Magnesium in PDB 9dpb: Human Lysrs Bound to Unmodified Trna-LYS3 (Undocked State, Ampcpp Bound)

All present enzymatic activity of Human Lysrs Bound to Unmodified Trna-LYS3 (Undocked State, Ampcpp Bound):
6.1.1.6;

The structure of Human Lysrs Bound to Unmodified Trna-LYS3 (Undocked State, Ampcpp Bound) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Human Lysrs Bound to Unmodified Trna-LYS3 (Undocked State, Ampcpp Bound) (pdb code 9dpb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Lysrs Bound to Unmodified Trna-LYS3 (Undocked State, Ampcpp Bound), PDB code: 9dpb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Lysrs Bound to Unmodified Trna-LYS3 (Undocked State, Ampcpp Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Lysrs Bound to Unmodified Trna-LYS3 (Undocked State, Ampcpp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:150.1 occ:1.00 OE2 A:GLU494 2.3 102.1 1.0 O3' A:APC602 3.2 132.3 1.0 O A:ILE495 3.4 92.1 1.0 CD A:GLU494 3.5 102.1 1.0 O2' A:APC602 3.7 132.3 1.0 OD1 A:ASN497 3.9 105.4 1.0 C4' A:APC602 3.9 122.8 1.0 C A:ILE495 4.0 92.1 1.0 C3' A:APC602 4.1 132.3 1.0 N A:GLY550 4.2 95.2 1.0 CG A:ASN497 4.3 105.4 1.0 CG A:GLU494 4.3 102.1 1.0 CA A:MET549 4.4 91.3 1.0 OE1 A:GLU494 4.4 102.1 1.0 C2' A:APC602 4.5 132.3 1.0 N A:CYS496 4.5 92.1 1.0 N A:ASN497 4.5 110.9 1.0 O A:GLY548 4.5 91.3 1.0 CA A:CYS496 4.6 92.1 1.0 C A:CYS496 4.6 110.9 1.0 C A:MET549 4.6 91.3 1.0 C5' A:APC602 4.6 122.8 1.0 CB A:ASN497 4.8 105.4 1.0 CA A:ILE495 4.8 102.1 1.0 O A:GLU494 4.8 102.1 1.0 N A:MET549 4.8 91.3 1.0 ND2 A:ASN497 4.8 105.4 1.0 C A:GLY548 4.9 91.3 1.0 CA A:GLY550 5.0 95.2 1.0

Magnesium binding site 2 out of 4 in the Human Lysrs Bound to Unmodified Trna-LYS3 (Undocked State, Ampcpp Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Lysrs Bound to Unmodified Trna-LYS3 (Undocked State, Ampcpp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:150.1 occ:1.00 OE1 A:GLU494 3.2 102.1 1.0 OE2 A:GLU487 3.5 88.4 1.0 OE1 A:GLU487 3.8 88.4 1.0 CD A:GLU487 4.1 88.4 1.0 CD A:GLU494 4.5 102.1 1.0 O1G A:APC602 4.8 111.8 1.0

Magnesium binding site 3 out of 4 in the Human Lysrs Bound to Unmodified Trna-LYS3 (Undocked State, Ampcpp Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Lysrs Bound to Unmodified Trna-LYS3 (Undocked State, Ampcpp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:105.2 occ:1.00 OE2 B:GLU494 3.1 275.0 1.0 C4' B:APC602 3.2 101.3 1.0 C5' B:APC602 3.2 101.3 1.0 OD1 B:ASN497 3.5 295.3 1.0 O B:ILE495 3.7 275.0 1.0 C3' B:APC602 3.7 101.3 1.0 CD B:GLU494 3.8 275.0 1.0 O B:LYS601 3.8 113.2 1.0 O3' B:APC602 3.8 105.2 1.0 O B:GLY548 4.1 250.7 1.0 N B:GLY550 4.3 250.7 1.0 CG B:GLU494 4.3 275.0 1.0 C B:ILE495 4.3 275.0 1.0 CG B:ASN497 4.4 295.3 1.0 C B:GLY548 4.5 250.7 1.0 CA B:CYS496 4.5 295.3 1.0 O4' B:APC602 4.5 101.3 1.0 OE1 B:GLU494 4.6 275.0 1.0 CA B:MET549 4.6 250.7 1.0 O5' B:APC602 4.6 101.3 1.0 N B:ASN497 4.6 295.3 1.0 C B:MET549 4.6 250.7 1.0 N B:CYS496 4.7 295.3 1.0 N B:MET549 4.7 250.7 1.0 C B:CYS496 4.8 295.3 1.0 C B:LYS601 4.8 113.2 1.0 CB B:ASN497 4.9 295.3 1.0

Magnesium binding site 4 out of 4 in the Human Lysrs Bound to Unmodified Trna-LYS3 (Undocked State, Ampcpp Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Lysrs Bound to Unmodified Trna-LYS3 (Undocked State, Ampcpp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:105.2 occ:1.00 OE2 B:GLU487 2.5 88.4 1.0 OE1 B:GLU494 3.2 275.0 1.0 CD B:GLU487 3.4 88.4 1.0 OE1 B:GLU487 3.7 88.4 1.0 CD B:GLU494 4.2 275.0 1.0 NH2 B:ARG485 4.4 88.4 1.0 O1A B:APC602 4.5 101.3 1.0 CZ B:PHE489 4.6 103.5 1.0 OE2 B:GLU494 4.7 275.0 1.0 CG B:GLU487 4.8 88.4 1.0

S.C.Devarkar, C.R.Budding, C.Pathirage, A.Kavoor, C.Herbert, P.A.Limbach, K.Musier-Forsyth, Y.Xiong. Structural Basis For Aminoacylation of Cellular Modified TRNALYS3 By Human Lysyl-Trna Synthetase. Nucleic Acids Res. V. 53 2025.
ISSN: ESSN 1362-4962
PubMed: 40036503
DOI: 10.1093/NAR/GKAF114