAF443