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Potassium in PDB 5ze1: Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C

Enzymatic activity of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C

All present enzymatic activity of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C:
2.3.2.27;

Protein crystallography data

The structure of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C, PDB code: 5ze1 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) 36.68 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 132.760, 108.600, 157.090, 90.00, 114.20, 90.00
R / Rfree (%) 19.7 / 23.2

Other elements in 5ze1:

The structure of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C (pdb code 5ze1). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C, PDB code: 5ze1:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 5ze1

Go back to Potassium Binding Sites List in 5ze1
Potassium binding site 1 out of 2 in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2005

b:64.5
occ:1.00
O A:HOH2101 2.6 48.9 1.0
OE1 A:GLU649 2.8 44.0 1.0
O4' L:DC19 2.9 64.3 1.0
O2 L:DC19 3.1 64.6 1.0
OG A:SER963 3.1 63.7 1.0
N3 L:DA18 3.3 66.0 1.0
C2 L:DA18 3.4 60.7 1.0
C1' L:DC19 3.6 59.9 1.0
C4' L:DC19 3.7 56.6 1.0
C2 L:DC19 3.7 63.8 1.0
N2 F:DG28 3.9 64.7 1.0
CD A:GLU649 3.9 50.0 1.0
N1 L:DC19 4.0 60.4 1.0
CB A:SER963 4.0 54.0 1.0
OE2 A:GLU649 4.2 46.8 1.0
C4 L:DA18 4.4 63.0 1.0
C5' L:DC19 4.4 57.4 1.0
N1 L:DA18 4.5 59.4 1.0
N3 L:DC19 4.7 65.7 1.0
O A:ASN647 4.8 66.9 1.0
N A:GLU649 4.8 54.6 1.0
C3' L:DC19 4.8 54.9 1.0
C2' L:DC19 4.9 59.3 1.0
C2 F:DG28 5.0 58.4 1.0
O3' L:DC19 5.0 57.5 1.0

Potassium binding site 2 out of 2 in 5ze1

Go back to Potassium Binding Sites List in 5ze1
Potassium binding site 2 out of 2 in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K2004

b:56.3
occ:1.00
OE1 C:GLU649 2.7 60.0 1.0
O C:HOH2104 2.7 55.9 1.0
O G:HOH102 2.7 51.7 1.0
O2 M:DC19 2.8 60.8 1.0
O4' M:DC19 2.9 55.2 1.0
OG C:SER963 3.3 52.5 1.0
N3 M:DA18 3.6 57.6 1.0
C1' M:DC19 3.6 58.5 1.0
C2 M:DC19 3.6 61.7 1.0
C4' M:DC19 3.6 58.4 1.0
C2 M:DA18 3.6 57.7 1.0
CD C:GLU649 3.6 58.2 1.0
O C:HOH2113 3.6 54.0 1.0
N2 G:DG39 3.7 55.0 1.0
OE2 C:GLU649 3.8 58.3 1.0
CB C:SER963 3.9 52.3 1.0
N1 M:DC19 4.0 57.1 1.0
C5' M:DC19 4.4 60.8 1.0
C4 M:DA18 4.6 56.9 1.0
N1 M:DA18 4.6 57.9 1.0
N3 M:DC19 4.6 62.7 1.0
O C:HOH2111 4.6 49.8 1.0
O C:ASN647 4.8 58.4 1.0
C3' M:DC19 4.8 61.0 1.0
O4' M:DA20 4.9 64.0 1.0
N C:GLU649 4.9 55.0 1.0
O3' M:DC19 4.9 60.1 1.0
C2' M:DC19 4.9 61.2 1.0
C2 G:DG39 5.0 56.5 1.0
CG C:GLU649 5.0 53.0 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: Mon Dec 14 00:15:56 2020

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