Calcium in PDB 6oer: Cryo-Em Structure of Mouse RAG1/2 Nfc Complex (DNA2)

All present enzymatic activity of Cryo-Em Structure of Mouse RAG1/2 Nfc Complex (DNA2):
2.3.2.27;

The structure of Cryo-Em Structure of Mouse RAG1/2 Nfc Complex (DNA2) 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 (DNA2) (pdb code 6oer). 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 (DNA2), PDB code: 6oer:
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 (DNA2)


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 (DNA2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:94.7 occ:1.00 OD2 A:ASP708 1.7 69.5 1.0 OD1 A:ASP600 2.5 73.2 1.0 CG A:ASP708 2.8 69.5 1.0 OP1 I:DC17 2.8 0.8 1.0 O3' I:DA16 3.3 0.0 1.0 OD1 A:ASP708 3.5 69.5 1.0 CG A:ASP600 3.6 73.2 1.0 P I:DC17 3.7 0.8 1.0 CB A:ASP708 3.9 69.5 1.0 OE1 A:GLU662 4.0 66.6 1.0 OD2 A:ASP600 4.1 73.2 1.0 CA A:CA1103 4.1 99.1 1.0 N A:GLY601 4.4 71.7 1.0 C3' I:DA16 4.5 0.0 1.0 C4' I:DA16 4.5 0.0 1.0 OP2 I:DC17 4.6 0.8 1.0 OE2 A:GLU662 4.7 66.6 1.0 CD A:GLU662 4.8 66.6 1.0 CB A:ASP600 4.8 73.2 1.0 O A:GLY601 4.8 71.7 1.0 C5' I:DA16 4.9 0.0 1.0 O5' I:DC17 4.9 0.8 1.0 CA A:ASP600 4.9 73.2 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Mouse RAG1/2 Nfc Complex (DNA2)


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 (DNA2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:99.1 occ:1.00 OD2 A:ASP600 2.3 73.2 1.0 OE1 A:GLN962 2.5 75.3 1.0 OP1 I:DC17 2.5 0.8 1.0 CG A:ASP600 3.2 73.2 1.0 OD1 A:ASP600 3.6 73.2 1.0 CD A:GLN962 3.7 75.3 1.0 P I:DC17 3.8 0.8 1.0 OP1 I:DA18 3.9 0.7 1.0 ND2 A:ASN965 4.0 68.1 1.0 CA A:CA1102 4.1 94.7 1.0 OP2 I:DC17 4.2 0.8 1.0 NE2 A:GLN962 4.5 75.3 1.0 CB A:ASP600 4.5 73.2 1.0 O5' I:DC17 4.5 0.8 1.0 OP2 I:DA18 4.6 0.7 1.0 CG A:GLN962 4.6 75.3 1.0 CB A:GLN962 4.7 75.3 1.0 P I:DA18 4.8 0.7 1.0 CA A:GLN962 4.8 75.3 1.0 CA A:MET602 4.8 73.7 1.0 N A:MET602 4.8 73.7 1.0 O3' I:DA16 5.0 0.0 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Mouse RAG1/2 Nfc Complex (DNA2)


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 (DNA2) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1102 b:0.0 occ:1.00 OD2 C:ASP708 1.9 69.1 1.0 OD1 C:ASP600 2.5 74.7 1.0 CG C:ASP708 2.9 69.1 1.0 OP1 J:DC17 3.1 0.4 1.0 OD1 C:ASP708 3.5 69.1 1.0 CG C:ASP600 3.6 74.7 1.0 O3' J:DA16 3.8 0.1 1.0 CA C:CA1103 4.0 0.4 1.0 CB C:ASP708 4.0 69.1 1.0 OE1 C:GLU662 4.1 67.0 1.0 P J:DC17 4.1 0.4 1.0 O C:GLY601 4.2 72.0 1.0 OD2 C:ASP600 4.3 74.7 1.0 OE2 C:GLU662 4.3 67.0 1.0 CD2 C:LEU711 4.5 57.1 1.0 N C:GLY601 4.5 72.0 1.0 CD C:GLU662 4.6 67.0 1.0 CB C:ASP600 4.7 74.7 1.0 CA C:ASP600 4.7 74.7 1.0 C4' J:DA16 4.9 0.1 1.0 C3' J:DA16 4.9 0.1 1.0 C C:ASP600 4.9 74.7 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Mouse RAG1/2 Nfc Complex (DNA2)


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 (DNA2) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1103 b:0.4 occ:1.00 OD2 C:ASP600 2.0 74.7 1.0 OE1 C:GLN962 2.3 85.3 1.0 CG C:ASP600 2.8 74.7 1.0 OP1 J:DC17 2.9 0.4 1.0 OD1 C:ASP600 3.0 74.7 1.0 CD C:GLN962 3.6 85.3 1.0 CA C:CA1102 4.0 0.0 1.0 CB C:ASP600 4.2 74.7 1.0 OP2 J:DA18 4.3 0.6 1.0 P J:DC17 4.3 0.4 1.0 CB C:GLN962 4.4 85.3 1.0 O C:GLY601 4.4 72.0 1.0 NE2 C:GLN962 4.4 85.3 1.0 CG C:GLN962 4.5 85.3 1.0 CA C:GLN962 4.6 85.3 1.0 ND2 C:ASN965 4.8 76.2 1.0 O5' J:DC17 4.9 0.4 1.0 OP2 J:DC17 4.9 0.4 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