Atomistry » Magnesium » PDB 6or7-6p1p » 6p09
Atomistry »
  Magnesium »
    PDB 6or7-6p1p »
      6p09 »

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

Go back to Magnesium Binding Sites List in 6p09
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

Go back to Magnesium Binding Sites List in 6p09
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

Go back to Magnesium Binding Sites List in 6p09
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

Go back to Magnesium Binding Sites List in 6p09
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

Go back to Magnesium Binding Sites List in 6p09
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy