Atomistry » Magnesium » PDB 6oqz-6p1o » 6p0b
Atomistry »
  Magnesium »
    PDB 6oqz-6p1o »
      6p0b »

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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy