Calcium in PDB 6vez: Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min):
2.7.7.7;

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min), PDB code: 6vez 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)	24.58 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.966, 68.481, 110.194, 90, 90, 90
R / Rfree (%)	16.6 / 20.5

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min) (pdb code 6vez). 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, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min), PDB code: 6vez:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min)


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, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:26.5 occ:1.00 OD1 A:ASP330 2.2 37.8 1.0 O1B A:8GT501 2.3 29.1 1.0 OD2 A:ASP332 2.3 26.9 1.0 O2G A:8GT501 2.4 53.5 1.0 O2A A:8GT501 2.4 36.2 1.0 O A:HOH737 2.5 27.6 1.0 O A:ASP330 2.7 19.7 1.0 CG A:ASP330 3.4 38.7 1.0 PB A:8GT501 3.4 37.2 1.0 CG A:ASP332 3.4 25.6 1.0 C A:ASP330 3.5 20.5 1.0 PG A:8GT501 3.5 52.1 1.0 O3B A:8GT501 3.6 47.3 1.0 PA A:8GT501 3.7 38.3 1.0 CA A:CA503 3.8 23.6 1.0 O3A A:8GT501 3.9 38.0 1.0 OD1 A:ASP332 3.9 24.8 1.0 N A:ASP330 4.1 20.4 1.0 O A:HOH614 4.1 16.8 1.0 CA A:ASP330 4.1 22.8 1.0 OD2 A:ASP330 4.2 42.2 1.0 O3G A:8GT501 4.2 43.9 1.0 N A:VAL331 4.3 20.6 1.0 N A:GLY320 4.3 15.7 1.0 CB A:ASP330 4.3 32.0 1.0 O A:HOH622 4.4 26.2 1.0 CA A:VAL331 4.6 18.6 1.0 O5' A:8GT501 4.7 47.6 1.0 CA A:GLY319 4.7 16.1 1.0 CB A:ASP332 4.7 19.0 1.0 C A:VAL331 4.7 16.6 1.0 C5' A:8GT501 4.7 52.1 1.0 O1A A:8GT501 4.7 34.5 1.0 N A:ASP332 4.7 16.5 1.0 O2B A:8GT501 4.8 37.2 1.0 O1G A:8GT501 4.8 62.1 1.0 ND1 A:HIS329 4.8 65.4 1.0 CE1 A:HIS329 5.0 67.1 1.0

Calcium binding site 2 out of 3 in the Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min)


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, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:23.6 occ:1.00 OD2 A:ASP330 2.3 42.2 1.0 OD2 A:ASP418 2.3 25.3 1.0 O2A A:8GT501 2.4 36.2 1.0 OD1 A:ASP332 2.4 24.8 1.0 O P:HOH101 2.4 39.3 1.0 O3' P:DA4 2.5 36.5 1.0 OD1 A:ASP330 2.8 37.8 1.0 CG A:ASP330 2.9 38.7 1.0 CG A:ASP332 3.3 25.6 1.0 PA A:8GT501 3.4 38.3 1.0 CG A:ASP418 3.5 22.7 1.0 O5' A:8GT501 3.5 47.6 1.0 C3' P:DA4 3.5 34.2 1.0 OD2 A:ASP332 3.6 26.9 1.0 C5' P:DA4 3.7 39.1 1.0 C4' P:DA4 3.8 33.9 1.0 CA A:CA502 3.8 26.5 1.0 C5' A:8GT501 4.0 52.1 1.0 O1A A:8GT501 4.0 34.5 1.0 CB A:ASP418 4.2 18.1 1.0 OD1 A:ASP418 4.4 24.0 1.0 CB A:ASP330 4.4 32.0 1.0 NH2 A:ARG416 4.5 20.2 1.0 OP1 P:DA4 4.5 21.7 1.0 O5' P:DA4 4.5 33.1 1.0 CB A:ASP332 4.7 19.0 1.0 O3A A:8GT501 4.8 38.0 1.0 CZ3 A:TRP434 4.9 29.8 1.0 CE1 A:HIS329 4.9 67.1 1.0 C2' P:DA4 4.9 33.2 1.0 O A:VAL331 5.0 16.7 1.0

Calcium binding site 3 out of 3 in the Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min)


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, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:57.4 occ:0.72 O D:HOH114 2.3 31.2 0.7 O A:HOH656 2.4 35.4 0.8 O A:PHE205 2.4 32.8 1.0 O A:HOH818 2.5 45.5 0.9 O D:HOH104 2.6 31.6 0.7 C A:PHE205 3.6 28.1 1.0 O A:HOH747 4.3 47.3 1.0 O A:LEU202 4.4 26.1 1.0 CA A:GLY206 4.5 29.9 1.0 N A:GLY206 4.5 27.5 1.0 CA A:PHE205 4.6 22.6 1.0 CB A:PHE205 4.7 21.2 1.0 OP1 D:DC3 4.8 24.3 0.3 N A:PHE205 4.8 23.5 1.0 OP1 D:DC3 4.9 23.8 0.7 OP2 D:DC3 4.9 27.1 0.3

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min) To Be Published.