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Manganese in PDB 7m4a: Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min

Enzymatic activity of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min

All present enzymatic activity of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min, PDB code: 7m4a was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.17 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.05, 62.727, 140.405, 90, 90, 90
R / Rfree (%) 18.8 / 22

Other elements in 7m4a:

The structure of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min (pdb code 7m4a). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min, PDB code: 7m4a:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7m4a

Go back to Manganese Binding Sites List in 7m4a
Manganese binding site 1 out of 4 in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:37.8
occ:1.00
 OD2 A:ASP427 1.8 44.4 1.0
OD1 A:ASP429 2.0 36.3 1.0
OD2 A:ASP490 2.1 38.9 1.0
OP1 P:DT7 2.2 33.9 1.0
O A:HOH704 2.4 40.7 1.0
CG A:ASP427 2.7 48.5 1.0
O3' P:DC6 2.8 31.6 1.0
OD1 A:ASP427 3.0 40.6 1.0
CG A:ASP429 3.1 37.3 1.0
CG A:ASP490 3.1 32.5 1.0
P P:DT7 3.1 30.1 1.0
MN A:MN603 3.4 34.5 1.0
OD2 A:ASP429 3.5 33.7 1.0
CB A:ASP490 3.8 36.3 1.0
OD1 A:ASP490 4.0 34.3 1.0
C3' P:DC6 4.0 33.0 1.0
CB A:ASP427 4.1 33.0 1.0
OP2 P:DT7 4.2 32.9 1.0
O5' P:DT7 4.3 30.6 1.0
C4' P:DC6 4.3 30.8 1.0
CB A:ASP429 4.4 38.0 1.0
C5' P:DC6 4.4 32.8 1.0
C5' P:DT7 4.4 38.7 1.0
NH2 A:ARG488 4.5 35.7 1.0
O A:VAL428 4.7 32.3 1.0
O22 A:PPV601 4.8 52.4 0.6
O21 A:PPV601 4.8 47.2 0.4
CA A:ASP429 4.9 31.7 1.0
O22 A:PPV601 5.0 55.2 0.4
C A:VAL428 5.0 31.3 1.0
N A:ASP490 5.0 28.8 1.0

Manganese binding site 2 out of 4 in 7m4a

Go back to Manganese Binding Sites List in 7m4a
Manganese binding site 2 out of 4 in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn603

b:34.5
occ:1.00
 O21 A:PPV601 1.9 47.2 0.4
OD1 A:ASP427 2.0 40.6 1.0
OD2 A:ASP429 2.1 33.7 1.0
OP1 P:DT7 2.2 33.9 1.0
O21 A:PPV601 2.2 50.8 0.6
O32 A:PPV601 2.3 54.2 0.4
O A:HOH741 2.3 52.5 0.6
O22 A:PPV601 2.4 52.4 0.6
O22 A:PPV601 2.4 55.2 0.4
P2 A:PPV601 2.7 58.8 0.4
P1 A:PPV601 3.0 50.5 0.4
CG A:ASP429 3.1 37.3 1.0
CG A:ASP427 3.1 48.5 1.0
P1 A:PPV601 3.2 50.4 0.6
O31 A:PPV601 3.3 63.5 0.6
OPP A:PPV601 3.3 65.1 0.4
OD1 A:ASP429 3.3 36.3 1.0
MN A:MN602 3.4 37.8 1.0
O31 A:PPV601 3.4 53.9 0.4
P2 A:PPV601 3.5 55.3 0.6
P P:DT7 3.5 30.1 1.0
OD2 A:ASP427 3.6 44.4 1.0
OPP A:PPV601 3.8 52.7 0.6
O32 A:PPV601 3.8 54.9 0.6
O5' P:DT7 3.9 30.6 1.0
C5' P:DT7 4.0 38.7 1.0
O12 A:PPV601 4.2 56.4 0.4
O A:ASP427 4.3 30.7 1.0
O A:HOH704 4.3 40.7 1.0
OP2 P:DT7 4.4 32.9 1.0
O11 A:PPV601 4.4 48.3 0.4
CA A:GLY416 4.4 33.4 1.0
CB A:ASP427 4.4 33.0 1.0
CB A:ASP429 4.4 38.0 1.0
C A:ASP427 4.5 36.0 1.0
O3' P:DC6 4.5 31.6 1.0
N A:ASP427 4.6 35.3 1.0
O11 A:PPV601 4.6 47.5 0.6
N A:SER417 4.6 36.9 1.0
MN P:MN101 4.7 47.2 0.5
CA A:ASP427 4.7 30.0 1.0
OG A:SER417 4.8 50.3 1.0
O12 A:PPV601 4.8 58.9 0.6

