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

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

The structure of Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Paired-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 (Paired-Form) (pdb code 6xny). 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 (Paired-Form), PDB code: 6xny:
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 (Paired-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 (Paired-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:35.0 occ:1.00 O A:GLY601 1.6 31.6 1.0 OP2 y:DC36 2.1 39.9 1.0 P y:DC36 2.6 39.9 1.0 C A:GLY601 2.8 31.6 1.0 OP1 y:DC36 2.8 39.9 1.0 OE1 A:GLU962 2.8 31.3 1.0 O3' y:DG35 3.0 32.6 1.0 CD A:GLU962 3.7 31.3 1.0 N A:MET602 3.8 29.9 1.0 CA A:GLY601 3.8 31.6 1.0 N A:GLY601 3.8 31.6 1.0 OE2 A:GLU962 3.9 31.3 1.0 CA A:MET602 3.9 29.9 1.0 OP1 y:DG35 4.0 32.6 1.0 O5' y:DC36 4.2 39.9 1.0 MG A:MG1102 4.2 35.4 1.0 OD2 A:ASP600 4.3 30.4 1.0 ND2 A:ASN965 4.3 29.2 1.0 C3' y:DG35 4.4 32.6 1.0 C A:ASP600 4.5 30.4 1.0 O3' I:DC16 4.6 37.0 1.0 OD2 A:ASP708 4.6 34.5 1.0 CB A:ASP600 4.6 30.4 1.0 OD1 A:ASP708 4.7 34.5 1.0 CG A:ASP600 4.8 30.4 1.0 OP1 y:DG37 4.8 44.4 1.0 CB A:MET602 4.8 29.9 1.0 OE2 A:GLU662 4.9 34.2 1.0 C3' I:DC16 4.9 37.0 1.0 C4' y:DC36 4.9 39.9 1.0 C5' y:DC36 4.9 39.9 1.0 CG A:ASP708 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 (Paired-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 (Paired-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:35.4 occ:1.00 OD2 A:ASP708 2.1 34.5 1.0 OE2 A:GLU662 2.2 34.2 1.0 O3' I:DC16 2.4 37.0 1.0 CG A:ASP708 3.0 34.5 1.0 CD A:GLU662 3.2 34.2 1.0 C3' I:DC16 3.5 37.0 1.0 CB A:ASP708 3.6 34.5 1.0 CG A:GLU662 3.7 34.2 1.0 N A:GLY601 3.7 31.6 1.0 OD1 A:ASP708 3.9 34.5 1.0 C4' I:DC16 4.2 37.0 1.0 OE1 A:GLU662 4.2 34.2 1.0 CA A:GLY601 4.2 31.6 1.0 MG A:MG1101 4.2 35.0 1.0 OP1 y:DC36 4.3 39.9 1.0 CB A:LEU711 4.4 33.2 1.0 O A:GLY601 4.4 31.6 1.0 CB A:GLU662 4.7 34.2 1.0 N A:LEU711 4.7 33.2 1.0 C2' I:DC16 4.8 37.0 1.0 C A:GLY601 4.8 31.6 1.0 C A:ASP600 4.8 30.4 1.0 CB A:LYS710 4.8 34.9 1.0 CA A:ASP600 4.9 30.4 1.0 NZ A:LYS710 4.9 34.9 1.0 OP2 y:DC36 4.9 39.9 1.0 CA A:ASP708 5.0 34.5 1.0

Magnesium binding site 3 out of 4 in the Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Paired-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 (Paired-Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1101 b:32.7 occ:1.00 OP2 x:DC47 2.0 39.3 1.0 OD1 C:ASP600 2.1 30.4 1.0 OE1 C:GLU962 2.2 30.5 1.0 O C:GLY601 2.3 31.0 1.0 O3' x:DG46 2.4 31.4 1.0 OE2 C:GLU962 2.4 30.5 1.0 CD C:GLU962 2.6 30.5 1.0 P x:DC47 2.7 39.3 1.0 CG C:ASP600 3.1 30.4 1.0 ND2 C:ASN965 3.2 29.6 1.0 C C:GLY601 3.4 31.0 1.0 OD2 C:ASP600 3.4 30.4 1.0 O5' x:DC47 3.7 39.3 1.0 C3' x:DG46 3.8 31.4 1.0 OP1 x:DC47 3.9 39.3 1.0 CA C:MET602 3.9 31.6 1.0 N C:MET602 4.1 31.6 1.0 CG C:GLU962 4.1 30.5 1.0 C4' x:DG46 4.3 31.4 1.0 N C:GLY601 4.3 31.0 1.0 CB C:ASP600 4.4 30.4 1.0 CA C:GLY601 4.5 31.0 1.0 O C:MET602 4.5 31.6 1.0 CG C:ASN965 4.5 29.6 1.0 C C:ASP600 4.6 30.4 1.0 C2' x:DG46 4.6 31.4 1.0 O5' x:DG46 4.7 31.4 1.0 C C:MET602 4.7 31.6 1.0 CA C:ASP600 4.9 30.4 1.0 OD2 C:ASP708 4.9 34.1 1.0 OP1 x:DG48 4.9 44.6 1.0 CG C:MET602 5.0 31.6 1.0 MG C:MG1102 5.0 37.5 1.0 CB C:MET602 5.0 31.6 1.0

Magnesium binding site 4 out of 4 in the Structure of RAG1 (R848M/E649V)-RAG2-Dna Strand Transfer Complex (Paired-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 (Paired-Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1102 b:37.5 occ:1.00 OE2 C:GLU662 1.8 34.5 1.0 OD2 C:ASP708 1.9 34.1 1.0 O3' J:DC16 2.4 36.0 1.0 CG C:ASP708 2.5 34.1 1.0 OD1 C:ASP708 2.6 34.1 1.0 CD C:GLU662 2.9 34.5 1.0 OE1 C:GLU662 3.3 34.5 1.0 C3' J:DC16 3.5 36.0 1.0 N C:GLY601 3.7 31.0 1.0 CB C:ASP708 3.8 34.1 1.0 OP2 x:DC47 3.8 39.3 1.0 CG C:GLU662 4.2 34.5 1.0 O C:GLY601 4.2 31.0 1.0 CA C:GLY601 4.3 31.0 1.0 CB C:LEU711 4.3 33.0 1.0 C4' J:DC16 4.4 36.0 1.0 OD1 C:ASP600 4.6 30.4 1.0 C2' J:DC16 4.7 36.0 1.0 C C:GLY601 4.7 31.0 1.0 N C:LEU711 4.7 33.0 1.0 C C:ASP600 4.8 30.4 1.0 CA C:ASP600 4.8 30.4 1.0 CB C:GLU662 4.9 34.5 1.0 MG C:MG1101 5.0 32.7 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