Calcium in PDB 6v0v: Cryo-Em Structure of Mouse Wt RAG1/2 Nfc Complex (DNA0)

All present enzymatic activity of Cryo-Em Structure of Mouse Wt RAG1/2 Nfc Complex (DNA0):
2.3.2.27;

The structure of Cryo-Em Structure of Mouse Wt RAG1/2 Nfc Complex (DNA0) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Cryo-Em Structure of Mouse Wt RAG1/2 Nfc Complex (DNA0) (pdb code 6v0v). 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 Wt RAG1/2 Nfc Complex (DNA0), PDB code: 6v0v:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Mouse Wt RAG1/2 Nfc Complex (DNA0)


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 Wt RAG1/2 Nfc Complex (DNA0) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:0.5 occ:1.00 OD1 A:ASP600 2.2 92.7 1.0 OP1 I:DC17 2.7 0.1 1.0 O3' I:DA16 2.8 0.6 1.0 OD2 A:ASP708 2.8 88.2 1.0 CG A:ASP708 3.2 88.2 1.0 P I:DC17 3.2 0.1 1.0 CG A:ASP600 3.4 92.7 1.0 OD1 A:ASP708 3.7 88.2 1.0 C4' I:DA16 3.8 0.6 1.0 CB A:ASP708 3.8 88.2 1.0 C3' I:DA16 3.8 0.6 1.0 CA A:CA1102 3.9 0.1 1.0 OP2 I:DC17 3.9 0.1 1.0 OD2 A:ASP600 4.1 92.7 1.0 C5' I:DA16 4.1 0.6 1.0 OE1 A:GLU662 4.2 89.2 1.0 O A:GLY601 4.3 92.4 1.0 CB A:ASP600 4.4 92.7 1.0 O5' I:DC17 4.6 0.1 1.0 OE2 A:GLU662 4.7 89.2 1.0 N A:GLY601 4.7 92.4 1.0 CD A:GLU662 4.9 89.2 1.0 NE2 A:HIS795 4.9 89.7 1.0 CA A:ASP600 4.9 92.7 1.0 O5' I:DA16 4.9 0.6 1.0 C2' I:DA16 4.9 0.6 1.0 C5' I:DC17 4.9 0.1 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Mouse Wt RAG1/2 Nfc Complex (DNA0)


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 Wt RAG1/2 Nfc Complex (DNA0) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:0.1 occ:1.00 OP1 I:DC17 1.9 0.1 1.0 OE1 A:GLU962 2.0 0.2 1.0 OD2 A:ASP600 2.7 92.7 1.0 P I:DC17 2.8 0.1 1.0 OP2 I:DC17 2.9 0.1 1.0 CD A:GLU962 3.1 0.2 1.0 CG A:ASP600 3.4 92.7 1.0 OD1 A:ASP600 3.5 92.7 1.0 OE2 A:GLU962 3.5 0.2 1.0 O5' I:DC17 3.6 0.1 1.0 CA A:CA1101 3.9 0.5 1.0 O3' I:DA16 4.1 0.6 1.0 O A:GLY601 4.3 92.4 1.0 C5' I:DC17 4.4 0.1 1.0 CG A:GLU962 4.4 0.2 1.0 NE2 A:HIS795 4.6 89.7 1.0 ND2 A:ASN965 4.6 91.2 1.0 CB A:ASP600 4.6 92.7 1.0 CB A:GLU962 4.7 0.2 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