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Magnesium in PDB 6p0b: Human Dna Ligase 1 (E346A/E592A) Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+

Enzymatic activity of Human Dna Ligase 1 (E346A/E592A) Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+

All present enzymatic activity of Human Dna Ligase 1 (E346A/E592A) 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 (E346A/E592A) Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+, PDB code: 6p0b 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) 41.43 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.866, 101.398, 115.606, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Ligase 1 (E346A/E592A) Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+ (pdb code 6p0b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Dna Ligase 1 (E346A/E592A) Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+, PDB code: 6p0b:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6p0b

Go back to Magnesium Binding Sites List in 6p0b
Magnesium binding site 1 out of 4 in the Human Dna Ligase 1 (E346A/E592A) 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 (E346A/E592A) 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:48.9
occ:0.70
 O A:HOH1111 2.0 47.2 1.0
O A:HOH1174 2.1 29.6 0.9
O A:HOH1115 2.5 31.8 1.0
OP2 C:DG1 2.6 52.1 1.0
O A:HOH1152 2.7 58.6 1.0
HZ3 A:LYS568 3.1 54.7 1.0
OE2 A:GLU720 3.1 76.1 1.0
HA A:ASP570 3.4 41.6 1.0
HZ2 A:LYS568 3.5 54.7 1.0
HZ1 A:LYS568 3.5 54.7 1.0
NZ A:LYS568 3.6 45.6 1.0
H1' C:AMP101 3.7 51.2 1.0
CD A:GLU720 3.7 72.3 1.0
OE1 A:GLU720 3.7 71.2 1.0
H4' C:AMP101 3.7 52.5 1.0
C3' B:DC13 3.9 29.2 1.0
H A:GLY571 3.9 43.1 1.0
P C:DG1 3.9 59.1 1.0
H5'' B:DC13 3.9 33.7 1.0
OD1 A:ASP570 4.0 35.5 1.0
O A:TYR569 4.0 30.8 1.0
OE2 A:GLU621 4.1 45.1 1.0
O4' C:AMP101 4.2 44.8 1.0
H4' B:DC13 4.2 35.6 1.0
O A:GLY571 4.3 37.6 1.0
O5' C:DG1 4.4 52.8 1.0
CA A:ASP570 4.4 34.6 1.0
C1' C:AMP101 4.5 42.7 1.0
C4' B:DC13 4.5 29.7 1.0
N A:GLY571 4.5 35.9 1.0
C4' C:AMP101 4.5 43.7 1.0
OP1 C:DG1 4.7 59.6 1.0
C5' B:DC13 4.7 28.1 1.0
O C:HOH211 4.7 60.0 1.0
HG2 A:LYS568 4.8 41.3 1.0
H2'' B:DC13 4.8 37.7 1.0
O5' C:AMP101 4.8 47.5 1.0
CG A:ASP570 4.8 40.3 1.0
O2P C:AMP101 4.9 41.1 1.0
C A:ASP570 4.9 34.4 1.0
HG3 A:GLU720 4.9 81.0 1.0
C2' B:DC13 4.9 31.4 1.0
H8 C:AMP101 4.9 47.9 1.0
HH22 A:ARG871 5.0 51.5 1.0
CG A:GLU720 5.0 67.5 1.0
C A:TYR569 5.0 32.6 1.0

Magnesium binding site 2 out of 4 in 6p0b

Go back to Magnesium Binding Sites List in 6p0b
Magnesium binding site 2 out of 4 in the Human Dna Ligase 1 (E346A/E592A) 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 (E346A/E592A) 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:38.2
occ:1.00
 OP1 C:DG4 1.9 51.2 1.0
O C:HOH222 2.1 36.3 1.0
O A:HOH1156 2.1 45.0 1.0
O A:HOH1181 2.2 31.1 1.0
O A:GLY799 2.2 31.5 1.0
O A:HOH1259 2.3 40.9 1.0
P C:DG4 3.3 43.6 1.0
C A:GLY799 3.4 34.8 1.0
H5'' C:DG4 3.7 43.9 1.0
HA2 A:GLY799 3.7 41.3 1.0
O3' C:DC3 3.9 41.9 1.0
HA A:PHE800 4.0 46.8 1.0
CA A:GLY799 4.1 34.4 1.0
O5' C:DG4 4.2 38.5 1.0
O A:PHE875 4.2 34.9 1.0
C5' C:DG4 4.3 36.6 1.0
H5' C:DG4 4.3 43.9 1.0
O C:HOH231 4.3 50.6 1.0
OP2 C:DG4 4.3 48.3 1.0
OE2 A:GLU804 4.3 52.4 1.0
HD2 A:PHE875 4.4 42.3 1.0
HA3 A:GLY799 4.4 41.3 1.0
O C:HOH215 4.4 52.1 1.0
N A:PHE800 4.4 37.7 1.0
O C:HOH201 4.6 58.0 1.0
CA A:PHE800 4.6 39.0 1.0
HA A:ILE876 4.7 52.0 1.0
O A:HOH1361 4.8 57.5 1.0
H A:SER801 4.9 43.6 1.0
O A:ILE876 4.9 47.0 1.0