Manganese binding site 3 out of 4 in 7m4a

Go back to Manganese Binding Sites List in 7m4a
Manganese binding site 3 out of 4 in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn604

b:37.6
occ:0.50
 OD2 A:ASP382 2.1 46.2 1.0
ND1 A:HIS486 2.3 33.0 1.0
O A:HOH778 2.3 49.9 1.0
O A:HOH754 2.4 43.3 1.0
O A:HOH796 2.5 53.8 1.0
CE1 A:HIS486 3.1 39.9 1.0
CG A:ASP382 3.2 39.6 1.0
CG A:HIS486 3.4 31.9 1.0
N A:HIS486 3.6 33.6 1.0
OD1 A:ASP382 3.7 41.9 1.0
CB A:HIS486 3.8 31.6 1.0
ND1 A:HIS379 4.3 29.9 1.0
NE2 A:HIS486 4.3 32.7 1.0
CA A:HIS486 4.3 32.3 1.0
CB A:ASP382 4.4 30.3 1.0
C A:ARG485 4.5 33.9 1.0
CA A:ARG485 4.5 34.4 1.0
CD2 A:HIS486 4.5 31.5 1.0
O A:HOH789 4.5 30.0 1.0
CE1 A:HIS379 4.7 37.6 1.0
NH1 A:ARG478 4.8 45.0 1.0

Manganese binding site 4 out of 4 in 7m4a

Go back to Manganese Binding Sites List in 7m4a
Manganese binding site 4 out of 4 in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:47.2
occ:0.48
 OP2 P:DT7 2.2 32.9 1.0
O31 A:PPV601 2.2 53.9 0.4
O31 A:PPV601 2.4 63.5 0.6
O22 A:PPV601 3.2 52.4 0.6
P P:DT7 3.3 30.1 1.0
OPP A:PPV601 3.6 52.7 0.6
P1 A:PPV601 3.6 50.5 0.4
P1 A:PPV601 3.6 50.4 0.6
O5' P:DT7 3.6 30.6 1.0
P2 A:PPV601 3.8 55.3 0.6
OP1 P:DT7 3.9 33.9 1.0
O12 A:PPV601 3.9 58.9 0.6
O22 A:PPV601 3.9 55.2 0.4
C7 P:DT7 3.9 41.1 1.0
O21 A:PPV601 4.3 47.2 0.4
O11 A:PPV601 4.3 48.3 0.4
O A:HOH735 4.4 39.1 1.0
O11 A:PPV601 4.5 47.5 0.6
OPP A:PPV601 4.5 65.1 0.4
O3' P:DC6 4.7 31.6 1.0
O21 A:PPV601 4.7 50.8 0.6
MN A:MN603 4.7 34.5 1.0
C6 P:DT7 4.8 31.8 1.0
C5 P:DT7 4.9 38.0 1.0
C5' P:DT7 4.9 38.7 1.0
P2 A:PPV601 4.9 58.8 0.4
O A:HOH704 5.0 40.7 1.0

Reference:

J.A.Jamsen, D.D.Shock, S.H.Wilson. Watching Right and Wrong Nucleotide Insertion Captures Hidden Polymerase Fidelity Checkpoints. Nat Commun V. 13 3193 2022.
ISSN: ESSN 2041-1723
PubMed: 35680862
DOI: 10.1038/S41467-022-30141-W
Page generated: Sun Oct 6 10:01:36 2024

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