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Manganese in PDB 6ipf: Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP

Enzymatic activity of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP

All present enzymatic activity of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP:
2.7.7.7;

Protein crystallography data

The structure of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP, PDB code: 6ipf 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 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.778, 68.792, 109.620, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 21.8

Other elements in 6ipf:

The structure of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP (pdb code 6ipf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP, PDB code: 6ipf:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6ipf

Go back to Manganese Binding Sites List in 6ipf
Manganese binding site 1 out of 4 in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:22.0
occ:1.00
 OD1 A:ASP330 2.0 27.6 1.0
OD2 A:ASP332 2.1 22.4 1.0
O A:HOH606 2.1 25.0 1.0
O32 A:PPV503 2.1 25.6 1.0
OP1 P:8OG5 2.2 22.5 1.0
O21 A:PPV503 2.3 36.3 1.0
CG A:ASP330 3.1 29.2 1.0
CG A:ASP332 3.1 22.3 1.0
P2 A:PPV503 3.2 30.6 1.0
P1 A:PPV503 3.4 50.6 1.0
O22 A:PPV503 3.4 31.2 1.0
MN A:MN502 3.4 24.9 1.0
P P:8OG5 3.5 24.9 1.0
OD1 A:ASP332 3.5 22.7 1.0
OD2 A:ASP330 3.5 28.0 1.0
OPP A:PPV503 3.6 40.1 1.0
O A:ASP330 3.8 22.4 1.0
O5' P:8OG5 3.8 24.2 1.0
O A:HOH633 3.9 43.1 1.0
C5' P:8OG5 4.0 24.0 1.0
O11 A:PPV503 4.1 43.1 1.0
O A:HOH603 4.2 30.9 1.0
O A:HOH686 4.3 20.8 1.0
OP2 P:8OG5 4.3 24.6 1.0
C A:ASP330 4.3 23.7 1.0
O P:HOH208 4.3 25.1 1.0
CB A:ASP330 4.4 25.6 1.0
N A:GLY320 4.4 21.6 1.0
CB A:ASP332 4.4 21.4 1.0
O12 A:PPV503 4.5 27.9 1.0
CA A:GLY319 4.6 22.6 1.0
O3' P:DA4 4.6 21.2 1.0
O31 A:PPV503 4.7 45.7 1.0
CA A:ASP330 4.8 25.7 1.0
O A:HOH602 4.9 38.1 1.0
N A:ASP332 4.9 21.7 1.0

Manganese binding site 2 out of 4 in 6ipf

Go back to Manganese Binding Sites List in 6ipf
Manganese binding site 2 out of 4 in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:24.9
occ:1.00
 OD2 A:ASP330 1.8 28.0 1.0
OD2 A:ASP418 2.0 23.2 1.0
OD1 A:ASP332 2.0 22.7 1.0
OP1 P:8OG5 2.1 22.5 1.0
O P:HOH208 2.3 25.1 1.0
CG A:ASP330 2.7 29.2 1.0
O3' P:DA4 3.0 21.2 1.0
CG A:ASP418 3.0 24.5 1.0
CG A:ASP332 3.0 22.3 1.0
P P:8OG5 3.1 24.9 1.0
OD1 A:ASP330 3.1 27.6 1.0
OD2 A:ASP332 3.4 22.4 1.0
MN A:MN501 3.4 22.0 1.0
CB A:ASP418 3.7 24.6 1.0
OD1 A:ASP418 3.9 26.4 1.0
CB A:ASP330 4.0 25.6 1.0
OP2 P:8OG5 4.0 24.6 1.0
C3' P:DA4 4.1 21.0 1.0
C5' P:DA4 4.1 21.8 1.0
O A:HOH633 4.2 43.1 1.0
C4' P:DA4 4.2 21.1 1.0
O5' P:8OG5 4.3 24.2 1.0
CB A:ASP332 4.4 21.4 1.0
NH2 A:ARG416 4.5 26.0 1.0
C5' P:8OG5 4.6 24.0 1.0
OP1 P:DA4 4.7 22.9 1.0
O A:VAL331 4.7 22.1 1.0
O21 A:PPV503 4.7 36.3 1.0
CZ3 A:TRP434 4.8 23.4 1.0
N A:ASP418 4.8 24.2 1.0
CA A:ASP418 4.9 24.3 1.0
CA A:ASP332 4.9 21.6 1.0
O5' P:DA4 4.9 22.0 1.0
C A:VAL331 4.9 23.5 1.0

