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

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

The structure of Cryo-Em Structure of Mouse RAG1/2 12RSS-Nfc/23RSS-Prc 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-Nfc/23RSS-Prc Complex (DNA1) (pdb code 6oep). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Cryo-Em Structure of Mouse RAG1/2 12RSS-Nfc/23RSS-Prc Complex (DNA1), PDB code: 6oep:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Cryo-Em Structure of Mouse RAG1/2 12RSS-Nfc/23RSS-Prc 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-Nfc/23RSS-Prc Complex (DNA1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:0.2 occ:1.00 OD2 A:ASP600 2.1 83.7 1.0 OE1 A:GLN962 2.2 94.1 1.0 OP1 I:DC17 2.3 0.1 1.0 CG A:ASP600 3.2 83.7 1.0 CD A:GLN962 3.5 94.1 1.0 P I:DC17 3.6 0.1 1.0 OD1 A:ASP600 3.6 83.7 1.0 CA I:CA101 3.9 0.1 1.0 O A:GLY601 4.0 84.4 1.0 OP2 I:DC17 4.1 0.1 1.0 NE2 A:GLN962 4.2 94.1 1.0 CB A:ASP600 4.5 83.7 1.0 O5' I:DC17 4.5 0.1 1.0 CG A:GLN962 4.5 94.1 1.0 CE1 A:HIS795 4.5 0.8 1.0 CB A:GLN962 4.6 94.1 1.0 ND2 A:ASN965 4.6 81.6 1.0 OP2 I:DA18 4.6 0.8 1.0 O3' I:DA16 4.6 0.1 1.0 C5' I:DC17 4.7 0.1 1.0 CA A:GLN962 4.7 94.1 1.0 NE2 A:HIS795 4.7 0.8 1.0

Calcium binding site 2 out of 3 in the Cryo-Em Structure of Mouse RAG1/2 12RSS-Nfc/23RSS-Prc 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-Nfc/23RSS-Prc Complex (DNA1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1101 b:0.5 occ:1.00 OD2 C:ASP600 2.3 72.5 1.0 CG C:ASP600 3.1 72.5 1.0 OD1 C:ASP600 3.2 72.5 1.0 OP2 G:DA43 3.9 0.9 1.0 OP1 G:DA43 3.9 0.9 1.0 OD2 C:ASP708 4.3 81.0 1.0 P G:DA43 4.3 0.9 1.0 O C:GLY601 4.5 72.2 1.0 CB C:ASP600 4.5 72.5 1.0 N C:GLY601 4.6 72.2 1.0 C C:GLY601 5.0 72.2 1.0 O3' G:DT42 5.0 0.6 1.0

Calcium binding site 3 out of 3 in the Cryo-Em Structure of Mouse RAG1/2 12RSS-Nfc/23RSS-Prc Complex (DNA1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Mouse RAG1/2 12RSS-Nfc/23RSS-Prc Complex (DNA1) within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca101 b:0.1 occ:1.00 OD2 A:ASP708 2.5 81.5 1.0 OP1 I:DC17 2.6 0.1 1.0 OD1 A:ASP600 2.7 83.7 1.0 O3' I:DA16 2.8 0.1 1.0 P I:DC17 3.2 0.1 1.0 O A:GLY601 3.5 84.4 1.0 CG A:ASP600 3.5 83.7 1.0 CG A:ASP708 3.7 81.5 1.0 OD2 A:ASP600 3.7 83.7 1.0 OE1 A:GLU662 3.8 82.1 1.0 C5' I:DC17 3.8 0.1 1.0 CA A:CA1101 3.9 0.2 1.0 C3' I:DA16 4.0 0.1 1.0 O5' I:DC17 4.0 0.1 1.0 OD1 A:ASP708 4.2 81.5 1.0 N A:GLY601 4.4 84.4 1.0 C4' I:DA16 4.4 0.1 1.0 C2' I:DA16 4.5 0.1 1.0 OP2 I:DC17 4.5 0.1 1.0 C A:GLY601 4.5 84.4 1.0 CD A:GLU662 4.7 82.1 1.0 CB A:ASP708 4.8 81.5 1.0 OE2 A:GLU662 4.8 82.1 1.0 CA A:GLY601 4.8 84.4 1.0 CB A:ASP600 4.9 83.7 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