Chlorine in PDB 7kt3: Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)

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

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

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN), PDB code: 7kt3 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) 24.54 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.804, 68.579, 110.149, 90, 90, 90
R / Rfree (%) 16 / 18.8

Other elements in 7kt3:

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

Sodium (Na) 1 atom
Calcium (Ca) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) (pdb code 7kt3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN), PDB code: 7kt3:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7kt3

Go back to Chlorine Binding Sites List in 7kt3
Chlorine binding site 1 out of 3 in the Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl514

b:53.4
occ:0.66
 CL A:CL514 0.0 53.4 0.7
CL A:CL514 1.9 25.9 0.3
O A:HOH789 2.5 38.6 1.0
OG A:SER172 2.8 31.5 0.7
NH1 A:ARG175 3.4 32.8 0.5
CB A:SER172 3.9 26.8 0.7
O6 D:DG1 4.0 22.2 1.0
CA A:SER172 4.1 24.7 0.7
CA A:SER172 4.1 24.8 0.3
CB A:SER172 4.1 26.4 0.3
N A:GLY174 4.3 19.3 1.0
C A:SER172 4.5 23.5 0.7
C A:SER172 4.5 23.5 0.3
O D:HOH112 4.6 21.7 0.4
O A:HOH682 4.6 40.0 1.0
N A:ARG175 4.7 19.2 0.5
N A:ARG175 4.7 19.2 0.5
CA A:GLY174 4.7 17.6 1.0
CZ A:ARG175 4.7 27.8 0.5
CG A:ARG175 4.7 22.4 0.5
N A:GLU173 4.7 22.1 1.0
C6 D:DG1 4.7 21.7 1.0
CG A:ARG175 4.8 22.2 0.5
OG A:SER172 4.8 26.6 0.3
N4 T:DC4 4.9 22.7 1.0
N7 D:DG1 5.0 18.8 1.0

Chlorine binding site 2 out of 3 in 7kt3

Go back to Chlorine Binding Sites List in 7kt3
Chlorine binding site 2 out of 3 in the Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl514

b:25.9
occ:0.34
 CL A:CL514 0.0 25.9 0.3
OG A:SER172 1.9 31.5 0.7
CL A:CL514 1.9 53.4 0.7
O A:HOH789 2.7 38.6 1.0
N A:ARG175 2.9 19.2 0.5
N A:ARG175 2.9 19.2 0.5
CB A:SER172 3.0 26.8 0.7
N A:GLY174 3.0 19.3 1.0
CB A:SER172 3.1 26.4 0.3
C A:SER172 3.1 23.5 0.3
C A:SER172 3.1 23.5 0.7
CA A:SER172 3.2 24.7 0.7
CA A:SER172 3.2 24.8 0.3
O A:SER172 3.4 22.1 0.3
O A:SER172 3.4 22.1 0.7
CA A:GLY174 3.4 17.6 1.0
CG A:ARG175 3.5 22.4 0.5
C A:GLY174 3.6 17.3 1.0
N A:GLU173 3.6 22.1 1.0
CG A:ARG175 3.6 22.2 0.5
NH1 A:ARG175 3.7 32.8 0.5
CB A:ARG175 3.8 20.2 0.5
CB A:ARG175 3.8 20.3 0.5
CA A:ARG175 3.9 18.1 0.5
CA A:ARG175 3.9 18.1 0.5
C A:GLU173 4.0 20.3 1.0
CD A:ARG175 4.1 22.6 0.5
CD A:ARG175 4.2 22.4 0.5
O6 D:DG1 4.2 22.2 1.0
OG A:SER172 4.3 26.6 0.3
CA A:GLU173 4.4 23.0 1.0
C6 D:DG1 4.5 21.7 1.0
N A:SER172 4.6 22.8 0.7
N A:SER172 4.7 22.8 0.3
O A:HOH682 4.7 40.0 1.0
C5 D:DG1 4.7 20.1 1.0
CZ A:ARG175 4.8 27.8 0.5
N7 D:DG1 4.8 18.8 1.0
O A:GLY174 4.8 18.5 1.0
NE A:ARG175 4.9 23.9 0.5
O A:GLU173 4.9 19.5 1.0
N A:LEU176 5.0 16.3 1.0

Chlorine binding site 3 out of 3 in 7kt3

Go back to Chlorine Binding Sites List in 7kt3
Chlorine binding site 3 out of 3 in the Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl515

b:22.9
occ:0.85
 OG A:SER458 2.8 20.3 1.0
O A:HOH687 3.2 22.4 1.0
N A:SER458 3.2 13.0 1.0
C1' T:DA7 3.5 22.2 1.0
CB A:SER458 3.5 17.7 1.0
NH2 A:ARG387 3.6 23.7 1.0
O4' T:DA7 3.6 25.6 1.0
C4' T:DA7 3.7 21.1 1.0
C2' T:DA7 3.7 22.0 1.0
CB A:ASN457 3.7 16.9 1.0
CA A:SER458 3.9 14.7 1.0
CE1 A:HIS459 3.9 28.1 1.0
CG A:ASN457 4.0 18.2 1.0
ND1 A:HIS459 4.1 32.8 1.0
C3' T:DA7 4.1 22.0 1.0
NE2 A:HIS459 4.3 31.5 1.0
C A:ASN457 4.3 15.6 1.0
O3' T:DA7 4.3 23.8 1.0
ND2 A:ASN457 4.3 27.5 1.0
C A:SER458 4.4 14.1 1.0
N A:HIS459 4.4 15.0 1.0
CA A:ASN457 4.5 16.3 1.0
CG A:HIS459 4.5 23.2 1.0
OD1 A:ASN457 4.5 15.3 1.0
CD2 A:HIS459 4.6 26.5 1.0
NH2 A:ARG445 4.7 16.8 1.0
CZ A:ARG387 4.8 21.6 1.0
NH1 A:ARG445 4.8 16.8 1.0
N9 T:DA7 4.9 22.3 1.0
O2 T:DT6 4.9 17.1 1.0
O1 A:EDO509 4.9 22.7 1.0
C5' T:DA7 5.0 23.6 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) To Be Published.
Page generated: Fri Dec 17 08:51:19 2021

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