Calcium in PDB 7ktj: Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)

Enzymatic activity of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)

All present enzymatic activity of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN), PDB code: 7ktj 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) 34.86 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.02, 62.099, 118.212, 90, 90, 90
R / Rfree (%) 16.1 / 18.4

Other elements in 7ktj:

The structure of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) (pdb code 7ktj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN), PDB code: 7ktj:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7ktj

Go back to Calcium Binding Sites List in 7ktj
Calcium binding site 1 out of 3 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:15.9
occ:1.00
 OD2 A:ASP418 2.3 28.7 1.0
O A:HOH744 2.4 24.9 1.0
OD1 A:ASP332 2.4 17.7 1.0
O P:HOH102 2.4 19.4 1.0
OD2 A:ASP330 2.4 21.3 1.0
O2A A:8DG506 2.4 16.8 1.0
OD1 A:ASP330 2.6 18.5 1.0
CG A:ASP330 2.8 16.1 1.0
CG A:ASP332 3.4 16.3 1.0
CG A:ASP418 3.4 20.9 1.0
PA A:8DG506 3.4 17.7 1.0
O5' A:8DG506 3.5 22.6 1.0
C5' A:8DG506 3.6 19.5 1.0
OD2 A:ASP332 3.7 17.2 1.0
CA A:CA502 3.8 16.0 1.0
CB A:ASP418 4.1 16.1 1.0
O1A A:8DG506 4.1 18.6 1.0
O A:HOH644 4.2 58.1 1.0
CB A:ASP330 4.3 15.8 1.0
OD1 A:ASP418 4.4 20.2 1.0
OP1 P:DA4 4.4 18.7 1.0
NH2 A:ARG416 4.5 17.4 1.0
CE1 A:HIS329 4.6 18.2 1.0
CB A:ASP332 4.7 14.5 1.0
O3A A:8DG506 4.8 16.9 1.0
O A:HOH887 4.8 26.2 0.5
NE2 A:HIS329 4.9 19.3 1.0

Calcium binding site 2 out of 3 in 7ktj

Go back to Calcium Binding Sites List in 7ktj
Calcium binding site 2 out of 3 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:16.0
occ:1.00
 OD1 A:ASP330 2.3 18.5 1.0
O2G A:8DG506 2.3 17.9 1.0
OD2 A:ASP332 2.3 17.2 1.0
O2B A:8DG506 2.3 16.9 1.0
O2A A:8DG506 2.4 16.8 1.0
O A:HOH743 2.5 18.0 1.0
O A:ASP330 2.8 20.2 1.0
CG A:ASP332 3.4 16.3 1.0
CG A:ASP330 3.4 16.1 1.0
PB A:8DG506 3.4 16.5 1.0
PG A:8DG506 3.5 16.8 1.0
C A:ASP330 3.6 18.0 1.0
O3B A:8DG506 3.6 17.1 1.0
PA A:8DG506 3.7 17.7 1.0
OD1 A:ASP332 3.7 17.7 1.0
CA A:CA501 3.8 15.9 1.0
O3A A:8DG506 3.8 16.9 1.0
N A:ASP330 4.1 15.8 1.0
OD2 A:ASP330 4.1 21.3 1.0
CA A:ASP330 4.2 17.4 1.0
O A:HOH635 4.2 15.4 1.0
O3G A:8DG506 4.2 18.0 1.0
O A:HOH647 4.4 17.9 1.0
CB A:ASP330 4.4 15.8 1.0
N A:VAL331 4.4 15.2 1.0
N A:GLY320 4.4 15.2 1.0
O1G A:8DG506 4.7 18.6 1.0
ND1 A:HIS329 4.7 18.6 1.0
CB A:ASP332 4.7 14.5 1.0
O1A A:8DG506 4.7 18.6 1.0
CA A:VAL331 4.7 15.9 1.0
C5' A:8DG506 4.7 19.5 1.0
CA A:GLY319 4.7 13.8 1.0
O5' A:8DG506 4.8 22.6 1.0
CE1 A:HIS329 4.8 18.2 1.0
N A:ASP332 4.8 14.5 1.0
O1B A:8DG506 4.8 19.7 1.0
C A:VAL331 4.9 14.6 1.0

Calcium binding site 3 out of 3 in 7ktj

Go back to Calcium Binding Sites List in 7ktj
Calcium binding site 3 out of 3 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:16.1
occ:0.75
 O A:VAL246 2.3 16.4 1.0
O A:THR241 2.3 19.3 1.0
O P:HOH109 2.3 21.5 1.0
O A:ILE243 2.4 17.6 1.0
O P:HOH110 2.5 25.2 1.0
OP1 P:DT3 2.5 16.6 1.0
C A:VAL246 3.4 15.1 1.0
C A:THR241 3.5 18.2 1.0
C A:ILE243 3.5 17.9 1.0
P P:DT3 3.7 16.8 1.0
N A:VAL246 3.8 14.9 1.0
OP2 P:DT3 3.9 17.6 1.0
N A:ILE243 4.1 16.9 1.0
CA A:VAL246 4.2 14.7 1.0
C A:GLN242 4.2 19.8 1.0
N A:GLY245 4.2 14.9 1.0
N A:PHE244 4.3 16.5 1.0
CA A:THR241 4.3 16.3 1.0
CA A:PHE244 4.3 15.8 1.0
N A:GLY247 4.4 15.8 1.0
N A:GLN242 4.4 19.6 1.0
CA A:ILE243 4.4 17.7 1.0
CA A:GLN242 4.5 20.6 1.0
O A:GLN242 4.6 21.6 1.0
CB A:VAL246 4.6 16.5 1.0
C A:PHE244 4.7 15.3 1.0
OP2 P:DA4 4.7 18.6 1.0
O3' P:DG2 4.7 16.3 1.0
CA A:GLY247 4.7 15.6 1.0
O5' P:DT3 4.7 16.8 1.0
C3' P:DA4 4.8 28.7 1.0
O3' P:DA4 4.8 35.8 1.0
C A:GLY245 4.9 16.8 1.0
O A:PHE240 4.9 17.9 1.0
CB A:THR241 4.9 17.0 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Watching A Double Strand Break Repair Polymerase Insert A Pro-Mutagenic Oxidized Nucleotide. Nat Commun V. 12 2059 2021.
ISSN: ESSN 2041-1723
PubMed: 33824325
DOI: 10.1038/S41467-021-21354-6
Page generated: Fri Jul 19 01:25:00 2024

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