Magnesium in PDB 6z2w: MEC1-DDC2 (F2244L Mutant) in Complex with Mg Amp-Pnp

Enzymatic activity of MEC1-DDC2 (F2244L Mutant) in Complex with Mg Amp-Pnp

All present enzymatic activity of MEC1-DDC2 (F2244L Mutant) in Complex with Mg Amp-Pnp:
2.7.11.1;

Other elements in 6z2w:

The structure of MEC1-DDC2 (F2244L Mutant) in Complex with Mg Amp-Pnp also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the MEC1-DDC2 (F2244L Mutant) in Complex with Mg Amp-Pnp (pdb code 6z2w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the MEC1-DDC2 (F2244L Mutant) in Complex with Mg Amp-Pnp, PDB code: 6z2w:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6z2w

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Magnesium binding site 1 out of 4 in the MEC1-DDC2 (F2244L Mutant) in Complex with Mg Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of MEC1-DDC2 (F2244L Mutant) in Complex with Mg Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg2403

b:99.7
occ:1.00
O1G E:ANP2401 2.1 100.0 1.0
OD2 E:ASP2243 2.1 96.2 1.0
ND2 E:ASN2229 2.2 92.3 1.0
O1A E:ANP2401 2.2 100.0 1.0
CG E:ASP2243 2.3 96.2 1.0
OD1 E:ASN2229 2.3 92.3 1.0
CG E:ASN2229 2.4 92.3 1.0
CB E:ASP2243 2.6 96.2 1.0
PG E:ANP2401 2.8 100.0 1.0
O2G E:ANP2401 3.0 100.0 1.0
OD1 E:ASP2243 3.1 96.2 1.0
N3B E:ANP2401 3.2 100.0 1.0
PA E:ANP2401 3.7 100.0 1.0
CA E:ASP2243 3.7 96.2 1.0
NE2 E:HIS2226 3.7 95.0 1.0
CB E:ASN2229 3.8 92.3 1.0
MG E:MG2404 4.0 94.6 1.0
CE1 E:HIS2226 4.1 95.0 1.0
O1B E:ANP2401 4.1 100.0 1.0
PB E:ANP2401 4.1 100.0 1.0
O3G E:ANP2401 4.3 100.0 1.0
C5' E:ANP2401 4.3 100.0 1.0
N E:ASP2243 4.4 96.2 1.0
O3A E:ANP2401 4.4 100.0 1.0
O2A E:ANP2401 4.5 100.0 1.0
O5' E:ANP2401 4.5 100.0 1.0
CD2 E:HIS2226 4.8 95.0 1.0
CA E:ASN2229 4.9 92.3 1.0
OD2 E:ASP2224 4.9 97.1 1.0
C E:ASP2243 4.9 96.2 1.0

Magnesium binding site 2 out of 4 in 6z2w

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Magnesium binding site 2 out of 4 in the MEC1-DDC2 (F2244L Mutant) in Complex with Mg Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of MEC1-DDC2 (F2244L Mutant) in Complex with Mg Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg2404

b:94.6
occ:1.00
O1B E:ANP2401 2.1 100.0 1.0
OD1 E:ASP2243 2.2 96.2 1.0
O2G E:ANP2401 2.2 100.0 1.0
OD2 E:ASP2243 2.5 96.2 1.0
CG E:ASP2243 2.7 96.2 1.0
O E:HOH2502 3.1 89.3 1.0
PB E:ANP2401 3.5 100.0 1.0
PG E:ANP2401 3.6 100.0 1.0
OD2 E:ASP2245 3.8 99.0 1.0
OD2 E:ASP2224 3.9 97.1 1.0
MG E:MG2403 4.0 99.7 1.0
N3B E:ANP2401 4.1 100.0 1.0
CB E:ASP2245 4.1 99.0 1.0
CB E:ASP2243 4.2 96.2 1.0
O3A E:ANP2401 4.2 100.0 1.0
CG E:ASP2245 4.2 99.0 1.0
O1A E:ANP2401 4.3 100.0 1.0
O1G E:ANP2401 4.4 100.0 1.0
O2B E:ANP2401 4.5 100.0 1.0
NZ E:LYS2080 4.6 1.0 1.0
O3G E:ANP2401 4.6 100.0 1.0
PA E:ANP2401 4.8 100.0 1.0
N E:ASP2245 4.8 99.0 1.0
CA E:ASP2243 4.9 96.2 1.0
C E:ASP2243 5.0 96.2 1.0

