Magnesium in PDB 6xnx: Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Dynamic-Form)

All present enzymatic activity of Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Dynamic-Form):
2.3.2.27;

The structure of Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Dynamic-Form) also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Dynamic-Form) (pdb code 6xnx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Dynamic-Form), PDB code: 6xnx:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Dynamic-Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Dynamic-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:44.1 occ:1.00 O A:GLY601 1.7 38.3 1.0 OP2 y:DC36 1.9 47.6 1.0 P y:DC36 2.7 47.6 1.0 C A:GLY601 2.8 38.3 1.0 O5' y:DC36 2.9 47.6 1.0 O3' y:DG35 3.2 37.1 1.0 N A:MET602 3.6 36.4 1.0 CA A:MET602 3.7 36.4 1.0 CA A:GLY601 3.8 38.3 1.0 OP1 y:DG35 3.9 37.1 1.0 N A:GLY601 4.1 38.3 1.0 OP1 y:DC36 4.1 47.6 1.0 O3' I:DC16 4.2 43.9 1.0 OP1 y:DG37 4.2 53.7 1.0 OE2 A:GLU662 4.2 40.5 1.0 OE1 A:GLU962 4.3 36.1 1.0 C5' y:DC36 4.3 47.6 1.0 OD2 A:ASP708 4.4 40.6 1.0 MG A:MG1102 4.4 42.3 1.0 C3' I:DC16 4.5 43.9 1.0 C3' y:DC36 4.5 47.6 1.0 C3' y:DG35 4.5 37.1 1.0 OE2 A:GLU962 4.5 36.1 1.0 CB A:MET602 4.7 36.4 1.0 C2' I:DC16 4.8 43.9 1.0 C A:MET602 4.8 36.4 1.0 N A:GLY603 4.8 39.1 1.0 CD A:GLU962 4.9 36.1 1.0 ND2 A:ASN965 5.0 34.5 1.0

Magnesium binding site 2 out of 4 in the Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Dynamic-Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Dynamic-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:42.3 occ:1.00 OE2 A:GLU662 2.0 40.5 1.0 OD2 A:ASP708 2.2 40.6 1.0 O3' I:DC16 2.4 43.9 1.0 OD1 A:ASP708 2.6 40.6 1.0 CG A:ASP708 2.7 40.6 1.0 CD A:GLU662 3.0 40.5 1.0 CG A:GLU662 3.5 40.5 1.0 C3' I:DC16 3.5 43.9 1.0 OE1 A:GLU662 4.1 40.5 1.0 N A:GLY601 4.1 38.3 1.0 OP2 y:DC36 4.1 47.6 1.0 CB A:ASP708 4.2 40.6 1.0 CB A:LYS710 4.2 41.1 1.0 CB A:LEU711 4.2 39.0 1.0 C4' I:DC16 4.2 43.9 1.0 N A:LEU711 4.3 39.0 1.0 MG A:MG1101 4.4 44.1 1.0 NZ A:LYS710 4.4 41.1 1.0 CG A:LYS710 4.4 41.1 1.0 CD A:LYS710 4.5 41.1 1.0 CA A:GLY601 4.6 38.3 1.0 CD2 A:LEU711 4.7 39.0 1.0 CB A:GLU662 4.7 40.5 1.0 CA A:LEU711 4.7 39.0 1.0 O A:GLY601 4.7 38.3 1.0 C2' I:DC16 4.8 43.9 1.0 CG A:LEU711 5.0 39.0 1.0

Magnesium binding site 3 out of 4 in the Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Dynamic-Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Dynamic-Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1101 b:41.9 occ:1.00 OD2 C:ASP708 2.1 39.4 1.0 OE2 C:GLU662 2.1 40.4 1.0 O3' J:DC16 2.1 42.5 1.0 MG x:MG101 2.9 45.2 1.0 CD C:GLU662 2.9 40.4 1.0 C3' J:DC16 3.0 42.5 1.0 OE1 C:GLU662 3.1 40.4 1.0 OP2 x:DC47 3.1 46.4 1.0 CG C:ASP708 3.2 39.4 1.0 O C:GLY601 3.7 37.4 1.0 N C:GLY601 3.7 37.4 1.0 OD1 C:ASP708 3.7 39.4 1.0 C4' J:DC16 4.1 42.5 1.0 C2' J:DC16 4.2 42.5 1.0 O5' x:DC47 4.2 46.4 1.0 CA C:GLY601 4.2 37.4 1.0 P x:DC47 4.3 46.4 1.0 C C:GLY601 4.3 37.4 1.0 CG C:GLU662 4.4 40.4 1.0 CB C:ASP708 4.5 39.4 1.0 C C:ASP600 4.7 35.8 1.0 CA C:ASP600 4.7 35.8 1.0

Magnesium binding site 4 out of 4 in the Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Dynamic-Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Dynamic-Form) within 5.0Å range: probe atom residue distance (Å) B Occ x:Mg101 b:45.2 occ:1.00 O C:GLY601 1.9 37.4 1.0 OP2 x:DC47 2.1 46.4 1.0 O5' x:DC47 2.1 46.4 1.0 P x:DC47 2.4 46.4 1.0 MG C:MG1101 2.9 41.9 1.0 O3' x:DG46 2.9 36.2 1.0 C C:GLY601 3.1 37.4 1.0 C5' x:DC47 3.1 46.4 1.0 OP1 x:DC47 3.9 46.4 1.0 OE1 C:GLU962 3.9 35.1 1.0 O3' J:DC16 3.9 42.5 1.0 CA C:GLY601 4.0 37.4 1.0 N C:GLY601 4.0 37.4 1.0 N C:MET602 4.0 36.9 1.0 C3' J:DC16 4.2 42.5 1.0 OE2 C:GLU662 4.2 40.4 1.0 CA C:MET602 4.2 36.9 1.0 OD2 C:ASP708 4.3 39.4 1.0 OE2 C:GLU962 4.3 35.1 1.0 C3' x:DG46 4.4 36.2 1.0 C4' x:DC47 4.4 46.4 1.0 O C:MET602 4.5 36.9 1.0 C2' J:DC16 4.5 42.5 1.0 CD C:GLU962 4.5 35.1 1.0 C C:MET602 4.7 36.9 1.0 CB C:ASP600 4.7 35.8 1.0 C C:ASP600 4.7 35.8 1.0 ND2 C:ASN965 4.9 34.6 1.0 O5' x:DG46 4.9 36.2 1.0

Y.Zhang, E.Corbett, S.Wu, D.G.Schatz. Structural Basis For the Activation and Suppression of Transposition During Evolution of the Rag Recombinase. Embo J. V. 39 05857 2020.
ISSN: ESSN 1460-2075
PubMed: 32945578
DOI: 10.15252/EMBJ.2020105857