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Zinc in PDB 6dbl: Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas

Enzymatic activity of Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas

All present enzymatic activity of Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas:
2.3.2.27;

Other elements in 6dbl:

The structure of Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas (pdb code 6dbl). 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 Rag in Complex with 12-Rss and 23-Rss Substrate Dnas, PDB code: 6dbl:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6dbl

Go back to Zinc Binding Sites List in 6dbl
Zinc binding site 1 out of 2 in the Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas


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 Rag in Complex with 12-Rss and 23-Rss Substrate Dnas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.2
occ:1.00
NE2 A:HIS964 1.7 0.2 1.0
SG A:CYS749 2.0 0.3 1.0
NE2 A:HIS959 2.1 0.3 1.0
CE1 A:HIS959 2.7 0.1 1.0
CD2 A:HIS964 2.7 1.0 1.0
CE1 A:HIS964 2.7 0.8 1.0
CB A:CYS752 2.9 0.7 1.0
CB A:CYS749 3.2 0.4 1.0
CD2 A:HIS959 3.3 0.8 1.0
ND1 A:HIS964 3.8 0.6 1.0
CG A:HIS964 3.8 0.4 1.0
N A:CYS752 3.8 0.9 1.0
ND1 A:HIS959 3.9 0.2 1.0
CA A:CYS752 4.0 0.1 1.0
SG A:CYS752 4.0 0.5 1.0
CB A:ALA963 4.1 0.5 1.0
CG A:HIS959 4.3 0.7 1.0
CB A:HIS766 4.3 0.4 1.0
CB A:LEU751 4.4 0.6 1.0
C A:LEU751 4.6 0.2 1.0
CA A:CYS749 4.6 0.8 1.0
CG A:HIS766 4.6 0.5 1.0
C A:CYS752 4.9 0.9 1.0
CA A:LEU751 4.9 0.2 1.0
N A:LEU751 5.0 0.2 1.0

Zinc binding site 2 out of 2 in 6dbl

Go back to Zinc Binding Sites List in 6dbl
Zinc binding site 2 out of 2 in the Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas


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 Rag in Complex with 12-Rss and 23-Rss Substrate Dnas within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1101

b:0.2
occ:1.00
NE2 C:HIS964 1.8 0.5 1.0
CB C:CYS752 2.2 1.0 1.0
CD2 C:HIS964 2.5 0.4 1.0
SG C:CYS749 2.6 0.7 1.0
N C:CYS752 2.7 0.3 1.0
NE2 C:HIS959 2.7 0.2 1.0
CA C:CYS752 2.9 0.2 1.0
CE1 C:HIS964 3.0 0.4 1.0
C C:LEU751 3.4 0.3 1.0
CB C:LEU751 3.5 0.4 1.0
CB C:CYS749 3.5 0.0 1.0
CE1 C:HIS959 3.6 0.0 1.0
CD2 C:HIS959 3.7 0.3 1.0
CG C:HIS964 3.7 0.4 1.0
SG C:CYS752 3.9 0.9 1.0
ND1 C:HIS964 3.9 0.0 1.0
CA C:LEU751 3.9 0.2 1.0
C C:CYS752 4.0 0.9 1.0
O C:LEU751 4.1 0.1 1.0
N C:LEU751 4.2 0.3 1.0
CG C:LEU751 4.4 0.3 1.0
O C:CYS752 4.4 1.0 1.0
CD1 C:LEU751 4.7 0.5 1.0
ND1 C:HIS959 4.7 0.2 1.0
CG C:HIS959 4.8 0.1 1.0
CA C:CYS749 4.9 0.8 1.0
N C:ASP753 4.9 0.5 1.0
CB C:ALA963 5.0 0.1 1.0

Reference:

H.Ru, W.Mi, P.Zhang, F.W.Alt, D.G.Schatz, M.Liao, H.Wu. Dna Melting Initiates the Rag Catalytic Pathway. Nat. Struct. Mol. Biol. V. 25 732 2018.
ISSN: ESSN 1545-9985
PubMed: 30061602
DOI: 10.1038/S41594-018-0098-5
Page generated: Wed Dec 16 11:39:25 2020

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