Magnesium in PDB 8ezb: Nhej Long-Range Complex with Atp

Enzymatic activity of Nhej Long-Range Complex with Atp

All present enzymatic activity of Nhej Long-Range Complex with Atp:
2.7.11.1; 6.5.1.1;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Nhej Long-Range Complex with Atp (pdb code 8ezb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Nhej Long-Range Complex with Atp, PDB code: 8ezb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8ezb

Go back to Magnesium Binding Sites List in 8ezb
Magnesium binding site 1 out of 2 in the Nhej Long-Range Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nhej Long-Range Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg4200

b:62.5
occ:1.00
OD1 C:ASN3927 2.1 48.6 1.0
OD2 C:ASP3941 2.1 52.1 1.0
O1B C:ATP4201 2.3 86.5 1.0
O1G C:ATP4201 2.6 86.5 1.0
CG C:ASP3941 3.0 52.1 1.0
CB C:ASP3941 3.2 52.1 1.0
CG C:ASN3927 3.2 48.6 1.0
PG C:ATP4201 3.4 86.5 1.0
O2G C:ATP4201 3.5 86.5 1.0
PB C:ATP4201 3.6 86.5 1.0
NE2 C:HIS3924 3.8 45.2 1.0
CE1 C:HIS3924 3.8 45.2 1.0
O3B C:ATP4201 3.8 86.5 1.0
ND2 C:ASN3927 3.9 48.6 1.0
OD1 C:ASP3941 4.1 52.1 1.0
O C:ASN3926 4.2 49.2 1.0
CB C:ASN3927 4.4 48.6 1.0
O1A C:ATP4201 4.5 86.5 1.0
O3A C:ATP4201 4.5 86.5 1.0
C C:ASN3926 4.5 49.2 1.0
CA C:ASN3927 4.5 48.6 1.0
N C:ASN3927 4.6 48.6 1.0
O2B C:ATP4201 4.7 86.5 1.0
CA C:ASP3941 4.8 52.1 1.0
CB C:ASN3926 4.8 49.2 1.0
O3G C:ATP4201 4.8 86.5 1.0

Magnesium binding site 2 out of 2 in 8ezb

Go back to Magnesium Binding Sites List in 8ezb
Magnesium binding site 2 out of 2 in the Nhej Long-Range Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nhej Long-Range Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg4200

b:62.5
occ:1.00
OD1 L:ASN3927 2.1 48.6 1.0
OD2 L:ASP3941 2.1 52.1 1.0
O1B L:ATP4201 2.3 86.5 1.0
O1G L:ATP4201 2.6 86.5 1.0
CG L:ASP3941 3.0 52.1 1.0
CB L:ASP3941 3.2 52.1 1.0
CG L:ASN3927 3.2 48.6 1.0
PG L:ATP4201 3.4 86.5 1.0
O2G L:ATP4201 3.5 86.5 1.0
PB L:ATP4201 3.6 86.5 1.0
NE2 L:HIS3924 3.8 45.2 1.0
CE1 L:HIS3924 3.8 45.2 1.0
O3B L:ATP4201 3.8 86.5 1.0
ND2 L:ASN3927 3.9 48.6 1.0
OD1 L:ASP3941 4.1 52.1 1.0
O L:ASN3926 4.2 49.2 1.0
CB L:ASN3927 4.4 48.6 1.0
O1A L:ATP4201 4.5 86.5 1.0
O3A L:ATP4201 4.5 86.5 1.0
C L:ASN3926 4.5 49.2 1.0
CA L:ASN3927 4.5 48.6 1.0
N L:ASN3927 4.6 48.6 1.0
O2B L:ATP4201 4.7 86.5 1.0
CA L:ASP3941 4.8 52.1 1.0
CB L:ASN3926 4.8 49.2 1.0
O3G L:ATP4201 4.8 86.5 1.0

Reference:

S.Chen, A.Vogt, L.Lee, T.Naila, R.Mckeown, A.E.Tomkinson, S.P.Lees-Miller, Y.He. Cryo-Em Visualization of Dna-Pkcs Structural Intermediates in Nhej. Sci Adv V. 9 G2838 2023.
ISSN: ESSN 2375-2548
PubMed: 37256947
DOI: 10.1126/SCIADV.ADG2838
Page generated: Fri Oct 4 01:25:12 2024

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