Calcium in PDB 6oeq: Cryo-Em Structure of Mouse RAG1/2 12RSS-Prc/23RSS-Nfc Complex (DNA1)

All present enzymatic activity of Cryo-Em Structure of Mouse RAG1/2 12RSS-Prc/23RSS-Nfc Complex (DNA1):
2.3.2.27;

The structure of Cryo-Em Structure of Mouse RAG1/2 12RSS-Prc/23RSS-Nfc Complex (DNA1) also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of Mouse RAG1/2 12RSS-Prc/23RSS-Nfc Complex (DNA1) (pdb code 6oeq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of Mouse RAG1/2 12RSS-Prc/23RSS-Nfc Complex (DNA1), PDB code: 6oeq:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Mouse RAG1/2 12RSS-Prc/23RSS-Nfc Complex (DNA1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Mouse RAG1/2 12RSS-Prc/23RSS-Nfc Complex (DNA1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1101 b:0.2 occ:1.00 OD1 C:ASP600 1.8 78.5 1.0 OD2 C:ASP708 1.9 85.3 1.0 OP1 J:DC17 2.3 0.5 1.0 O3' J:DA16 2.8 0.9 1.0 P J:DC17 2.9 0.5 1.0 CG C:ASP600 2.9 78.5 1.0 CG C:ASP708 3.1 85.3 1.0 OP2 J:DC17 3.4 0.5 1.0 OD2 C:ASP600 3.6 78.5 1.0 CA C:CA1102 3.9 0.5 1.0 OD1 C:ASP708 3.9 85.3 1.0 C3' J:DA16 4.0 0.9 1.0 CB C:ASP708 4.0 85.3 1.0 CB C:ASP600 4.1 78.5 1.0 C4' J:DA16 4.2 0.9 1.0 C5' J:DA16 4.3 0.9 1.0 O5' J:DC17 4.3 0.5 1.0 CA C:ASP600 4.5 78.5 1.0 N C:GLY601 4.7 78.8 1.0 O C:GLY601 4.7 78.8 1.0 CD2 C:LEU711 4.7 66.4 1.0 C5' J:DC17 4.8 0.5 1.0 C C:ASP600 4.9 78.5 1.0 OE1 C:GLU662 4.9 75.0 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Mouse RAG1/2 12RSS-Prc/23RSS-Nfc Complex (DNA1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Mouse RAG1/2 12RSS-Prc/23RSS-Nfc Complex (DNA1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1102 b:0.5 occ:1.00 OE1 C:GLN962 1.7 85.3 1.0 OD2 C:ASP600 1.9 78.5 1.0 OP2 J:DC17 2.5 0.5 1.0 OP1 J:DC17 2.6 0.5 1.0 CD C:GLN962 2.9 85.3 1.0 P J:DC17 2.9 0.5 1.0 CG C:ASP600 2.9 78.5 1.0 OD1 C:ASP600 3.3 78.5 1.0 O5' J:DC17 3.6 0.5 1.0 CG C:GLN962 3.6 85.3 1.0 NE2 C:GLN962 3.9 85.3 1.0 CA C:CA1101 3.9 0.2 1.0 O C:GLY601 4.0 78.8 1.0 C5' J:DC17 4.2 0.5 1.0 CB C:ASP600 4.3 78.5 1.0 OP2 J:DA18 4.3 0.3 1.0 CB C:GLN962 4.3 85.3 1.0 O3' J:DA16 4.4 0.9 1.0 NE2 C:HIS795 4.9 80.0 1.0

X.Chen, Y.Cui, Z.H.Zhou, W.Yang, M.Gellert. Cutting Antiparallel Dna Strands in A Single Active Site Nat.Struct.Mol.Biol. 2020.
ISSN: ESSN 1545-9985