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Manganese in PDB 4phd: Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp and Manganese

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp and Manganese

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp and Manganese:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp and Manganese, PDB code: 4phd was solved by M.C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.245, 79.954, 54.403, 90.00, 108.88, 90.00
R / Rfree (%) 24.3 / 29.5

Other elements in 4phd:

The structure of Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp and Manganese also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp and Manganese (pdb code 4phd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp and Manganese, PDB code: 4phd:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4phd

Go back to Manganese Binding Sites List in 4phd
Manganese binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:22.0
occ:1.00
O2B A:0KX405 1.9 16.9 1.0
O1A A:0KX405 1.9 23.4 1.0
OD1 A:ASP190 2.0 15.6 1.0
OD1 A:ASP192 2.2 18.5 1.0
O2G A:0KX405 2.4 29.8 1.0
PB A:0KX405 3.0 21.1 1.0
CG A:ASP190 3.1 20.6 1.0
PA A:0KX405 3.2 16.4 1.0
CG A:ASP192 3.2 20.8 1.0
PG A:0KX405 3.3 21.9 1.0
O3B A:0KX405 3.4 20.4 1.0
N3A A:0KX405 3.4 24.4 1.0
OD2 A:ASP192 3.5 17.1 1.0
MN A:MN402 3.6 19.4 1.0
OD2 A:ASP190 3.7 28.0 1.0
O A:HOH550 3.8 23.6 1.0
O5' A:0KX405 4.0 25.4 1.0
O A:ASP190 4.0 20.2 1.0
O2A A:0KX405 4.1 20.2 1.0
O3G A:0KX405 4.1 22.7 1.0
C5' A:0KX405 4.1 28.0 1.0
OG A:SER180 4.2 20.1 1.0
N A:ASP190 4.2 17.6 1.0
C A:ASP190 4.3 17.1 1.0
O1G A:0KX405 4.3 33.7 1.0
N A:SER180 4.3 23.2 1.0
O1B A:0KX405 4.3 22.9 1.0
CB A:ASP190 4.4 18.6 1.0
CA A:GLY179 4.4 23.8 1.0
CA A:ASP190 4.5 14.0 1.0
CB A:ASP192 4.6 21.0 1.0
O A:HOH528 4.7 17.7 1.0
N A:ASP192 4.8 22.8 1.0
N A:MET191 4.9 18.6 1.0
C A:GLY179 4.9 26.4 1.0

Manganese binding site 2 out of 2 in 4phd

Go back to Manganese Binding Sites List in 4phd
Manganese binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:19.4
occ:1.00
OD2 A:ASP190 2.1 28.0 1.0
O3' P:DA10 2.2 20.1 1.0
OD2 A:ASP256 2.2 24.5 1.0
OD2 A:ASP192 2.3 17.1 1.0
O A:HOH528 2.3 17.7 1.0
O1A A:0KX405 2.5 23.4 1.0
CG A:ASP190 3.0 20.6 1.0
OD1 A:ASP190 3.2 15.6 1.0
CG A:ASP192 3.3 20.8 1.0
PA A:0KX405 3.3 16.4 1.0
C3' P:DA10 3.4 20.9 1.0
CG A:ASP256 3.4 23.1 1.0
O5' A:0KX405 3.6 25.4 1.0
MN A:MN401 3.6 22.0 1.0
O2A A:0KX405 3.6 20.2 1.0
OD1 A:ASP192 3.7 18.5 1.0
O A:HOH550 4.0 23.6 1.0
C5' A:0KX405 4.0 28.0 1.0
C4' P:DA10 4.0 18.4 1.0
CB A:ASP256 4.0 19.8 1.0
C5' P:DA10 4.1 18.1 1.0
OD1 A:ASP256 4.4 20.9 1.0
CB A:ASP190 4.4 18.6 1.0
O5' P:DA10 4.5 19.2 1.0
OP1 P:DA10 4.6 18.7 1.0
C2' P:DA10 4.6 21.9 1.0
CB A:ASP192 4.6 21.0 1.0
O2B A:0KX405 4.8 16.9 1.0
O A:MET191 5.0 22.4 1.0

Reference:

M.C.Koag, K.Nam, S.Lee. The Spontaneous Replication Error and the Mismatch Discrimination Mechanisms of Human Dna Polymerase Beta. Nucleic Acids Res. V. 42 11233 2015.
ISSN: ESSN 1362-4962
PubMed: 25200079
DOI: 10.1093/NAR/GKU789
Page generated: Tue Dec 15 04:26:12 2020

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