Atomistry » Manganese » PDB 7sd0-7u7z » 7u74
Atomistry »
  Manganese »
    PDB 7sd0-7u7z »
      7u74 »

Manganese in PDB 7u74: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 30S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 30S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 30S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 30S, PDB code: 7u74 was solved by C.Chang, Y.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.30 / 1.52
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.675, 98.675, 82.213, 90, 90, 120
R / Rfree (%) 19 / 22.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 30S (pdb code 7u74). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 30S, PDB code: 7u74:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 7u74

Go back to Manganese Binding Sites List in 7u74
Manganese binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 30S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 30S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:24.0
occ:0.50
 OE1 A:GLU116 2.1 37.2 1.0
O1A A:DGT505 2.2 23.8 0.7
OD1 A:ASP115 2.2 30.6 0.8
OD1 A:ASP13 2.2 35.2 0.6
OD2 A:ASP13 2.2 32.6 0.4
O A:HOH660 2.2 37.1 1.0
O A:HOH845 2.3 33.4 0.6
O3' P:DT8 2.5 35.5 0.4
OD1 A:ASP115 2.9 23.0 0.2
CG A:ASP115 3.0 25.4 0.8
CD A:GLU116 3.2 40.9 1.0
CG A:ASP115 3.2 22.8 0.2
OD2 A:ASP115 3.2 27.6 0.8
CG A:ASP13 3.3 25.4 0.4
CG A:ASP13 3.3 25.3 0.6
PA A:DGT505 3.4 25.9 0.7
C3' P:DT8 3.5 31.2 0.4
OD2 A:ASP115 3.5 22.5 0.2
MN A:MN502 3.6 22.5 0.8
OD1 A:ASP13 3.8 26.1 0.4
CB A:GLU116 3.8 31.2 1.0
OG A:SER113 3.8 30.1 1.0
O5' A:DGT505 3.9 22.7 0.7
OE2 A:GLU116 3.9 42.1 1.0
OD2 A:ASP13 4.0 32.6 0.6
O2A A:DGT505 4.0 28.6 0.7
CG A:GLU116 4.1 28.4 1.0
CB A:ASP115 4.1 22.9 0.2
C5' A:DGT505 4.1 22.0 0.7
O A:HOH750 4.2 40.6 1.0
O P:HOH203 4.3 33.3 0.7
C4' P:DT8 4.3 35.3 0.4
C A:ASP115 4.3 25.6 1.0
CB A:ASP115 4.4 23.1 0.8
O A:ASP115 4.4 26.8 1.0
NZ A:LYS224 4.4 38.0 1.0
CB A:ASP13 4.4 23.0 0.6
CB A:ASP13 4.4 23.0 0.4
N A:GLU116 4.5 20.0 1.0
O P:HOH221 4.6 36.1 0.7
O1G A:DGT505 4.7 24.2 0.7
O3A A:DGT505 4.7 23.7 0.7
C2' P:DT8 4.7 31.6 0.4
CA A:ASP115 4.7 21.0 0.2
CA A:GLU116 4.8 26.7 1.0
CA A:ASP115 4.8 20.9 0.8
O5' P:DT8 4.9 42.1 0.4
O2B A:DGT505 4.9 18.3 0.7
C5' P:DT8 4.9 35.4 0.4
CB A:SER113 4.9 25.6 1.0

