Zinc in PDB 6dbw: Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna

Enzymatic activity of Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna

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

Other elements in 6dbw:

The structure of Cryo-Em Structure of Rag in Complex with 12-Rss Substrate Dna 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 Substrate Dna (pdb code 6dbw). 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 Substrate Dna, PDB code: 6dbw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6dbw

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


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 Substrate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:0.5
occ:1.00
NE2 A:HIS964 1.9 0.0 1.0
SG A:CYS749 2.3 0.2 1.0
CB A:CYS752 2.4 0.2 1.0
N A:CYS752 2.4 0.5 1.0
NE2 A:HIS959 2.4 1.0 1.0
CD2 A:HIS964 2.6 0.1 1.0
CA A:CYS752 2.9 0.5 1.0
SG A:CYS752 2.9 0.1 1.0
CE1 A:HIS964 3.0 1.0 1.0
CE1 A:HIS959 3.0 97.7 1.0
CB A:CYS749 3.1 0.5 1.0
C A:LEU751 3.4 0.6 1.0
CD2 A:HIS959 3.6 89.6 1.0
CG A:HIS964 3.7 0.3 1.0
ND1 A:HIS964 3.9 0.6 1.0
C A:CYS752 3.9 0.5 1.0
O A:CYS752 4.0 0.7 1.0
CB A:LEU751 4.1 0.5 1.0
CA A:LEU751 4.1 0.3 1.0
O A:LEU751 4.2 0.8 1.0
N A:LEU751 4.2 0.8 1.0
ND1 A:HIS959 4.3 66.0 1.0
CA A:CYS749 4.6 0.2 1.0
CG A:HIS959 4.6 64.3 1.0
O A:SER767 4.8 0.1 1.0
N A:ASP753 5.0 0.9 1.0
CB A:HIS766 5.0 0.6 1.0

Zinc binding site 2 out of 2 in 6dbw

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


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 Substrate Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1101

b:0.0
occ:1.00
NE2 C:HIS964 2.2 0.1 1.0
NE2 C:HIS959 2.3 0.1 1.0
SG C:CYS749 2.3 0.3 1.0
CE1 C:HIS959 2.4 0.3 1.0
CE1 C:HIS964 2.7 0.9 1.0
CB C:CYS749 3.1 0.4 1.0
CB C:CYS752 3.3 0.7 1.0
CD2 C:HIS964 3.3 0.8 1.0
ND1 C:HIS959 3.5 0.9 1.0
CB C:HIS766 3.6 0.6 1.0
CD2 C:HIS959 3.7 0.8 1.0
CD2 C:HIS766 3.8 0.4 1.0
CG C:HIS766 3.9 0.4 1.0
ND1 C:HIS964 3.9 0.9 1.0
N C:CYS752 4.0 0.7 1.0
CA C:CYS752 4.2 0.0 1.0
CG C:HIS964 4.2 0.0 1.0
CA C:CYS749 4.4 0.7 1.0
CG C:HIS959 4.4 0.2 1.0
SG C:CYS752 4.4 0.2 1.0
O C:SER767 4.5 0.5 1.0
NE2 C:HIS766 4.8 84.1 1.0
C C:CYS752 4.9 0.7 1.0
CB C:ALA963 4.9 0.1 1.0
ND1 C:HIS766 4.9 0.2 1.0
CA C:HIS766 5.0 0.4 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 11:39:37 2020

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy