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Manganese in PDB 7m4b: Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 Min

Enzymatic activity of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 Min

All present enzymatic activity of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 Min:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 Min, PDB code: 7m4b 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) 31.14 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.981, 62.634, 140.334, 90, 90, 90
R / Rfree (%) 18.1 / 20.2

Other elements in 7m4b:

The structure of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 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, 60 Min (pdb code 7m4b). 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, 60 Min, PDB code: 7m4b:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7m4b

Go back to Manganese Binding Sites List in 7m4b
Manganese binding site 1 out of 4 in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 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, 60 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:25.2
occ:1.00
 O21 A:PPV607 2.1 28.4 0.9
OD1 A:ASP427 2.1 32.1 0.4
O22 A:PPV607 2.1 37.9 0.6
OD2 A:ASP429 2.1 27.8 1.0
OP1 P:DT7 2.1 26.6 1.0
OD1 A:ASP427 2.2 31.8 0.6
O12 A:PPV607 2.2 29.2 0.4
O A:HOH732 2.4 36.2 0.8
O22 A:PPV607 2.6 45.9 0.4
P2 A:PPV607 2.8 42.0 0.4
CG A:ASP427 2.9 29.9 0.4
CG A:ASP429 3.1 26.9 1.0
P1 A:PPV607 3.1 34.7 0.8
OD2 A:ASP427 3.1 37.0 0.4
CG A:ASP427 3.3 31.8 0.6
O31 A:PPV607 3.3 42.5 0.5
P2 A:PPV607 3.3 38.1 0.6
OD1 A:ASP429 3.4 27.4 1.0
P P:DT7 3.4 24.4 1.0
MN A:MN602 3.5 28.7 0.9
OPP A:PPV607 3.5 43.7 0.8
OD2 A:ASP427 3.8 33.1 0.6
O12 A:PPV607 3.9 33.3 0.6
C5' P:DT7 4.0 24.2 1.0
O5' P:DT7 4.0 23.6 1.0
O A:ASP427 4.2 24.7 0.6
O32 A:PPV607 4.3 35.5 0.4
OP2 P:DT7 4.3 22.1 1.0
CB A:ASP427 4.3 27.2 0.4
O A:HOH720 4.4 30.8 1.0
O11 A:PPV607 4.4 30.6 1.0
CA A:GLY416 4.5 26.1 1.0
CB A:ASP429 4.5 24.2 1.0
C A:ASP427 4.5 23.6 0.6
CB A:ASP427 4.5 25.1 0.6
O32 A:PPV607 4.6 37.6 0.6
N A:ASP427 4.6 29.0 0.6
O3' P:DC6 4.6 23.6 1.0
N A:SER417 4.6 29.5 1.0
O A:ASP427 4.6 24.6 0.4
C A:ASP427 4.7 24.5 0.4
MN P:MN101 4.7 31.4 0.4
OG A:SER417 4.7 46.1 1.0
N A:ASP427 4.7 29.5 0.4
CA A:ASP427 4.8 23.1 0.6
CA A:ASP427 4.8 24.5 0.4
O A:HOH831 4.8 28.0 0.4

Manganese binding site 2 out of 4 in 7m4b

Go back to Manganese Binding Sites List in 7m4b
Manganese binding site 2 out of 4 in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 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, 60 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:28.7
occ:0.95
 OD2 A:ASP427 2.0 33.1 0.6
OD2 A:ASP490 2.1 27.2 1.0
OD1 A:ASP429 2.1 27.4 1.0
OP1 P:DT7 2.2 26.6 1.0
O A:HOH720 2.4 30.8 1.0
O A:HOH831 2.6 28.0 0.4
O3' P:DC6 2.8 23.6 1.0
CG A:ASP427 2.8 31.8 0.6
OD1 A:ASP427 2.9 32.1 0.4
CG A:ASP490 3.1 26.0 1.0
OD1 A:ASP427 3.1 31.8 0.6
P P:DT7 3.1 24.4 1.0
CG A:ASP429 3.2 26.9 1.0
CG A:ASP427 3.4 29.9 0.4
MN A:MN601 3.5 25.2 1.0
OD2 A:ASP429 3.6 27.8 1.0
OD2 A:ASP427 3.7 37.0 0.4
CB A:ASP490 3.8 24.5 1.0
OD1 A:ASP490 4.0 26.2 1.0
C3' P:DC6 4.1 23.1 1.0
OP2 P:DT7 4.1 22.1 1.0
CB A:ASP427 4.2 25.1 0.6
CB A:ASP427 4.2 27.2 0.4
C4' P:DC6 4.3 24.2 1.0
C5' P:DC6 4.3 24.0 1.0
O5' P:DT7 4.3 23.6 1.0
NH2 A:ARG488 4.4 25.7 1.0
C5' P:DT7 4.4 24.2 1.0
CB A:ASP429 4.5 24.2 1.0
O A:VAL428 4.7 25.7 1.0
O22 A:PPV607 4.7 37.9 0.6
CA A:ASP429 4.9 24.2 1.0
C A:VAL428 5.0 24.5 1.0
N A:ASP490 5.0 22.6 1.0
O5' P:DC6 5.0 24.1 1.0
CA A:ASP490 5.0 24.3 1.0

