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Manganese in PDB 6akh: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp:
2.7.7.7;

Protein crystallography data

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp, PDB code: 6akh was solved by Y.K.Chang, W.J.Wu, M.D.Tsai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.838, 68.800, 109.680, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19

Other elements in 6akh:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp (pdb code 6akh). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp, PDB code: 6akh:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6akh

Go back to Manganese Binding Sites List in 6akh
Manganese binding site 1 out of 2 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:9.3
occ:1.00
OD2 A:ASP332 2.1 8.8 1.0
OD1 A:ASP330 2.1 10.6 1.0
O2B A:DUP505 2.2 8.9 1.0
O3G A:DUP505 2.2 12.6 1.0
O2A A:DUP505 2.2 9.8 1.0
O A:HOH764 2.3 9.5 1.0
CG A:ASP332 3.1 9.4 1.0
CG A:ASP330 3.2 11.4 1.0
PB A:DUP505 3.2 10.1 1.0
PA A:DUP505 3.4 10.2 1.0
PG A:DUP505 3.4 12.9 1.0
OD1 A:ASP332 3.5 9.9 1.0
OD2 A:ASP330 3.6 11.4 1.0
N3A A:DUP505 3.6 9.7 1.0
MN A:MN503 3.6 9.9 1.0
O3B A:DUP505 3.6 10.5 1.0
O A:ASP330 4.1 10.2 1.0
ND1 A:HIS329 4.1 21.2 1.0
C5' A:DUP505 4.2 9.3 1.0
O1G A:DUP505 4.2 13.2 1.0
O A:HOH675 4.2 14.9 1.0
O A:HOH730 4.3 10.6 1.0
N A:GLY320 4.3 9.2 1.0
O5' A:DUP505 4.3 9.4 1.0
C A:ASP330 4.3 11.1 1.0
CE1 A:HIS329 4.3 20.7 1.0
CB A:ASP330 4.5 11.2 1.0
CB A:ASP332 4.5 9.5 1.0
CA A:GLY319 4.5 9.8 1.0
O1A A:DUP505 4.5 10.5 1.0
N A:ASP330 4.6 12.0 1.0
O2G A:DUP505 4.6 13.8 1.0
O1B A:DUP505 4.6 9.6 1.0
CA A:ASP330 4.7 11.7 1.0
N A:ASP332 4.7 9.9 1.0
O P:HOH102 4.8 13.0 1.0
N A:VAL331 4.9 10.8 1.0
C A:GLY319 5.0 9.6 1.0
C A:VAL331 5.0 10.8 1.0

Manganese binding site 2 out of 2 in 6akh

Go back to Manganese Binding Sites List in 6akh
Manganese binding site 2 out of 2 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:9.9
occ:1.00
OD2 A:ASP330 2.1 11.4 1.0
OD1 A:ASP332 2.1 9.9 1.0
OD2 A:ASP418 2.1 12.0 1.0
O P:HOH102 2.2 13.0 1.0
O2A A:DUP505 2.2 9.8 1.0
O3' P:DA4 2.3 12.3 1.0
CG A:ASP330 3.1 11.4 1.0
CG A:ASP332 3.1 9.4 1.0
CG A:ASP418 3.2 12.5 1.0
PA A:DUP505 3.4 10.2 1.0
OD1 A:ASP330 3.4 10.6 1.0
C3' P:DA4 3.5 13.4 1.0
OD2 A:ASP332 3.5 8.8 1.0
MN A:MN502 3.6 9.3 1.0
O1A A:DUP505 3.7 10.5 1.0
O5' A:DUP505 3.8 9.4 1.0
CB A:ASP418 3.9 12.2 1.0
C4' P:DA4 4.0 13.9 1.0
C5' P:DA4 4.0 14.1 1.0
CE1 A:HIS329 4.1 20.7 1.0
C5' A:DUP505 4.1 9.3 1.0
OD1 A:ASP418 4.2 12.3 1.0
CB A:ASP330 4.5 11.2 1.0
CB A:ASP332 4.5 9.5 1.0
OP1 P:DA4 4.5 14.2 1.0
O5' P:DA4 4.6 14.9 1.0
CZ3 A:TRP434 4.6 14.5 1.0
NH2 A:ARG416 4.6 13.1 1.0
C2' P:DA4 4.8 13.8 1.0
O3G A:DUP505 4.8 12.6 1.0
ND1 A:HIS329 4.9 21.2 1.0
N3A A:DUP505 4.9 9.7 1.0
NE2 A:HIS329 4.9 23.2 1.0

Reference:

Y.K.Chang, Y.P.Huang, X.X.Liu, T.P.Ko, Y.Bessho, Y.Kawano, M.Maestre-Reyna, W.J.Wu, M.D.Tsai. Human Dna Polymerase Mu Can Use A Noncanonical Mechanism For Multiple MN2+-Mediated Functions. J.Am.Chem.Soc. V. 141 8489 2019.
ISSN: ESSN 1520-5126
PubMed: 31067051
DOI: 10.1021/JACS.9B01741
Page generated: Sun Oct 6 03:51:07 2024

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