Magnesium binding site 3 out of 4 in 6p0b

Go back to Magnesium Binding Sites List in 6p0b
Magnesium binding site 3 out of 4 in the Human Dna Ligase 1 (E346A/E592A) 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 (E346A/E592A) 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:51.9
occ:1.00
 O A:HOH1371 1.9 51.5 1.0
O A:HOH1191 2.1 42.9 1.0
O A:HOH1377 2.2 37.9 1.0
O A:HOH1373 2.3 41.0 1.0
O A:HOH1126 2.3 40.8 1.0
O A:HOH1372 2.4 50.7 1.0
OD2 A:ASP833 4.0 42.2 1.0
O A:HOH1362 4.1 42.8 1.0
HD2 A:ARG768 4.2 47.4 1.0
O A:HOH1117 4.3 44.6 1.0
HB3 A:TYR765 4.3 41.7 1.0
OD1 A:ASP833 4.4 42.0 1.0
O A:LEU766 4.5 31.3 1.0
O A:HOH1165 4.5 38.3 1.0
HB1 A:ALA374 4.5 57.1 1.0
HB2 A:ALA374 4.6 57.1 1.0
CG A:ASP833 4.6 43.0 1.0
HB2 A:LEU766 4.7 51.4 1.0
O D:HOH143 4.7 53.7 1.0
HD2 A:TYR765 4.8 44.5 1.0
HA A:ALA374 4.8 55.7 1.0
HG3 A:ARG768 4.9 42.6 1.0
H A:LEU766 4.9 41.6 1.0
HH11 A:ARG768 4.9 75.6 1.0
CB A:ALA374 5.0 47.6 1.0

Magnesium binding site 4 out of 4 in 6p0b

Go back to Magnesium Binding Sites List in 6p0b
Magnesium binding site 4 out of 4 in the Human Dna Ligase 1 (E346A/E592A) 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 (E346A/E592A) Bound to An Adenylated, Dideoxy Terminated Dna Nick with 200 Mm MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:44.7
occ:1.00
 O B:HOH218 2.0 39.1 1.0
O B:HOH223 2.0 44.8 1.0
O B:HOH214 2.0 39.6 1.0
O B:HOH224 2.1 33.5 1.0
O D:HOH106 2.2 39.4 1.0
O D:HOH139 2.4 40.3 1.0
H4' B:DT8 3.5 53.8 1.0
H5' B:DG9 3.7 51.8 1.0
O A:HOH1288 3.8 49.9 1.0
H2 B:DA7 4.1 53.7 1.0
O2 D:DT22 4.1 41.3 1.0
O D:HOH140 4.1 43.0 1.0
O4' B:DG9 4.1 36.1 1.0
O4' B:DT8 4.2 41.0 1.0
H4' B:DG9 4.2 47.6 1.0
O D:HOH126 4.2 55.6 1.0
H1' B:DT8 4.2 48.9 1.0
C4' B:DT8 4.3 44.8 1.0
H4' D:DC23 4.4 55.9 1.0
C5' B:DG9 4.5 43.2 1.0
C4' B:DG9 4.5 39.7 1.0
O2 B:DT8 4.5 34.6 1.0
O4' D:DC23 4.5 44.0 1.0
O A:HOH1229 4.6 40.9 1.0
C2 B:DA7 4.7 44.7 1.0
H5' D:DC23 4.8 57.9 1.0
C1' B:DT8 4.8 40.8 1.0
N3 B:DA7 4.8 44.7 1.0
H5'' B:DG9 4.8 51.8 1.0
O3' B:DT8 4.9 47.2 1.0
C4' D:DC23 4.9 46.6 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 13:46:05 2024

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