Manganese binding site 3 out of 4 in 7m4b

Go back to Manganese Binding Sites List in 7m4b
Manganese binding site 3 out of 4 in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 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, 60 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn603

b:32.7
occ:0.58
 OD2 A:ASP382 2.1 38.7 1.0
ND1 A:HIS486 2.3 23.5 1.0
O A:HOH847 2.4 42.7 1.0
O A:HOH772 2.5 33.8 1.0
O A:HOH804 2.7 33.2 0.9
CE1 A:HIS486 3.2 28.2 1.0
CG A:ASP382 3.2 32.9 1.0
CG A:HIS486 3.5 23.8 1.0
NH2 A:ARG485 3.5 44.1 0.5
N A:HIS486 3.6 24.8 1.0
OD1 A:ASP382 3.8 34.8 1.0
CB A:HIS486 3.9 23.8 1.0
CZ A:ARG485 3.9 26.3 0.5
NE A:ARG485 4.3 30.4 0.5
ND1 A:HIS379 4.3 25.0 1.0
CA A:HIS486 4.4 22.8 1.0
NE2 A:HIS486 4.4 31.8 1.0
CB A:ASP382 4.4 28.8 1.0
CA A:ARG485 4.5 25.0 0.5
C A:ARG485 4.5 25.0 0.5
C A:ARG485 4.5 24.8 0.5
CA A:ARG485 4.5 26.0 0.5
CD2 A:HIS486 4.5 29.0 1.0
O A:HOH839 4.5 25.4 1.0
NH1 A:ARG485 4.6 31.1 0.5
O A:HOH860 4.6 61.7 1.0
CE1 A:HIS379 4.7 27.7 1.0
NH1 A:ARG478 4.9 38.4 1.0
O A:HOH842 4.9 31.7 1.0

Manganese binding site 4 out of 4 in 7m4b

Go back to Manganese Binding Sites List in 7m4b
Manganese binding site 4 out of 4 in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 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, 60 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:31.4
occ:0.43
 O31 A:PPV607 2.1 42.5 0.5
O A:HOH799 2.2 36.4 0.6
OP2 P:DT7 2.3 22.1 1.0
O P:HOH227 3.1 47.3 0.8
P P:DT7 3.3 24.4 1.0
O22 A:PPV607 3.5 45.9 0.4
P1 A:PPV607 3.6 34.7 0.8
O22 A:PPV607 3.6 37.9 0.6
O5' P:DT7 3.7 23.6 1.0
O32 A:PPV607 3.8 37.6 0.6
OP1 P:DT7 3.9 26.6 1.0
OPP A:PPV607 4.0 43.7 0.8
C7 P:DT7 4.0 31.5 1.0
P2 A:PPV607 4.1 38.1 0.6
O A:HOH721 4.3 32.2 1.0
O11 A:PPV607 4.4 30.6 1.0
P2 A:PPV607 4.5 42.0 0.4
O21 A:PPV607 4.5 28.4 0.9
MN A:MN601 4.7 25.2 1.0
O3' P:DC6 4.7 23.6 1.0
OD2 A:ASP427 4.9 37.0 0.4
C6 P:DT7 4.9 24.7 1.0
C5 P:DT7 4.9 24.8 1.0
C5' P:DT7 4.9 24.2 1.0
O A:HOH720 5.0 30.8 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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