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Manganese in PDB 5tb9: Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.

Enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.

All present enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.:
2.7.7.7;

Protein crystallography data

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+., PDB code: 5tb9 was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.87 / 2.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.190, 82.310, 54.280, 90.00, 110.97, 90.00
R / Rfree (%) 20.5 / 26.7

Other elements in 5tb9:

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+. also contains other interesting chemical elements:

Fluorine (F) 1 atom
Sodium (Na) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+. (pdb code 5tb9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+., PDB code: 5tb9:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5tb9

Go back to Manganese Binding Sites List in 5tb9
Manganese binding site 1 out of 6 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:23.9
occ:1.00
 OD2 A:ASP256 1.9 22.2 1.0
O A:HOH501 1.9 29.3 1.0
OD2 A:ASP190 1.9 23.0 1.0
OAD A:1RY401 2.0 24.5 1.0
OD1 A:ASP192 2.0 25.0 1.0
O3' P:DC10 2.4 48.9 1.0
CG A:ASP190 3.0 23.3 1.0
CG A:ASP256 3.1 22.4 1.0
CG A:ASP192 3.1 23.7 1.0
C3' P:DC10 3.1 50.8 1.0
PBA A:1RY401 3.1 25.4 1.0
OD1 A:ASP190 3.3 24.4 1.0
MN A:MN403 3.4 24.7 1.0
OD2 A:ASP192 3.5 23.6 1.0
OAH A:1RY401 3.7 26.1 1.0
OAO A:1RY401 3.7 26.1 1.0
CB A:ASP256 3.8 21.6 1.0
C4' P:DC10 4.0 50.5 1.0
OD1 A:ASP256 4.0 23.5 1.0
CB A:ASP190 4.3 22.2 1.0
CAL A:1RY401 4.3 26.8 1.0
CB A:ASP192 4.4 23.0 1.0
C2' P:DC10 4.4 49.9 1.0
C5' P:DC10 4.5 47.9 1.0
OAF A:1RY401 4.6 26.2 1.0
OAR A:1RY401 4.6 25.6 1.0
OXT A:ACT411 4.8 36.3 1.0
SAS A:1RY401 4.8 27.6 1.0
CA A:ASP192 4.9 22.8 1.0
OAI A:1RY401 5.0 24.0 1.0

Manganese binding site 2 out of 6 in 5tb9

Go back to Manganese Binding Sites List in 5tb9
Manganese binding site 2 out of 6 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:24.7
occ:1.00
 OD1 A:ASP190 1.9 24.4 1.0
OAD A:1RY401 1.9 24.5 1.0
OAI A:1RY401 1.9 24.0 1.0
OAF A:1RY401 1.9 26.2 1.0
OD2 A:ASP192 2.2 23.6 1.0
O A:HOH509 2.2 13.0 1.0
PBA A:1RY401 2.8 25.4 1.0
PBB A:1RY401 2.9 24.6 1.0
CG A:ASP190 2.9 23.3 1.0
OAR A:1RY401 3.0 25.6 1.0
CG A:ASP192 3.1 23.7 1.0
PAZ A:1RY401 3.2 25.5 1.0
OD2 A:ASP190 3.3 23.0 1.0
OD1 A:ASP192 3.4 25.0 1.0
MN A:MN402 3.4 23.9 1.0
OAQ A:1RY401 3.4 24.9 1.0
OAO A:1RY401 3.8 26.1 1.0
OAG A:1RY401 3.9 25.9 1.0
CAL A:1RY401 3.9 26.8 1.0
O A:HOH501 3.9 29.3 1.0
OAH A:1RY401 4.1 26.1 1.0
CB A:ASP190 4.2 22.2 1.0
OXT A:ACT411 4.2 36.3 1.0
OAE A:1RY401 4.3 23.8 1.0
O A:ASP190 4.3 20.0 1.0
N A:ASP190 4.3 21.5 1.0
CA A:GLY179 4.4 24.5 1.0
C A:ASP190 4.4 21.8 1.0
OAC A:1RY401 4.5 26.9 1.0
N A:SER180 4.5 25.9 1.0
CB A:ASP192 4.5 23.0 1.0
CA A:ASP190 4.5 21.7 1.0
O A:HOH517 4.5 16.4 1.0
OG A:SER180 4.6 24.6 1.0
N A:ASP192 4.9 23.1 1.0
O3' P:DC10 5.0 48.9 1.0

Manganese binding site 3 out of 6 in 5tb9

Go back to Manganese Binding Sites List in 5tb9
Manganese binding site 3 out of 6 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:44.9
occ:1.00
 O A:HOH527 1.9 28.0 1.0
NE2 A:HIS339 2.3 39.5 1.0
O A:HOH545 2.3 29.6 1.0
NE2 A:HIS337 2.4 33.1 1.0
O A:HOH541 2.5 23.2 1.0
CE1 A:HIS339 2.9 38.8 1.0
CD2 A:HIS337 3.3 33.4 1.0
CE1 A:HIS337 3.4 33.3 1.0
CD2 A:HIS339 3.5 39.1 1.0
ND1 A:HIS339 4.1 38.9 1.0
CG A:HIS339 4.4 37.6 1.0
CG A:HIS337 4.5 33.0 1.0
ND1 A:HIS337 4.5 33.5 1.0
CG A:GLU9 4.8 55.7 1.0
OE1 A:GLU9 5.0 57.2 1.0
OG1 A:THR10 5.0 35.0 1.0

Manganese binding site 4 out of 6 in 5tb9

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Manganese binding site 4 out of 6 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:72.6
occ:1.00
 O A:HOH556 2.5 35.7 1.0
NE2 A:HIS340 2.9 41.5 1.0
CD2 A:HIS340 3.5 40.6 1.0
O A:THR10 3.9 32.3 1.0
CE1 A:HIS340 4.0 41.4 1.0
O A:HOH521 4.4 32.6 1.0
CG A:HIS340 4.8 40.0 1.0
C A:THR10 4.9 32.2 1.0
ND1 A:HIS340 5.0 41.0 1.0

Manganese binding site 5 out of 6 in 5tb9

Go back to Manganese Binding Sites List in 5tb9
Manganese binding site 5 out of 6 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn406

b:51.9
occ:1.00
 O A:GLU117 2.8 30.2 1.0
C A:GLU117 3.5 29.9 1.0
CA A:GLU117 3.9 29.9 1.0
N A:GLY118 4.3 29.4 1.0
CB A:GLU117 4.3 30.7 1.0
CA A:GLY118 4.6 28.7 1.0

Manganese binding site 6 out of 6 in 5tb9

Go back to Manganese Binding Sites List in 5tb9
Manganese binding site 6 out of 6 in the Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)Ftc-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn407

b:32.4
occ:1.00
 O A:LYS48 2.1 28.8 1.0
O A:HOH546 2.2 16.5 1.0
NE2 A:HIS338 2.4 29.5 1.0
NE2 A:HIS336 2.4 33.1 1.0
C A:LYS48 3.1 29.9 1.0
CE1 A:HIS338 3.2 30.0 1.0
CD2 A:HIS336 3.3 33.4 1.0
CD2 A:HIS338 3.4 29.7 1.0
CE1 A:HIS336 3.5 33.3 1.0
CA A:LYS48 3.6 31.5 1.0
CB A:LYS48 3.8 33.4 1.0
N A:TYR49 4.3 29.8 1.0
ND1 A:HIS338 4.4 29.6 1.0
CG A:HIS336 4.5 33.8 1.0
CG A:HIS338 4.5 30.3 1.0
ND1 A:HIS336 4.5 34.0 1.0
N A:PRO50 4.7 31.6 1.0
C A:TYR49 4.7 30.2 1.0
CG A:LYS48 4.7 35.1 1.0
CA A:TYR49 4.8 29.8 1.0
CD A:PRO50 4.8 32.3 1.0
CB A:PRO50 4.9 32.9 1.0

Reference:

A.J.Reed, R.Vyas, A.T.Raper, Z.Suo. Structural Insights Into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed By A Dna Polymerase. J. Am. Chem. Soc. V. 139 465 2017.
ISSN: ESSN 1520-5126
PubMed: 27959534
DOI: 10.1021/JACS.6B11258
Page generated: Sun Oct 6 02:56:12 2024

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