Magnesium binding site 3 out of 4 in 6z2w

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Magnesium binding site 3 out of 4 in the MEC1-DDC2 (F2244L Mutant) in Complex with Mg Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of MEC1-DDC2 (F2244L Mutant) in Complex with Mg Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2403

b:99.7
occ:1.00
O1G F:ANP2401 2.1 0.3 1.0
ND2 F:ASN2229 2.1 92.8 1.0
OD2 F:ASP2243 2.2 96.3 1.0
O1A F:ANP2401 2.2 0.3 1.0
CG F:ASP2243 2.3 96.3 1.0
OD1 F:ASN2229 2.4 92.8 1.0
CG F:ASN2229 2.5 92.8 1.0
CB F:ASP2243 2.6 96.3 1.0
PG F:ANP2401 2.8 0.3 1.0
O2G F:ANP2401 3.0 0.3 1.0
OD1 F:ASP2243 3.1 96.3 1.0
N3B F:ANP2401 3.2 0.3 1.0
PA F:ANP2401 3.6 0.3 1.0
CA F:ASP2243 3.7 96.3 1.0
NE2 F:HIS2226 3.8 95.0 1.0
CB F:ASN2229 3.9 92.8 1.0
O1B F:ANP2401 4.0 0.3 1.0
PB F:ANP2401 4.1 0.3 1.0
CE1 F:HIS2226 4.1 95.0 1.0
C5' F:ANP2401 4.3 0.3 1.0
O3G F:ANP2401 4.3 0.3 1.0
O3A F:ANP2401 4.4 0.3 1.0
MG F:MG2404 4.4 92.7 1.0
N F:ASP2243 4.4 96.3 1.0
O2A F:ANP2401 4.5 0.3 1.0
O5' F:ANP2401 4.5 0.3 1.0
CD2 F:HIS2226 4.8 95.0 1.0
CA F:ASN2229 4.9 92.8 1.0
C F:ASP2243 4.9 96.3 1.0
OD2 F:ASP2224 4.9 97.4 1.0

Magnesium binding site 4 out of 4 in 6z2w

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Magnesium binding site 4 out of 4 in the MEC1-DDC2 (F2244L Mutant) in Complex with Mg Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of MEC1-DDC2 (F2244L Mutant) in Complex with Mg Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2404

b:92.7
occ:1.00
O1B F:ANP2401 2.1 0.3 1.0
O2G F:ANP2401 2.2 0.3 1.0
OD1 F:ASP2243 2.7 96.3 1.0
OD2 F:ASP2243 2.9 96.3 1.0
O F:HOH2502 3.0 90.3 1.0
CG F:ASP2243 3.2 96.3 1.0
PB F:ANP2401 3.5 0.3 1.0
PG F:ANP2401 3.7 0.3 1.0
OD2 F:ASP2245 3.7 99.3 1.0
OD2 F:ASP2224 4.0 97.4 1.0
N3B F:ANP2401 4.2 0.3 1.0
CB F:ASP2245 4.2 99.3 1.0
CG F:ASP2245 4.3 99.3 1.0
MG F:MG2403 4.4 99.7 1.0
O2B F:ANP2401 4.4 0.3 1.0
O3A F:ANP2401 4.4 0.3 1.0
O3G F:ANP2401 4.5 0.3 1.0
O1G F:ANP2401 4.6 0.3 1.0
O1A F:ANP2401 4.6 0.3 1.0
NZ F:LYS2080 4.7 0.9 1.0
CB F:ASP2243 4.7 96.3 1.0

Reference:

E.A.Tannous, L.A.Yates, X.Zhang, P.M.Burgers. Mechanism of Auto-Inhibition and Activation of MEC1 Atr Checkpoint Kinase. Nat.Struct.Mol.Biol. 2020.
ISSN: ESSN 1545-9985
PubMed: 33169019
DOI: 10.1038/S41594-020-00522-0
Page generated: Tue Dec 15 02:54:01 2020

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