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Calcium in PDB 7u7d: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S, PDB code: 7u7d 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) 42.13 / 1.57
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 98.081, 98.081, 82.346, 90, 90, 120
R / Rfree (%) 18.2 / 21.8

Other elements in 7u7d:

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S (pdb code 7u7d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S, PDB code: 7u7d:

Calcium binding site 1 out of 1 in 7u7d

Go back to Calcium Binding Sites List in 7u7d
Calcium binding site 1 out of 1 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 30S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:21.6
occ:0.80
 MN A:MN503 0.0 21.9 0.2
OD2 A:ASP13 2.1 31.3 0.7
OD2 A:ASP115 2.1 32.2 1.0
O2B A:DGT504 2.2 19.4 0.8
OD2 A:ASP13 2.2 31.2 0.3
O A:MET14 2.2 24.6 1.0
O1G A:DGT504 2.2 23.9 0.8
O1A A:DGT504 2.4 24.7 0.8
CG A:ASP13 2.9 25.8 0.3
CG A:ASP13 2.9 25.8 0.7
OD1 A:ASP13 3.0 33.9 0.3
PB A:DGT504 3.2 20.8 0.8
CG A:ASP115 3.2 27.2 1.0
OD1 A:ASP13 3.2 34.0 0.7
C A:MET14 3.4 21.2 1.0
PG A:DGT504 3.4 22.9 0.8
O3A A:DGT504 3.5 23.1 0.8
PA A:DGT504 3.5 23.2 0.8
MN A:MN501 3.6 22.7 0.7
O3B A:DGT504 3.6 20.2 0.8
OD1 A:ASP115 3.7 28.1 1.0
N A:MET14 3.9 17.6 1.0
O A:HOH744 3.9 35.8 1.0
NZ A:LYS231 3.9 29.4 1.0
O3G A:DGT504 4.0 21.2 0.8
C5' A:DGT504 4.1 22.9 0.8
CA A:MET14 4.2 17.1 1.0
CB A:ASP13 4.2 21.8 0.7
CB A:ASP13 4.2 21.9 0.3
C A:ASP13 4.2 18.3 1.0
O5' A:DGT504 4.3 21.1 0.8
CB A:ASP115 4.3 22.9 1.0
N A:ASP15 4.4 16.8 1.0
N A:CYS16 4.4 18.2 1.0
O A:HOH796 4.5 32.0 1.0
CA A:ASP15 4.5 17.9 1.0
O1B A:DGT504 4.5 21.6 0.8
C A:ASP15 4.5 22.4 1.0
O2G A:DGT504 4.6 28.0 0.8
O A:ASP13 4.6 21.8 1.0
N A:PHE17 4.7 16.7 1.0
O2A A:DGT504 4.7 26.1 0.8
CA A:ASP13 4.7 20.8 0.3
CB A:MET14 4.7 18.2 1.0
CA A:ASP13 4.7 20.7 0.7
O A:ASP115 4.9 24.6 1.0
CB A:PHE17 4.9 15.8 1.0
CE A:LYS231 4.9 39.1 1.0

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: Fri Jul 19 04:42:11 2024

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