Calcium in PDB 5zdz: Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+

Enzymatic activity of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+

All present enzymatic activity of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+:
2.3.2.27;

Protein crystallography data

The structure of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+, PDB code: 5zdz was solved by M.S.Kim, W.Chuenchor, X.Chen, M.Gellert, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.72 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 132.450, 109.000, 156.050, 90.00, 114.28, 90.00
R / Rfree (%) 20.2 / 24.2

Other elements in 5zdz:

The structure of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+ also contains other interesting chemical elements:

Potassium (K) 2 atoms
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+ (pdb code 5zdz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+, PDB code: 5zdz:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5zdz

Go back to Calcium Binding Sites List in 5zdz
Calcium binding site 1 out of 2 in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:84.0
occ:1.00
O F:HOH102 2.4 57.2 1.0
OD1 A:ASP600 2.5 69.0 1.0
O A:HOH2103 2.5 54.1 1.0
OP2 F:DT31 2.5 57.1 1.0
OE1 A:GLU962 3.2 61.0 1.0
CG A:ASP600 3.3 67.1 1.0
OD2 A:ASP708 3.3 52.5 1.0
OD2 A:ASP600 3.4 66.9 1.0
P F:DT31 3.5 52.8 1.0
O3' F:DG30 3.6 52.8 1.0
O A:GLY601 3.6 53.8 1.0
O3' I:DA16 3.9 61.5 1.0
C3' I:DA16 4.0 56.1 1.0
OP1 F:DT31 4.1 56.2 1.0
CD A:GLU962 4.1 58.9 1.0
OE2 A:GLU962 4.2 59.7 1.0
NE2 A:HIS795 4.4 50.1 1.0
CG A:ASP708 4.5 56.2 1.0
CE1 A:HIS795 4.6 52.9 1.0
N A:GLY601 4.7 56.7 1.0
CB A:ASP600 4.7 57.1 1.0
C A:GLY601 4.7 55.5 1.0
C3' F:DG30 4.9 51.0 1.0
O5' F:DT31 4.9 69.5 1.0
C2' I:DA16 4.9 57.2 1.0

Calcium binding site 2 out of 2 in 5zdz

Go back to Calcium Binding Sites List in 5zdz
Calcium binding site 2 out of 2 in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2001

b:69.6
occ:1.00
O C:HOH2103 2.5 42.9 1.0
O C:HOH2108 2.5 54.5 1.0
OD1 C:ASP600 2.7 66.2 1.0
O C:HOH2111 2.7 46.9 1.0
OE1 C:GLU962 2.8 54.7 1.0
O C:GLY601 2.9 49.6 1.0
OP2 G:DT42 3.0 49.2 1.0
O C:HOH2110 3.2 56.7 1.0
CD C:GLU962 3.7 51.1 1.0
CG C:ASP600 3.7 60.7 1.0
OE2 C:GLU962 3.7 53.8 1.0
O3' G:DG41 3.7 53.5 1.0
CB C:ASP600 3.9 51.6 1.0
P G:DT42 4.0 53.9 1.0
N C:GLY601 4.0 48.8 1.0
C C:GLY601 4.0 50.4 1.0
OD2 C:ASP708 4.1 52.9 1.0
CA C:GLY601 4.7 50.5 1.0
CA C:ASP600 4.7 51.1 1.0
O3' J:DA16 4.7 57.7 1.0
C C:ASP600 4.7 50.8 1.0
OP1 G:DT42 4.8 53.9 1.0
OD2 C:ASP600 4.9 56.4 1.0
C3' G:DG41 5.0 46.5 1.0

Reference:

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
Page generated: Sat Dec 12 05:55:54 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy