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Manganese in PDB 5tb8: Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+.

Enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+.

All present enzymatic activity of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-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 (-)3TC-Tp and MN2+., PDB code: 5tb8 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) 46.41 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.480, 81.400, 53.570, 90.00, 110.28, 90.00
R / Rfree (%) 18.2 / 23

Other elements in 5tb8:

The structure of Precatalytic Ternary Complex of Human Dna Polymerase Beta in Closed Conformation with Gapped Dna Substrate Incoming (-)3TC-Tp and MN2+. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 5 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 (-)3TC-Tp and MN2+. (pdb code 5tb8). 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 (-)3TC-Tp and MN2+., PDB code: 5tb8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5tb8

Go back to Manganese Binding Sites List in 5tb8
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 (-)3TC-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 (-)3TC-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:49.0
occ:1.00
 O A:HOH647 1.9 46.1 1.0
O A:HOH511 2.1 23.1 1.0
NE2 A:HIS337 2.3 34.8 1.0
NE2 A:HIS339 2.5 35.0 1.0
CD2 A:HIS337 3.2 33.7 1.0
CE1 A:HIS337 3.2 32.8 1.0
CD2 A:HIS339 3.3 34.0 1.0
CE1 A:HIS339 3.5 34.1 1.0
ND1 A:HIS337 4.3 34.4 1.0
CG A:HIS337 4.3 32.0 1.0
CG A:HIS339 4.5 31.5 1.0
ND1 A:HIS339 4.6 33.7 1.0

Manganese binding site 2 out of 6 in 5tb8

Go back to Manganese Binding Sites List in 5tb8
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 (-)3TC-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 (-)3TC-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:23.0
occ:1.00
 O A:GLU117 2.3 16.5 1.0
OXT A:ACT417 2.8 35.3 1.0
O A:ACT417 2.9 41.7 1.0
C A:ACT417 3.2 38.9 1.0
C A:GLU117 3.3 16.7 1.0
CA A:GLU117 4.0 16.8 1.0
O A:HOH631 4.2 14.0 1.0
N A:GLY118 4.2 16.3 1.0
CB A:GLU117 4.4 17.7 1.0
CA A:GLY118 4.4 16.3 1.0
CH3 A:ACT417 4.7 35.5 1.0

Manganese binding site 3 out of 6 in 5tb8

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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 (-)3TC-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 (-)3TC-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:20.5
occ:1.00
 O A:HOH592 2.1 20.3 1.0
NE2 A:HIS338 2.1 24.4 1.0
O A:LYS48 2.1 16.2 1.0
NE2 A:HIS336 2.3 18.9 1.0
CE1 A:HIS338 2.8 26.2 1.0
C A:LYS48 3.1 18.4 1.0
CE1 A:HIS336 3.3 19.1 1.0
CD2 A:HIS338 3.3 25.2 1.0
CD2 A:HIS336 3.4 17.1 1.0
CA A:LYS48 3.6 18.6 1.0
CB A:LYS48 3.8 19.9 1.0
ND1 A:HIS338 4.1 25.3 1.0
CG A:HIS338 4.3 24.2 1.0
N A:TYR49 4.3 18.4 1.0
ND1 A:HIS336 4.4 18.3 1.0
CG A:HIS336 4.5 18.9 1.0
N A:PRO50 4.7 18.7 1.0
CG A:LYS48 4.7 20.8 1.0
C A:TYR49 4.8 18.1 1.0
CD A:PRO50 4.8 21.2 1.0
CA A:TYR49 4.8 19.3 1.0
CB A:PRO50 4.8 19.2 1.0

Manganese binding site 4 out of 6 in 5tb8

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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 (-)3TC-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 (-)3TC-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:12.5
occ:1.00
 O2A A:1RZ401 2.0 14.4 1.0
OD2 A:ASP192 2.0 15.2 1.0
OD1 A:ASP190 2.1 12.3 1.0
O3G A:1RZ401 2.1 15.5 1.0
O1B A:1RZ401 2.2 12.8 1.0
O A:HOH530 2.3 15.1 1.0
CG A:ASP192 3.0 14.4 1.0
CG A:ASP190 3.1 13.8 1.0
PB A:1RZ401 3.1 13.8 1.0
PA A:1RZ401 3.2 15.4 1.0
PG A:1RZ401 3.3 16.0 1.0
OD1 A:ASP192 3.4 12.6 1.0
O3A A:1RZ401 3.4 14.5 1.0
OD2 A:ASP190 3.5 13.4 1.0
MN A:MN406 3.6 12.5 1.0
O3B A:1RZ401 3.6 14.5 1.0
O1G A:1RZ401 3.9 16.6 1.0
O A:ASP190 4.0 13.2 1.0
O A:HOH600 4.1 24.4 1.0
O A:HOH616 4.2 9.1 1.0
O5' A:1RZ401 4.3 15.2 1.0
C A:ASP190 4.3 14.5 1.0
C5' A:1RZ401 4.3 14.5 1.0
N A:ASP190 4.4 15.4 1.0
CB A:ASP190 4.4 14.0 1.0
CB A:ASP192 4.4 14.3 1.0
OG A:SER180 4.4 14.4 1.0
N A:SER180 4.4 15.3 1.0
CA A:GLY179 4.5 14.1 1.0
O1A A:1RZ401 4.5 15.1 1.0
O2C A:1RZ401 4.6 18.1 1.0
O2B A:1RZ401 4.6 12.7 1.0
CA A:ASP190 4.6 14.5 1.0
O A:HOH557 4.6 12.7 1.0
N A:ASP192 4.8 13.8 1.0
O A:HOH603 4.9 12.4 1.0
N A:MET191 4.9 15.2 1.0

Manganese binding site 5 out of 6 in 5tb8

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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 (-)3TC-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 (-)3TC-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn406

b:12.5
occ:1.00
 OD1 A:ASP192 2.0 12.6 1.0
O A:HOH557 2.1 12.7 1.0
OD2 A:ASP256 2.1 13.4 1.0
OD2 A:ASP190 2.2 13.4 1.0
O A:HOH603 2.2 12.4 1.0
O2A A:1RZ401 2.4 14.4 1.0
CG A:ASP190 3.1 13.8 1.0
CG A:ASP192 3.1 14.4 1.0
C3' P:DC10 3.1 29.3 0.4
CG A:ASP256 3.2 13.6 1.0
OD1 A:ASP190 3.3 12.3 1.0
PA A:1RZ401 3.4 15.4 1.0
OD2 A:ASP192 3.5 15.2 1.0
MN A:MN405 3.6 12.5 1.0
C2' P:DC10 3.8 29.0 0.4
O1A A:1RZ401 3.8 15.1 1.0
O3' P:DC10 3.9 28.9 0.4
CB A:ASP256 4.0 12.0 1.0
O5' A:1RZ401 4.1 15.2 1.0
C4' P:DC10 4.1 29.4 0.4
OD1 A:ASP256 4.2 13.5 1.0
C5' P:DC10 4.3 29.6 0.4
O A:HOH600 4.3 24.4 1.0
CB A:ASP192 4.4 14.3 1.0
CB A:ASP190 4.5 14.0 1.0
O3G A:1RZ401 4.7 15.5 1.0
C5' A:1RZ401 4.8 14.5 1.0
O3A A:1RZ401 4.8 14.5 1.0
NH2 A:ARG254 5.0 22.3 1.0
CA A:ASP192 5.0 13.0 1.0

Manganese binding site 6 out of 6 in 5tb8

Go back to Manganese Binding Sites List in 5tb8
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 (-)3TC-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 (-)3TC-Tp and MN2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn407

b:41.0
occ:1.00
 ND1 A:HIS285 2.4 21.0 1.0
OE1 A:GLU288 2.6 42.3 1.0
CE1 A:HIS285 3.3 20.7 1.0
CD A:GLU288 3.4 37.4 1.0
CG A:HIS285 3.4 22.5 1.0
OE2 A:GLU288 3.5 41.8 1.0
CB A:HIS285 3.7 19.5 1.0
CA A:HIS285 4.1 18.6 1.0
O A:HOH637 4.4 28.2 1.0
NE2 A:HIS285 4.4 22.1 1.0
CD2 A:HIS285 4.5 22.1 1.0
CG A:GLU288 4.7 33.4 1.0
NE1 A:TRP325 5.0 24.5 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 02:54:49 2024

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