Calcium in PDB 6oeo: Cryo-Em Structure of Mouse RAG1/2 Nfc Complex (DNA1)

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

The structure of Cryo-Em Structure of Mouse RAG1/2 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 Nfc Complex (DNA1) (pdb code 6oeo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of Mouse RAG1/2 Nfc Complex (DNA1), PDB code: 6oeo:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of Mouse RAG1/2 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 Nfc Complex (DNA1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:0.9 occ:1.00 OD1 A:ASP600 1.9 82.5 1.0 OD2 A:ASP708 2.0 84.0 1.0 OP1 I:DC17 2.8 0.7 1.0 O3' I:DA16 3.0 0.4 1.0 CG A:ASP600 3.0 82.5 1.0 CG A:ASP708 3.2 84.0 1.0 P I:DC17 3.5 0.7 1.0 OD2 A:ASP600 3.6 82.5 1.0 CA A:CA1102 3.9 0.0 1.0 CB A:ASP708 3.9 84.0 1.0 OD1 A:ASP708 4.1 84.0 1.0 C3' I:DA16 4.1 0.4 1.0 O A:GLY601 4.1 77.6 1.0 C4' I:DA16 4.2 0.4 1.0 CB A:ASP600 4.3 82.5 1.0 OP2 I:DC17 4.4 0.7 1.0 OE2 A:GLU662 4.5 72.6 1.0 N A:GLY601 4.5 77.6 1.0 C5' I:DA16 4.6 0.4 1.0 O5' I:DC17 4.6 0.7 1.0 C5' I:DC17 4.7 0.7 1.0 CA A:ASP600 4.7 82.5 1.0 CD2 A:LEU711 4.8 71.7 1.0 C A:ASP600 4.9 82.5 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Mouse RAG1/2 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 Nfc Complex (DNA1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:0.0 occ:1.00 OP1 I:DC17 2.0 0.7 1.0 OD2 A:ASP600 2.1 82.5 1.0 OE1 A:GLN962 2.2 86.0 1.0 CG A:ASP600 3.1 82.5 1.0 P I:DC17 3.3 0.7 1.0 CD A:GLN962 3.3 86.0 1.0 OD1 A:ASP600 3.5 82.5 1.0 OP1 I:DA18 3.8 0.8 1.0 O A:GLY601 3.9 77.6 1.0 OP2 I:DC17 3.9 0.7 1.0 CA A:CA1101 3.9 0.9 1.0 O5' I:DC17 4.0 0.7 1.0 NE2 A:GLN962 4.1 86.0 1.0 ND2 A:ASN965 4.1 73.3 1.0 CG A:GLN962 4.4 86.0 1.0 C5' I:DC17 4.4 0.7 1.0 CB A:ASP600 4.4 82.5 1.0 O3' I:DA16 4.5 0.4 1.0 CB A:GLN962 4.5 86.0 1.0 OP2 I:DA18 4.6 0.8 1.0 P I:DA18 4.7 0.8 1.0 CE1 A:HIS795 4.8 0.1 1.0 CA A:GLN962 4.9 86.0 1.0 C A:GLY601 5.0 77.6 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Mouse RAG1/2 Nfc 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 Nfc Complex (DNA1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1101 b:97.7 occ:1.00 OD1 C:ASP600 1.9 67.8 1.0 OD2 C:ASP708 2.0 64.9 1.0 OP1 J:DC17 2.2 0.7 1.0 CG C:ASP600 2.9 67.8 1.0 CG C:ASP708 3.2 64.9 1.0 P J:DC17 3.3 0.7 1.0 OD2 C:ASP600 3.4 67.8 1.0 O3' J:DA16 3.5 0.6 1.0 OD1 C:ASP708 3.8 64.9 1.0 CA C:CA1102 3.9 82.0 1.0 OE1 C:GLU662 4.0 59.2 1.0 OP2 J:DC17 4.1 0.7 1.0 CB C:ASP600 4.2 67.8 1.0 CB C:ASP708 4.3 64.9 1.0 N C:GLY601 4.3 65.8 1.0 CA C:ASP600 4.6 67.8 1.0 O5' J:DC17 4.6 0.7 1.0 C3' J:DA16 4.7 0.6 1.0 C4' J:DA16 4.7 0.6 1.0 O C:GLY601 4.8 65.8 1.0 C5' J:DC17 4.8 0.7 1.0 C5' J:DA16 4.9 0.6 1.0 C C:ASP600 4.9 67.8 1.0 CD C:GLU662 4.9 59.2 1.0 NE2 C:HIS795 5.0 76.8 1.0 OE2 C:GLU662 5.0 59.2 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Mouse RAG1/2 Nfc Complex (DNA1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Mouse RAG1/2 Nfc Complex (DNA1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1102 b:82.0 occ:1.00 OD2 C:ASP600 1.9 67.8 1.0 OE1 C:GLN962 2.0 73.5 1.0 OP1 J:DC17 2.5 0.7 1.0 CG C:ASP600 3.1 67.8 1.0 CD C:GLN962 3.1 73.5 1.0 P J:DC17 3.4 0.7 1.0 OD1 C:ASP600 3.6 67.8 1.0 O5' J:DC17 3.7 0.7 1.0 OP2 J:DC17 3.8 0.7 1.0 CG C:GLN962 3.9 73.5 1.0 CA C:CA1101 3.9 97.7 1.0 O C:GLY601 3.9 65.8 1.0 C5' J:DC17 4.0 0.7 1.0 NE2 C:GLN962 4.0 73.5 1.0 CB C:ASP600 4.3 67.8 1.0 NE2 C:HIS795 4.5 76.8 1.0 CE1 C:HIS795 4.6 76.8 1.0 CB C:GLN962 4.6 73.5 1.0 O3' J:DA16 4.9 0.6 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