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Manganese in PDB 7m49: Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 Min

Enzymatic activity of Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 Min

All present enzymatic activity of Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 Min:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 Min, PDB code: 7m49 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) 40.11 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.146, 62.771, 140.568, 90, 90, 90
R / Rfree (%) 18.8 / 21.6

Other elements in 7m49:

The structure of Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 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+ Reaction State Ternary Complex, 5 Min (pdb code 7m49). 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+ Reaction State Ternary Complex, 5 Min, PDB code: 7m49:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7m49

Go back to Manganese Binding Sites List in 7m49
Manganese binding site 1 out of 4 in the Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 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+ Reaction State Ternary Complex, 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn604

b:28.4
occ:0.98
 OD2 A:ASP427 2.0 33.6 1.0
OD1 A:ASP429 2.1 29.5 1.0
OD2 A:ASP490 2.1 28.1 1.0
OP1 P:DT7 2.1 36.6 0.6
O2A A:TTP607 2.3 23.0 0.4
O A:HOH730 2.3 31.7 1.0
O3' P:DC6 2.4 26.8 0.4
O3' P:DC6 2.6 26.0 0.6
CG A:ASP427 2.9 29.8 1.0
P P:DT7 3.0 22.9 0.6
CG A:ASP490 3.1 26.9 1.0
CG A:ASP429 3.2 30.4 1.0
OD1 A:ASP427 3.2 30.2 1.0
PA A:TTP607 3.4 32.7 0.4
MN A:MN605 3.6 26.6 1.0
OD2 A:ASP429 3.6 30.0 1.0
C3' P:DC6 3.6 27.4 0.4
O1A A:TTP607 3.7 28.8 0.4
CB A:ASP490 3.8 27.4 1.0
C3' P:DC6 3.9 22.6 0.6
OD1 A:ASP490 4.0 29.2 1.0
C4' P:DC6 4.1 24.9 0.4
C4' P:DC6 4.1 24.2 0.6
O5' P:DT7 4.1 41.3 0.6
C5' P:DC6 4.1 20.9 0.4
O5' A:TTP607 4.2 17.6 0.4
OP2 P:DT7 4.2 20.1 0.6
O A:HOH845 4.2 28.8 0.4
C5' P:DC6 4.2 23.5 0.6
C5' P:DT7 4.2 35.9 0.6
CB A:ASP427 4.3 28.6 1.0
C5' A:TTP607 4.4 20.5 0.4
CB A:ASP429 4.4 25.4 1.0
NH2 A:ARG488 4.5 28.7 1.0
O A:HOH845 4.6 44.1 0.6
O22 A:PPV608 4.8 27.6 0.6
O3A A:TTP607 4.8 35.2 0.4
OP1 P:DC6 4.8 24.2 0.4
O5' P:DC6 4.9 31.9 0.4
O5' P:DC6 4.9 20.3 0.6
C2' P:DC6 4.9 25.6 0.4
C2' P:DC6 4.9 26.4 0.6
O A:VAL428 4.9 28.3 1.0
CA A:ASP429 4.9 25.5 1.0
O2G A:TTP607 5.0 27.7 0.4

Manganese binding site 2 out of 4 in 7m49

Go back to Manganese Binding Sites List in 7m49
Manganese binding site 2 out of 4 in the Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 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+ Reaction State Ternary Complex, 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn605

b:26.6
occ:1.00
 O2A A:TTP607 2.0 23.0 0.4
O2B A:TTP607 2.1 31.7 0.4
OD1 A:ASP427 2.1 30.2 1.0
O2G A:TTP607 2.1 27.7 0.4
OD2 A:ASP429 2.2 30.0 1.0
O21 A:PPV608 2.2 24.4 0.6
O22 A:PPV608 2.3 27.6 0.6
O A:HOH722 2.4 31.8 1.0
OP1 P:DT7 2.4 36.6 0.6
PB A:TTP607 3.0 51.1 0.4
PA A:TTP607 3.1 32.7 0.4
CG A:ASP429 3.1 30.4 1.0
O3A A:TTP607 3.1 35.2 0.4
P1 A:PPV608 3.2 24.6 0.6
CG A:ASP427 3.2 29.8 1.0
PG A:TTP607 3.3 32.6 0.4
P2 A:PPV608 3.3 34.0 0.6
O31 A:PPV608 3.4 37.8 0.6
OD1 A:ASP429 3.5 29.5 1.0
MN A:MN604 3.6 28.4 1.0
O3B A:TTP607 3.6 37.9 0.4
OPP A:PPV608 3.6 40.1 0.6
P P:DT7 3.7 22.9 0.6
OD2 A:ASP427 3.7 33.6 1.0
O12 A:PPV608 3.9 36.9 0.6
O A:HOH845 3.9 44.1 0.6
O A:HOH845 3.9 28.8 0.4
O5' A:TTP607 4.1 17.6 0.4
C5' A:TTP607 4.1 20.5 0.4
C5' P:DT7 4.1 35.9 0.6
O5' P:DT7 4.1 41.3 0.6
O1G A:TTP607 4.2 29.1 0.4
O1A A:TTP607 4.3 28.8 0.4
O A:ASP427 4.3 27.9 1.0
O1B A:TTP607 4.3 29.2 0.4
OG A:SER417 4.4 37.2 1.0
O A:HOH730 4.4 31.7 1.0
O3G A:TTP607 4.4 35.7 0.4
N A:ASP427 4.4 31.5 1.0
CB A:ASP429 4.5 25.4 1.0
CA A:GLY416 4.5 28.9 1.0
CB A:ASP427 4.5 28.6 1.0
N A:SER417 4.5 32.4 1.0
C A:ASP427 4.5 26.7 1.0
O11 A:PPV608 4.5 34.7 0.6
OP2 P:DT7 4.6 20.1 0.6
O32 A:PPV608 4.7 33.7 0.6
O A:HOH794 4.7 29.3 1.0
CA A:ASP427 4.7 28.0 1.0
O3' P:DC6 4.8 26.0 0.6
MN P:MN101 4.8 40.1 0.6
O3' P:DC6 4.8 26.8 0.4
N A:ASP429 4.9 25.7 1.0

