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Magnesium in PDB 6p09: Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+

Enzymatic activity of Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+

All present enzymatic activity of Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+:
6.5.1.1;

Protein crystallography data

The structure of Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+, PDB code: 6p09 was solved by M.J.Schellenberg, R.S.Williams, P.S.Tumbale, A.A.Riccio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.02 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.039, 101.083, 115.450, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+ (pdb code 6p09). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+, PDB code: 6p09:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6p09

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Magnesium binding site 1 out of 5 in the Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:25.2
occ:1.00
 OP1 B:DG11 1.8 33.8 1.0
O A:HOH1285 2.0 32.3 1.0
O B:HOH119 2.1 20.8 1.0
OE1 A:GLU592 2.1 29.6 1.0
O A:HOH1355 2.1 26.1 1.0
O A:HOH1207 2.2 31.1 1.0
CD A:GLU592 3.1 30.2 1.0
P B:DG11 3.3 30.4 1.0
OE2 A:GLU592 3.5 33.5 1.0
H5'' B:DG11 3.6 37.9 1.0
HG2 A:GLU346 3.8 42.0 1.0
O A:HOH1382 3.8 44.3 1.0
HA2 A:GLY344 4.0 42.0 1.0
O B:HOH116 4.0 35.7 1.0
O3' B:DC10 4.1 32.9 1.0
O5' B:DG11 4.1 29.7 1.0
O A:HOH1185 4.2 33.0 1.0
C5' B:DG11 4.2 31.6 1.0
H5' B:DG11 4.2 37.9 1.0
O B:HOH125 4.3 34.5 1.0
OP2 B:DG11 4.3 32.4 1.0
OE2 A:GLU346 4.4 34.4 1.0
O A:HOH1517 4.4 42.7 1.0
CG A:GLU592 4.4 26.1 1.0
O A:PRO341 4.5 36.7 1.0
HG3 A:GLU346 4.5 42.0 1.0
HA A:PRO341 4.5 39.4 1.0
CG A:GLU346 4.5 35.0 1.0
HG2 A:GLU592 4.6 31.4 1.0
O A:LEU345 4.6 33.7 1.0
HG3 A:GLU592 4.7 31.4 1.0
CA A:GLY344 4.9 35.0 1.0
CD A:GLU346 4.9 36.2 1.0
HB3 A:PRO341 5.0 40.5 1.0

Magnesium binding site 2 out of 5 in 6p09

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Magnesium binding site 2 out of 5 in the Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:56.3
occ:1.00
 O A:HOH1497 2.0 41.7 1.0
O A:HOH1509 2.2 54.6 1.0
O A:HOH1258 2.2 42.0 1.0
O A:HOH1529 2.2 45.9 1.0
O A:HOH1308 2.2 39.2 1.0
O A:HOH1498 2.4 44.7 1.0
HB2 A:GLU346 3.6 42.8 1.0
O A:HOH1419 3.9 66.5 1.0
O A:HOH1315 4.1 34.5 1.0
HA3 A:GLY348 4.2 38.0 1.0
O B:HOH123 4.2 41.2 1.0
OE1 A:GLU346 4.3 37.6 1.0
O A:HOH1111 4.3 46.4 1.0
HZ1 A:LYS423 4.4 52.9 1.0
O A:GLU346 4.5 39.9 1.0
CB A:GLU346 4.5 35.6 1.0
H4' D:DT22 4.6 48.3 1.0
O D:HOH148 4.6 57.4 1.0
HB3 A:GLU346 4.7 42.8 1.0
H5'' D:DT22 4.8 47.8 1.0
CA A:GLY348 4.9 31.7 1.0
HA2 A:GLY348 4.9 38.0 1.0
HG22 A:THR415 5.0 53.2 1.0

Magnesium binding site 3 out of 5 in 6p09

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Magnesium binding site 3 out of 5 in the Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:42.1
occ:1.00
 O A:HOH1192 2.0 45.6 1.0
OP1 C:DG4 2.1 33.1 1.0
O A:GLY799 2.1 31.3 1.0
O A:HOH1323 2.1 34.5 1.0
O C:HOH222 2.2 37.1 1.0
O A:HOH1307 2.2 41.3 1.0
C A:GLY799 3.3 29.5 1.0
P C:DG4 3.5 31.7 1.0
HA2 A:GLY799 3.7 33.7 1.0
HA A:PHE800 3.9 40.1 1.0
H5'' C:DG4 4.0 35.7 1.0
O A:PHE875 4.0 34.5 1.0
CA A:GLY799 4.0 28.1 1.0
O3' C:DC3 4.0 29.5 1.0
HD2 A:PHE875 4.0 38.7 1.0
OE2 A:GLU804 4.2 45.3 1.0
O A:HOH1278 4.2 48.4 1.0
HA3 A:GLY799 4.2 33.7 1.0
N A:PHE800 4.3 31.5 1.0
O C:HOH232 4.4 41.9 1.0
O C:HOH220 4.5 37.6 1.0
O5' C:DG4 4.5 29.9 1.0
H5' C:DG4 4.5 35.7 1.0
OP2 C:DG4 4.5 30.7 1.0
C5' C:DG4 4.5 29.8 1.0
CA A:PHE800 4.5 33.4 1.0
HA A:ILE876 4.5 39.4 1.0
O A:ILE876 4.6 35.9 1.0
H A:SER801 4.8 38.2 1.0
CD2 A:PHE875 4.9 32.2 1.0
HE2 A:PHE875 4.9 40.3 1.0

