Calcium 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:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of Rag in Complex with 12-Rss and 23-Rss Substrate Dnas, PDB code: 6dbl:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6dbl

Go back to Calcium Binding Sites List in 6dbl
Calcium binding site 1 out of 4 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 Calcium with other atoms in the Ca 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:Ca1802

b:0.5
occ:1.00
OE2 A:GLU984 2.2 0.6 1.0
OP1 E:DC17 2.7 0.6 1.0
OP2 E:DC17 3.0 0.6 1.0
CD A:GLU984 3.1 0.5 1.0
P E:DC17 3.2 0.5 1.0
NE2 A:HIS817 3.4 0.5 1.0
CA E:CA101 3.5 0.0 1.0
OD2 A:ASP620 3.7 0.8 1.0
CG A:GLU984 3.8 0.3 1.0
OE1 A:GLU984 4.0 0.9 1.0
CE1 A:HIS817 4.0 0.1 1.0
O5' E:DC17 4.1 0.5 1.0
CD2 A:HIS817 4.5 0.6 1.0
O3' E:DA16 4.5 0.6 1.0
C3' E:DA16 4.8 0.2 1.0
CG A:ASP620 4.9 0.4 1.0

Calcium binding site 2 out of 4 in 6dbl

Go back to Calcium Binding Sites List in 6dbl
Calcium binding site 2 out of 4 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 Calcium with other atoms in the Ca 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:Ca1102

b:0.2
occ:1.00
OP1 G:DC17 2.3 0.8 1.0
OD1 C:ASP620 2.4 0.6 1.0
OE2 C:GLU984 2.5 0.3 1.0
OP2 G:DC17 3.0 0.8 1.0
P G:DC17 3.0 0.2 1.0
CG C:ASP620 3.3 0.2 1.0
CD C:GLU984 3.6 0.4 1.0
OD2 C:ASP730 3.7 0.8 1.0
OD2 C:ASP620 3.7 0.6 1.0
O5' G:DC17 4.2 0.1 1.0
O3' G:DA16 4.2 0.3 1.0
CG C:GLU984 4.2 0.8 1.0
NE2 C:HIS817 4.2 0.4 1.0
CB C:ASP620 4.5 0.4 1.0
OE1 C:GLU984 4.6 0.4 1.0
O C:GLY621 4.7 0.8 1.0
CG C:ASP730 4.7 0.5 1.0
C3' G:DA16 4.7 0.4 1.0
CE1 C:HIS817 4.9 0.2 1.0
CB C:ASP730 5.0 0.0 1.0

Calcium binding site 3 out of 4 in 6dbl

Go back to Calcium Binding Sites List in 6dbl
Calcium binding site 3 out of 4 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 Calcium with other atoms in the Ca binding site number 3 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
E:Ca101

b:0.0
occ:1.00
OP2 E:DA18 2.3 0.5 1.0
O5' E:DC17 2.7 0.5 1.0
OE2 A:GLU984 3.3 0.6 1.0
C3' E:DC17 3.3 0.0 1.0
P E:DC17 3.5 0.5 1.0
CA A:CA1802 3.5 0.5 1.0
P E:DA18 3.5 0.7 1.0
OP1 E:DC17 3.6 0.6 1.0
OE1 A:GLU984 3.6 0.9 1.0
O3' E:DC17 3.8 0.4 1.0
CD A:GLU984 3.8 0.5 1.0
C5' E:DC17 3.9 0.7 1.0
C4' E:DC17 4.0 0.5 1.0
OP2 E:DC17 4.0 0.6 1.0
O5' E:DA18 4.3 0.4 1.0
C2' E:DC17 4.4 0.5 1.0
OP1 E:DA18 4.8 0.0 1.0
OD2 A:ASP620 4.9 0.8 1.0
O3' E:DA16 5.0 0.6 1.0

Calcium binding site 4 out of 4 in 6dbl

Go back to Calcium Binding Sites List in 6dbl
Calcium binding site 4 out of 4 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 Calcium with other atoms in the Ca binding site number 4 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
G:Ca101

b:0.4
occ:1.00
OP2 G:DC17 3.2 0.8 1.0
C3' G:DC17 3.7 0.6 1.0
C2' G:DC17 3.8 0.2 1.0
O5' G:DC17 3.9 0.1 1.0
OE2 C:GLU984 3.9 0.3 1.0
OE1 C:GLU984 4.2 0.4 1.0
P G:DC17 4.2 0.2 1.0
C5' G:DC17 4.2 0.6 1.0
CD C:GLU984 4.3 0.4 1.0
C4' G:DC17 4.5 0.3 1.0
OP2 G:DA18 4.6 0.8 1.0
O5' G:DA18 4.7 0.9 1.0
O3' G:DC17 4.7 0.2 1.0
C6 G:DC17 4.8 0.2 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: Sat Dec 12 06:03:02 2020

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