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Calcium in PDB 7m4k: Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex

Enzymatic activity of Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex

All present enzymatic activity of Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex, PDB code: 7m4k 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) 31.12 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.001, 62.507, 140.191, 90, 90, 90
R / Rfree (%) 19.6 / 22.7

Other elements in 7m4k:

The structure of Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex (pdb code 7m4k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex, PDB code: 7m4k:

Calcium binding site 1 out of 1 in 7m4k

Go back to Calcium Binding Sites List in 7m4k
Calcium binding site 1 out of 1 in the Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:45.6
occ:1.00
 OD1 A:ASP427 2.1 47.5 1.0
O1A A:YQS612 2.3 66.7 1.0
O1B A:YQS612 2.3 65.2 1.0
O1G A:YQS612 2.3 96.2 1.0
OD2 A:ASP429 2.4 54.8 1.0
O A:HOH753 2.8 46.3 1.0
PB A:YQS612 3.2 44.9 1.0
CG A:ASP427 3.3 57.2 1.0
PA A:YQS612 3.3 50.8 1.0
CG A:ASP429 3.3 59.2 1.0
PG A:YQS612 3.4 62.0 1.0
O3A A:YQS612 3.4 106.5 1.0
O A:ASP427 3.5 37.2 1.0
OD1 A:ASP429 3.6 47.5 1.0
NA A:NA602 3.7 48.7 1.0
O3B A:YQS612 3.7 83.2 1.0
C A:ASP427 3.8 39.3 1.0
O2G A:YQS612 3.9 88.7 1.0
N A:ASP427 4.0 30.9 1.0
OD2 A:ASP427 4.0 48.6 1.0
CA A:ASP427 4.2 45.5 1.0
O A:HOH764 4.3 40.5 1.0
C5' A:YQS612 4.3 69.3 1.0
CB A:ASP427 4.3 52.9 1.0
O5' A:YQS612 4.3 80.7 1.0
OG A:SER417 4.4 39.2 1.0
N A:SER417 4.5 31.0 1.0
O A:HOH772 4.5 35.8 1.0
N A:VAL428 4.5 28.9 1.0
CA A:GLY416 4.5 33.0 1.0
O2B A:YQS612 4.6 51.4 1.0
O3G A:YQS612 4.7 45.2 1.0
CB A:ASP429 4.7 49.1 1.0
S2A A:YQS612 4.7 42.7 1.0
N A:ASP429 4.9 26.1 1.0
C A:GLY426 4.9 34.2 1.0
CA A:VAL428 5.0 29.1 1.0
C A:VAL428 5.0 28.3 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: Fri Jul 19 01:55:36 2024

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