Manganese binding site 3 out of 4 in 7m49

Go back to Manganese Binding Sites List in 7m49
Manganese binding site 3 out of 4 in the Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 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+ Reaction State Ternary Complex, 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn606

b:36.7
occ:0.34
 OD2 A:ASP382 2.2 38.0 1.0
ND1 A:HIS486 2.4 28.6 1.0
O A:HOH776 2.6 34.2 0.9
O A:HOH759 3.0 36.9 0.9
CE1 A:HIS486 3.2 29.9 1.0
CG A:ASP382 3.3 26.6 1.0
NH2 A:ARG485 3.4 51.0 1.0
CG A:HIS486 3.5 27.1 1.0
N A:HIS486 3.6 28.3 1.0
CZ A:ARG485 3.8 45.7 1.0
OD1 A:ASP382 3.8 32.7 1.0
CB A:HIS486 3.9 26.2 1.0
NE A:ARG485 4.1 42.5 1.0
CA A:ARG485 4.3 30.0 1.0
CA A:HIS486 4.4 28.9 1.0
O A:HOH866 4.4 72.8 1.0
NH1 A:ARG485 4.4 42.5 1.0
C A:ARG485 4.4 27.2 1.0
NE2 A:HIS486 4.4 34.2 1.0
CB A:ASP382 4.5 30.5 1.0
ND1 A:HIS379 4.5 28.0 1.0
CD2 A:HIS486 4.6 28.7 1.0
O A:HOH842 4.7 27.5 1.0
NH1 A:ARG478 4.8 43.0 1.0
CE1 A:HIS379 4.9 27.9 1.0
CB A:ARG485 4.9 34.2 1.0
O A:HOH837 4.9 34.0 1.0
O A:ARG484 4.9 35.6 1.0

Manganese binding site 4 out of 4 in 7m49

Go back to Manganese Binding Sites List in 7m49
Manganese binding site 4 out of 4 in the Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 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+ Reaction State Ternary Complex, 5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:40.1
occ:0.56
 O3A A:TTP607 1.9 35.2 0.4
O A:HOH809 2.1 34.4 0.6
OP2 P:DT7 2.1 20.1 0.6
O A:HOH845 2.2 44.1 0.6
O1A A:TTP607 2.3 28.8 0.4
O31 A:PPV608 2.4 37.8 0.6
O P:HOH226 2.4 49.3 0.6
PA A:TTP607 2.7 32.7 0.4
P P:DT7 3.2 22.9 0.6
PB A:TTP607 3.3 51.1 0.4
O3B A:TTP607 3.6 37.9 0.4
O5' A:TTP607 3.6 17.6 0.4
O22 A:PPV608 3.6 27.6 0.6
O5' P:DT7 3.7 41.3 0.6
P1 A:PPV608 3.7 24.6 0.6
O32 A:PPV608 3.7 33.7 0.6
OP1 P:DT7 3.8 36.6 0.6
OPP A:PPV608 3.8 40.1 0.6
O2A A:TTP607 3.9 23.0 0.4
O3G A:TTP607 3.9 35.7 0.4
C7 P:DT7 3.9 34.9 0.6
O1B A:TTP607 3.9 29.2 0.4
O A:HOH845 4.0 28.8 0.4
P2 A:PPV608 4.0 34.0 0.6
C5M A:TTP607 4.0 29.1 0.4
PG A:TTP607 4.2 32.6 0.4
O A:HOH740 4.4 35.9 1.0
O2G A:TTP607 4.4 27.7 0.4
O2B A:TTP607 4.5 31.7 0.4
O11 A:PPV608 4.6 34.7 0.6
O3' P:DC6 4.6 26.0 0.6
O A:HOH730 4.7 31.7 1.0
O21 A:PPV608 4.7 24.4 0.6
MN A:MN605 4.8 26.6 1.0
C5' A:TTP607 4.8 20.5 0.4
C6 P:DT7 4.9 34.3 0.6
C5 P:DT7 4.9 37.3 0.6
C6 A:TTP607 4.9 20.2 0.4
C5 A:TTP607 4.9 21.5 0.4
C5' P:DT7 5.0 35.9 0.6

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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