Zinc in PDB 6cij: Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A)

All present enzymatic activity of Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A):
2.3.2.27;

The structure of Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A) (pdb code 6cij). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A), PDB code: 6cij:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:85.4 occ:1.00 SG A:CYS730 2.0 76.3 1.0 NE2 A:HIS937 2.2 72.4 1.0 SG A:CYS727 2.2 75.3 1.0 CD2 A:HIS937 2.4 72.4 1.0 CB A:CYS727 2.5 75.3 1.0 NE2 A:HIS942 2.5 71.5 1.0 CD2 A:HIS942 3.1 71.5 1.0 CB A:CYS730 3.4 76.3 1.0 CE1 A:HIS937 3.4 72.4 1.0 N A:CYS730 3.7 76.3 1.0 CE1 A:HIS942 3.7 71.5 1.0 CG A:HIS937 3.7 72.4 1.0 CA A:CYS727 4.0 75.3 1.0 CA A:CYS730 4.0 76.3 1.0 ND1 A:HIS937 4.2 72.4 1.0 O A:CYS730 4.2 76.3 1.0 CG A:HIS942 4.4 71.5 1.0 C A:CYS730 4.4 76.3 1.0 ND1 A:HIS942 4.6 71.5 1.0 CG2 A:THR732 4.7 72.6 1.0 CB A:ALA941 4.7 72.2 1.0 N A:CYS727 4.8 75.3 1.0 C A:LEU729 4.8 73.0 1.0 C A:CYS727 4.8 75.3 1.0 CB A:LEU729 4.9 73.0 1.0 N A:LEU729 5.0 73.0 1.0 CB A:HIS937 5.0 72.4 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Mouse RAG1/2 Hfc Complex Containing Partial HMGB1 Linker(3.9 A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1101 b:87.6 occ:1.00 NE2 C:HIS937 2.1 73.3 1.0 NE2 C:HIS942 2.1 69.7 1.0 CD2 C:HIS937 2.3 73.3 1.0 SG C:CYS727 2.4 72.0 1.0 SG C:CYS730 2.4 75.1 1.0 CB C:CYS727 2.8 72.0 1.0 CD2 C:HIS942 3.0 69.7 1.0 CE1 C:HIS942 3.2 69.7 1.0 CE1 C:HIS937 3.4 73.3 1.0 CG C:HIS937 3.6 73.3 1.0 CB C:CYS730 3.9 75.1 1.0 ND1 C:HIS937 4.1 73.3 1.0 CG C:HIS942 4.2 69.7 1.0 N C:CYS730 4.2 75.1 1.0 ND1 C:HIS942 4.2 69.7 1.0 CA C:CYS727 4.2 72.0 1.0 CG2 C:THR732 4.3 76.6 1.0 CA C:CYS730 4.6 75.1 1.0 CB C:HIS937 4.8 73.3 1.0 O C:HIS937 4.9 73.3 1.0 CD2 C:HIS744 5.0 79.0 1.0

M.S.Kim, W.Chuenchor, X.Chen, Y.Cui, X.Zhang, Z.H.Zhou, M.Gellert, W.Yang. Cracking the Dna Code For V(D)J Recombination. Mol. Cell V. 70 358 2018.
ISSN: ISSN 1097-4164
PubMed: 29628308
DOI: 10.1016/J.MOLCEL.2018.03.008