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Manganese in PDB 5ddy: Binary Complex of Human Polymerase Lambda with Dctp

Enzymatic activity of Binary Complex of Human Polymerase Lambda with Dctp

All present enzymatic activity of Binary Complex of Human Polymerase Lambda with Dctp:
2.7.7.7;

Protein crystallography data

The structure of Binary Complex of Human Polymerase Lambda with Dctp, PDB code: 5ddy was solved by M.S.Liu, M.D.Tsai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.66 / 3.36
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 206.015, 206.015, 114.266, 90.00, 90.00, 90.00
R / Rfree (%) 26.2 / 29.7

Other elements in 5ddy:

The structure of Binary Complex of Human Polymerase Lambda with Dctp also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Binary Complex of Human Polymerase Lambda with Dctp (pdb code 5ddy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Binary Complex of Human Polymerase Lambda with Dctp, PDB code: 5ddy:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5ddy

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Manganese binding site 1 out of 8 in the Binary Complex of Human Polymerase Lambda with Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Binary Complex of Human Polymerase Lambda with Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:0.5
occ:1.00
 OD2 A:ASP490 2.4 0.8 1.0
OD1 A:ASP429 2.5 0.4 1.0
OD2 A:ASP427 2.8 0.0 1.0
O2A A:DCP603 2.9 0.2 1.0
CG A:ASP429 3.3 0.9 1.0
OD2 A:ASP429 3.3 0.9 1.0
O5' A:DCP603 3.4 0.5 1.0
O1A A:DCP603 3.4 0.1 1.0
PA A:DCP603 3.4 0.2 1.0
CG A:ASP490 3.6 0.5 1.0
CG A:ASP427 3.8 0.7 1.0
OD1 A:ASP427 3.9 0.1 1.0
C5' A:DCP603 3.9 0.1 1.0
CB A:ASP490 4.3 0.5 1.0
OD1 A:ASP490 4.6 0.9 1.0
MG A:MG601 4.6 0.0 1.0
CB A:ASP429 4.7 0.3 1.0
O3A A:DCP603 5.0 0.1 1.0

Manganese binding site 2 out of 8 in 5ddy

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Manganese binding site 2 out of 8 in the Binary Complex of Human Polymerase Lambda with Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Binary Complex of Human Polymerase Lambda with Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn604

b:0.8
occ:1.00
 O A:SER339 2.7 0.0 1.0
O A:ALA344 3.4 0.7 1.0
O A:ILE341 3.5 0.7 1.0
C A:SER339 3.8 0.8 1.0
O A:HOH702 4.0 88.7 1.0
CA A:ASN340 4.2 0.1 1.0
C A:ASN340 4.2 0.4 1.0
C A:ILE341 4.4 1.0 1.0
O A:ASN340 4.4 0.9 1.0
N A:ASN340 4.5 0.1 1.0
C A:ALA344 4.5 0.7 1.0
O A:HOH701 4.6 0.3 1.0
N A:ILE341 4.7 0.4 1.0
OG A:SER339 4.8 0.2 1.0
CA A:TRP342 4.8 0.6 1.0
N A:ALA344 4.8 1.0 1.0
N A:GLY343 5.0 0.6 1.0
N A:TRP342 5.0 0.7 1.0

Manganese binding site 3 out of 8 in 5ddy

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Manganese binding site 3 out of 8 in the Binary Complex of Human Polymerase Lambda with Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Binary Complex of Human Polymerase Lambda with Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn602

b:0.9
occ:1.00
 OD2 C:ASP429 2.1 0.6 1.0
OD2 C:ASP427 2.4 0.5 1.0
OD2 C:ASP490 2.4 0.3 1.0
O2A C:DCP603 2.7 0.7 1.0
CG C:ASP429 3.0 0.8 1.0
OD1 C:ASP429 3.1 0.6 1.0
CG C:ASP427 3.2 1.0 1.0
OD1 C:ASP427 3.3 0.0 1.0
PA C:DCP603 3.4 0.2 1.0
O5' C:DCP603 3.4 0.5 1.0
CG C:ASP490 3.5 0.3 1.0
O1A C:DCP603 3.6 0.8 1.0
C5' C:DCP603 3.9 0.3 1.0
CB C:ASP490 4.2 0.5 1.0
MG C:MG601 4.3 0.1 1.0
CB C:ASP429 4.4 1.0 1.0
OD1 C:ASP490 4.5 0.4 1.0
CB C:ASP427 4.6 0.4 1.0
O2G C:DCP603 4.9 0.9 1.0
O3A C:DCP603 4.9 0.8 1.0
O2B C:DCP603 5.0 0.0 1.0

Manganese binding site 4 out of 8 in 5ddy

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Manganese binding site 4 out of 8 in the Binary Complex of Human Polymerase Lambda with Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Binary Complex of Human Polymerase Lambda with Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn604

b:0.0
occ:1.00
 O C:SER339 3.0 1.0 1.0
O C:HOH701 3.0 0.2 1.0
O C:ALA344 3.8 0.1 1.0
O C:ILE341 3.9 0.8 1.0
C C:SER339 4.1 0.2 1.0
CA C:ASN340 4.3 0.1 1.0
C C:ASN340 4.4 0.5 1.0
O C:ASN340 4.4 0.4 1.0
N C:ASN340 4.7 1.0 1.0
C C:ILE341 4.7 0.7 1.0
OG C:SER339 4.7 0.7 1.0
C C:ALA344 4.9 0.8 1.0
N C:ILE341 4.9 0.9 1.0