Manganese binding site 3 out of 4 in 6ipf

Go back to Manganese Binding Sites List in 6ipf
Manganese binding site 3 out of 4 in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:32.7
occ:0.50
 O P:HOH204 2.1 40.2 1.0
O22 A:PPV503 2.3 31.2 1.0
MN P:MN102 2.4 35.8 0.5
O A:HOH602 2.4 38.1 1.0
OP2 P:8OG5 2.4 24.6 1.0
O A:HOH795 2.5 24.3 0.5
O8 P:8OG5 2.5 30.9 1.0
O5' P:8OG5 3.1 24.2 1.0
P P:8OG5 3.3 24.9 1.0
C8 P:8OG5 3.7 29.6 1.0
P2 A:PPV503 3.7 30.6 1.0
O P:HOH214 3.7 22.2 0.5
O P:HOH219 3.9 26.5 0.5
O A:HOH711 3.9 24.9 1.0
O31 A:PPV503 4.1 45.7 1.0
O21 A:PPV503 4.1 36.3 1.0
O12 A:PPV503 4.1 27.9 1.0
C3' P:8OG5 4.2 25.8 1.0
OP1 P:8OG5 4.2 22.5 1.0
N7 P:8OG5 4.3 29.4 1.0
O A:HOH633 4.4 43.1 1.0
C5' P:8OG5 4.4 24.0 1.0
P1 A:PPV503 4.5 50.6 1.0
OPP A:PPV503 4.5 40.1 1.0
O3' P:DA4 4.6 21.2 1.0
O32 A:PPV503 4.6 25.6 1.0
O P:HOH213 4.7 31.1 1.0
N9 P:8OG5 4.7 27.1 1.0
C4' P:8OG5 4.8 24.8 1.0
CB A:LYS438 4.8 24.4 1.0
C3' P:DA4 4.9 21.0 1.0
C2' P:8OG5 4.9 26.9 1.0
O4' P:8OG5 4.9 24.1 1.0
O3' P:8OG5 4.9 25.3 1.0

Manganese binding site 4 out of 4 in 6ipf

Go back to Manganese Binding Sites List in 6ipf
Manganese binding site 4 out of 4 in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn102

b:35.8
occ:0.50
 O P:HOH214 2.0 22.2 0.5
O A:HOH602 2.1 38.1 1.0
O P:HOH219 2.2 26.5 0.5
O P:HOH204 2.3 40.2 1.0
OP2 P:8OG5 2.3 24.6 1.0
MN P:MN101 2.4 32.7 0.5
O A:HOH633 3.2 43.1 1.0
P P:8OG5 3.8 24.9 1.0
O22 A:PPV503 3.9 31.2 1.0
O8 P:8OG5 4.0 30.9 1.0
O A:HOH795 4.1 24.3 0.5
O P:HOH213 4.3 31.1 1.0
OP2 P:DA4 4.3 23.2 1.0
O P:HOH208 4.4 25.1 1.0
O21 A:PPV503 4.4 36.3 1.0
O31 A:PPV503 4.4 45.7 1.0
O5' P:8OG5 4.5 24.2 1.0
OP1 P:8OG5 4.5 22.5 1.0
O5' P:DA4 4.7 22.0 1.0
C3' P:DA4 4.7 21.0 1.0
O3' P:DA4 4.7 21.2 1.0
OP1 P:DA4 4.8 22.9 1.0
P P:DA4 4.8 23.8 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 04:54:17 2024

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