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Zinc in PDB 6dbr: Cryo-Em Structure of Rag in Complex with One Melted Rss and One Unmelted Rss

Enzymatic activity of Cryo-Em Structure of Rag in Complex with One Melted Rss and One Unmelted Rss

All present enzymatic activity of Cryo-Em Structure of Rag in Complex with One Melted Rss and One Unmelted Rss:
2.3.2.27;

Other elements in 6dbr:

The structure of Cryo-Em Structure of Rag in Complex with One Melted Rss and One Unmelted Rss 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 One Melted Rss and One Unmelted Rss (pdb code 6dbr). 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 One Melted Rss and One Unmelted Rss, PDB code: 6dbr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6dbr

Go back to Zinc Binding Sites List in 6dbr
Zinc binding site 1 out of 2 in the Cryo-Em Structure of Rag in Complex with One Melted Rss and One Unmelted Rss


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 One Melted Rss and One Unmelted Rss within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:59.3
occ:1.00
NE2 A:HIS964 2.0 57.7 1.0
NE2 A:HIS959 2.0 47.7 1.0
SG A:CYS749 2.3 57.9 1.0
SG A:CYS752 2.3 76.4 1.0
CE1 A:HIS964 2.3 60.8 1.0
CB A:CYS752 2.9 75.6 1.0
CE1 A:HIS959 2.9 52.3 1.0
CB A:CYS749 2.9 58.5 1.0
CD2 A:HIS959 3.1 47.0 1.0
CD2 A:HIS964 3.4 56.7 1.0
N A:CYS752 3.5 74.2 1.0
ND1 A:HIS964 3.6 58.0 1.0
CA A:CYS752 3.8 81.9 1.0
ND1 A:HIS959 4.0 50.1 1.0
CG A:HIS964 4.1 57.6 1.0
CG A:HIS959 4.2 46.4 1.0
OG A:SER754 4.3 77.7 1.0
CA A:CYS749 4.4 57.2 1.0
C A:CYS752 4.5 76.0 1.0
CB A:ALA963 4.6 73.7 1.0
C A:LEU751 4.7 62.9 1.0
O A:CYS752 4.8 70.2 1.0
CB A:HIS766 4.9 73.1 1.0
C A:CYS749 5.0 52.8 1.0
CG A:HIS766 5.0 74.6 1.0
N A:LEU751 5.0 54.0 1.0

Zinc binding site 2 out of 2 in 6dbr

Go back to Zinc Binding Sites List in 6dbr
Zinc binding site 2 out of 2 in the Cryo-Em Structure of Rag in Complex with One Melted Rss and One Unmelted Rss


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 One Melted Rss and One Unmelted Rss within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1101

b:23.7
occ:1.00
NE2 C:HIS964 1.8 29.9 1.0
NE2 C:HIS959 1.9 24.5 1.0
SG C:CYS752 2.0 59.7 1.0
SG C:CYS749 2.3 61.3 1.0
CE1 C:HIS959 2.4 25.9 1.0
CE1 C:HIS964 2.5 32.4 1.0
CB C:CYS752 2.9 52.6 1.0
CB C:CYS749 2.9 26.0 1.0
CD2 C:HIS964 3.1 26.0 1.0
CD2 C:HIS959 3.2 24.8 1.0
ND1 C:HIS959 3.7 24.1 1.0
ND1 C:HIS964 3.8 31.3 1.0
CA C:CYS752 4.0 48.2 1.0
N C:CYS752 4.0 47.4 1.0
CG C:HIS964 4.0 30.2 1.0
CG C:HIS959 4.1 20.9 1.0
CA C:CYS749 4.4 24.3 1.0
CD2 C:HIS766 4.4 58.8 1.0
CB C:HIS766 4.4 54.0 1.0
CG C:HIS766 4.5 59.2 1.0
C C:CYS752 4.5 46.2 1.0
O C:CYS752 4.6 44.3 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 11:39:29 2020

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