Magnesium binding site 4 out of 5 in 6p09

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Magnesium binding site 4 out of 5 in the Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:52.8
occ:1.00
 O A:HOH1526 2.1 41.5 1.0
O A:HOH1538 2.2 51.2 1.0
O A:HOH1216 2.2 39.1 1.0
O A:HOH1530 2.2 36.9 1.0
O A:HOH1248 2.3 37.4 1.0
O A:HOH1510 2.3 43.4 1.0
O A:HOH1522 4.1 48.2 1.0
HD2 A:ARG768 4.1 52.5 1.0
O A:HOH1349 4.3 47.2 1.0
OD2 A:ASP833 4.3 36.0 1.0
HB2 A:ALA374 4.4 58.0 1.0
HB3 A:TYR765 4.5 37.5 1.0
HB1 A:ALA374 4.5 58.0 1.0
OD1 A:ASP833 4.6 41.9 1.0
O A:HOH1189 4.6 37.3 1.0
O D:HOH149 4.7 38.5 1.0
HA A:ALA374 4.8 61.0 1.0
HD2 A:TYR765 4.8 40.4 1.0
O A:LEU766 4.8 30.1 1.0
CG A:ASP833 4.9 39.0 1.0
HH11 A:ARG768 4.9 63.6 1.0
CB A:ALA374 4.9 48.3 1.0

Magnesium binding site 5 out of 5 in 6p09

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Magnesium binding site 5 out of 5 in the Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:37.6
occ:1.00
 O A:HOH1135 1.9 36.3 1.0
O A:HOH1149 2.1 25.8 1.0
O A:HOH1335 2.1 35.2 1.0
OP2 C:DG1 2.2 41.4 1.0
O A:HOH1146 2.2 32.2 1.0
HZ3 A:LYS568 3.2 42.9 1.0
H1' C:AMP101 3.2 33.9 1.0
H4' C:AMP101 3.5 33.5 1.0
HZ1 A:LYS568 3.6 42.9 1.0
P C:DG1 3.7 43.1 1.0
HA A:ASP570 3.7 34.5 1.0
OE2 A:GLU621 3.7 30.1 1.0
NZ A:LYS568 3.7 35.8 1.0
C3' B:DC13 3.8 26.8 1.0
H5'' B:DC13 3.8 32.7 1.0
HZ2 A:LYS568 3.8 42.9 1.0
OE1 A:GLU720 3.9 47.4 1.0
O A:TYR569 3.9 27.6 1.0
O4' C:AMP101 3.9 30.2 1.0
H A:GLY571 4.0 28.9 1.0
C1' C:AMP101 4.1 28.2 1.0
OE2 A:GLU720 4.1 46.5 1.0
O5' C:DG1 4.2 37.9 1.0
H4' B:DC13 4.2 33.7 1.0
C4' C:AMP101 4.2 27.9 1.0
O C:HOH208 4.3 32.5 1.0
O A:GLY571 4.3 23.5 1.0
CD A:GLU720 4.4 46.5 1.0
C4' B:DC13 4.4 28.1 1.0
OP1 C:DG1 4.4 44.0 1.0
C5' B:DC13 4.5 27.2 1.0
H8 C:AMP101 4.6 31.7 1.0
OD1 A:ASP570 4.6 27.5 1.0
O2' C:AMP101 4.6 25.2 1.0
O C:HOH209 4.7 27.7 1.0
O3P C:AMP101 4.7 25.7 1.0
N A:GLY571 4.7 24.1 1.0
CA A:ASP570 4.7 28.7 1.0
CD A:GLU621 4.8 28.7 1.0
O5' C:AMP101 4.8 30.1 1.0
H2'' B:DC13 4.8 32.6 1.0
HG2 A:LYS568 4.8 37.3 1.0
O2P C:AMP101 4.8 30.7 1.0
C2' C:AMP101 4.9 24.4 1.0
C2' B:DC13 4.9 27.2 1.0
C A:TYR569 5.0 28.7 1.0

Reference:

P.P.Tumbale, T.J.Jurkiw, M.J.Schellenberg, A.A.Riccio, P.J.O'brien, R.S.Williams. Two-Tiered Enforcement of High-Fidelity Dna Ligation. Nat Commun V. 10 5431 2019.
ISSN: ESSN 2041-1723
PubMed: 31780661
DOI: 10.1038/S41467-019-13478-7
Page generated: Tue Oct 1 13:45:11 2024

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