Manganese binding site 5 out of 8 in 5ddy

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Manganese binding site 5 out of 8 in the Binary Complex of Human Polymerase Lambda with Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Binary Complex of Human Polymerase Lambda with Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn602

b:0.8
occ:1.00
 OD2 E:ASP490 2.1 0.5 1.0
OD1 E:ASP429 2.3 0.0 1.0
OD2 E:ASP427 2.6 0.4 1.0
O2A E:DCP603 3.1 0.7 1.0
CG E:ASP429 3.3 0.3 1.0
CG E:ASP490 3.4 0.2 1.0
O5' E:DCP603 3.5 0.1 1.0
PA E:DCP603 3.6 0.9 1.0
CG E:ASP427 3.7 0.0 1.0
O1A E:DCP603 3.7 0.4 1.0
OD2 E:ASP429 3.8 0.7 1.0
C5' E:DCP603 3.9 0.9 1.0
OD1 E:ASP427 3.9 0.4 1.0
OD1 E:ASP490 4.2 0.7 1.0
CB E:ASP490 4.3 0.9 1.0
CB E:ASP429 4.6 0.3 1.0
MG E:MG601 4.9 0.3 1.0
CB E:ASP427 5.0 0.3 1.0

Manganese binding site 6 out of 8 in 5ddy

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Manganese binding site 6 out of 8 in the Binary Complex of Human Polymerase Lambda with Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Binary Complex of Human Polymerase Lambda with Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn604

b:0.6
occ:1.00
 O E:SER339 2.9 0.3 1.0
O E:ILE341 3.6 0.2 1.0
O E:ALA344 3.8 0.8 1.0
C E:SER339 4.1 1.0 1.0
O E:ASN340 4.2 0.9 1.0
C E:ASN340 4.2 0.8 1.0
C E:ILE341 4.3 0.2 1.0
CA E:ASN340 4.5 0.9 1.0
N E:ILE341 4.7 0.6 1.0
N E:ASN340 4.8 0.5 1.0
CA E:TRP342 4.8 0.3 1.0
N E:TRP342 4.8 0.6 1.0
OG E:SER339 4.9 0.2 1.0
C E:ALA344 5.0 0.8 1.0

Manganese binding site 7 out of 8 in 5ddy

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Manganese binding site 7 out of 8 in the Binary Complex of Human Polymerase Lambda with Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Binary Complex of Human Polymerase Lambda with Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn602

b:0.6
occ:1.00
 OD2 G:ASP490 2.2 0.8 1.0
O2A G:DCP603 3.0 0.4 1.0
OD1 G:ASP429 3.2 0.0 1.0
O1A G:DCP603 3.3 0.7 1.0
CG G:ASP490 3.4 0.8 1.0
PA G:DCP603 3.4 0.4 1.0
O5' G:DCP603 3.4 0.8 1.0
OD2 G:ASP427 3.6 0.2 1.0
OD1 G:ASP427 3.8 0.0 1.0
C5' G:DCP603 3.9 0.8 1.0
CG G:ASP427 3.9 0.8 1.0
OD1 G:ASP490 4.1 0.9 1.0
CG G:ASP429 4.3 0.8 1.0
CB G:ASP490 4.4 0.5 1.0
OD2 G:ASP429 4.9 0.3 1.0
CB G:ASP427 4.9 0.8 1.0
O3A G:DCP603 5.0 0.0 1.0

Manganese binding site 8 out of 8 in 5ddy

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Manganese binding site 8 out of 8 in the Binary Complex of Human Polymerase Lambda with Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Binary Complex of Human Polymerase Lambda with Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn604

b:0.2
occ:1.00
 O G:SER339 2.8 0.3 1.0
O G:ALA344 2.8 0.8 1.0
O G:ILE341 3.0 0.5 1.0
C G:ALA344 3.7 0.9 1.0
N G:ALA344 3.8 0.9 1.0
C G:SER339 4.0 0.6 1.0
C G:ILE341 4.0 0.5 1.0
N G:GLY343 4.1 0.6 1.0
CA G:ALA344 4.2 0.7 1.0
C G:ASN340 4.5 0.1 1.0
N G:GLY345 4.6 0.8 1.0
O G:ASN340 4.6 0.4 1.0
CA G:TRP342 4.6 0.1 1.0
N G:ILE341 4.7 0.3 1.0
CB G:ALA344 4.7 0.8 1.0
N G:TRP342 4.8 0.9 1.0
C G:GLY343 4.8 0.1 1.0
C G:TRP342 4.8 0.0 1.0
OG G:SER339 4.9 0.7 1.0
CA G:SER339 4.9 0.5 1.0
CA G:GLY345 4.9 0.2 1.0
CA G:ASN340 4.9 0.7 1.0
CA G:GLY343 4.9 0.4 1.0
N G:ASN340 4.9 0.4 1.0

Reference:

M.S.Liu, H.Y.Tsai, X.X.Liu, M.C.Ho, W.J.Wu, M.D.Tsai. Structural Mechanism For the Fidelity Modulation of Dna Polymerase Lambda J.Am.Chem.Soc. V. 138 2389 2016.
ISSN: ESSN 1520-5126
PubMed: 26836966
DOI: 10.1021/JACS.5B13368
Page generated: Sat Oct 5 23:53:57 2024

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