Atomistry » Manganese » PDB 6i90-6jr1 » 6ipf
Atomistry »
  Manganese »
    PDB 6i90-6jr1 »
      6ipf »

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

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