Manganese binding site 2 out of 3 in 7u74

Go back to Manganese Binding Sites List in 7u74
Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 30S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 30S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:22.5
occ:0.80
 OD1 A:ASP13 1.8 26.1 0.4
OD2 A:ASP115 2.0 27.6 0.8
O A:MET14 2.1 26.9 1.0
O1G A:DGT505 2.2 24.2 0.7
O2B A:DGT505 2.2 18.3 0.7
OD2 A:ASP13 2.2 32.6 0.6
O1A A:DGT505 2.4 23.8 0.7
OD1 A:ASP13 2.7 35.2 0.6
CG A:ASP13 2.7 25.3 0.6
CG A:ASP13 2.7 25.4 0.4
OD2 A:ASP13 3.0 32.6 0.4
CG A:ASP115 3.1 25.4 0.8
PB A:DGT505 3.2 20.5 0.7
C A:MET14 3.3 19.6 1.0
PG A:DGT505 3.4 22.3 0.7
PA A:DGT505 3.5 25.9 0.7
O3A A:DGT505 3.5 23.7 0.7
MN A:MN501 3.6 24.0 0.5
O3B A:DGT505 3.7 20.8 0.7
O A:HOH663 3.7 20.4 0.5
OD1 A:ASP115 3.7 30.6 0.8
N A:MET14 3.8 17.2 1.0
OD2 A:ASP115 3.8 22.5 0.2
O A:HOH750 4.0 40.6 1.0
O3G A:DGT505 4.0 19.8 0.7
CA A:MET14 4.1 18.4 1.0
CG A:ASP115 4.1 22.8 0.2
C5' A:DGT505 4.1 22.0 0.7
CB A:ASP13 4.1 23.0 0.4
CB A:ASP13 4.1 23.0 0.6
C A:ASP13 4.1 17.7 1.0
CB A:ASP115 4.2 22.9 0.2
O5' A:DGT505 4.2 22.7 0.7
N A:ASP15 4.3 16.4 1.0
CB A:ASP115 4.3 23.1 0.8
N A:CYS16 4.4 20.6 1.0
CA A:ASP15 4.4 17.3 1.0
O A:HOH660 4.5 37.1 1.0
C A:ASP15 4.5 20.0 1.0
O A:ASP13 4.6 20.7 1.0
CA A:ASP13 4.6 21.7 0.4
CA A:ASP13 4.6 21.6 0.6
CB A:MET14 4.6 19.7 1.0
O A:ASP115 4.7 26.8 1.0
O2G A:DGT505 4.7 24.9 0.7
O1B A:DGT505 4.7 19.2 0.7
N A:PHE17 4.7 18.2 1.0
O2A A:DGT505 4.7 28.6 0.7
OD1 A:ASP115 4.9 23.0 0.2
NZ A:LYS231 4.9 26.4 0.5

Manganese binding site 3 out of 3 in 7u74

Go back to Manganese Binding Sites List in 7u74
Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 30S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 0.5 Mm MN2+ For 1800S Then with 10 Mm MN2+ For 30S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:29.6
occ:0.10
 O A:HOH636 2.1 35.2 1.0
O3A A:DGT505 2.3 23.7 0.7
O P:HOH219 2.3 37.0 0.5
O2A A:DGT505 2.6 28.6 0.7
NH1 A:ARG61 2.9 26.6 0.2
O A:HOH912 3.1 31.0 1.0
O2G A:DGT505 3.1 24.9 0.7
PA A:DGT505 3.1 25.9 0.7
O3B A:DGT505 3.2 20.8 0.7
PB A:DGT505 3.4 20.5 0.7
O A:HOH817 3.6 31.4 0.8
CZ A:ARG61 3.6 26.3 0.2
PG A:DGT505 3.7 22.3 0.7
O3' P:DT8 3.7 31.6 0.6
NH2 A:ARG61 3.7 25.9 0.2
O1G A:DGT505 4.0 24.2 0.7
O1B A:DGT505 4.0 19.2 0.7
O1A A:DGT505 4.1 23.8 0.7
O A:HOH750 4.2 40.6 1.0
O A:HOH645 4.3 22.6 1.0
O5' A:DGT505 4.3 22.7 0.7
C3' P:DT8 4.4 33.1 0.6
NH2 A:ARG55 4.4 24.6 1.0
O2B A:DGT505 4.6 18.3 0.7
NE A:ARG61 4.7 27.1 0.2
O A:HOH926 4.8 36.4 1.0
NZ A:LYS231 4.8 37.6 0.6

Reference:

C.Chang, C.Lee Luo, Y.Gao. In Crystallo Observation of Three Metal Ion Promoted Dna Polymerase Misincorporation. Nat Commun V. 13 2346 2022.
ISSN: ESSN 2041-1723
PubMed: 35487947
DOI: 10.1038/S41467-022-30005-3
Page generated: Sun Oct 6 10:41:20 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy