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Manganese in PDB 5u9h: Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S

Enzymatic activity of Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S

All present enzymatic activity of Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S, PDB code: 5u9h was solved by B.D.Freudenthal, S.H.Wilson, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.18 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.980, 80.048, 55.074, 90.00, 108.05, 90.00
R / Rfree (%) 19.5 / 23.3

Other elements in 5u9h:

The structure of Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S (pdb code 5u9h). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S, PDB code: 5u9h:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5u9h

Go back to Manganese Binding Sites List in 5u9h
Manganese binding site 1 out of 4 in the Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:30.0
occ:1.00
 O T:HOH240 1.9 54.0 1.0
O T:HOH241 2.3 46.3 1.0
O A:HOH709 2.3 53.8 1.0
O D:HOH106 2.4 52.1 1.0
O A:HOH717 4.0 36.7 1.0
O T:HOH220 4.3 39.3 1.0
O T:HOH236 4.4 42.1 1.0
O D:HOH105 4.4 37.6 1.0
N3 T:DA4 4.5 37.1 1.0
O4' T:DC5 4.5 33.0 1.0
O T:HOH232 4.6 44.9 1.0
OE2 A:GLU288 4.6 56.8 1.0
C4' T:DC5 4.7 36.2 1.0
C5' T:DC5 4.8 33.0 1.0
O2 D:DC3 4.8 40.0 1.0
C2 T:DA4 5.0 35.5 1.0

Manganese binding site 2 out of 4 in 5u9h

Go back to Manganese Binding Sites List in 5u9h
Manganese binding site 2 out of 4 in the Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:23.8
occ:1.00
 OD2 A:ASP190 2.0 28.4 1.0
OD2 A:ASP256 2.1 20.0 1.0
OD1 A:ASP192 2.1 18.7 1.0
OP1 P:C7R11 2.2 21.5 1.0
O A:HOH551 2.2 27.2 1.0
CG A:ASP190 2.7 22.0 1.0
OD1 A:ASP190 2.8 22.2 1.0
O3' P:DC10 2.8 26.5 1.0
P P:C7R11 3.0 28.0 1.0
CG A:ASP192 3.1 17.1 1.0
CG A:ASP256 3.2 21.7 1.0
MN A:MN403 3.4 23.7 1.0
OD2 A:ASP192 3.5 20.5 1.0
CB A:ASP256 3.8 20.2 1.0
C3' P:DC10 4.1 19.8 1.0
OD1 A:ASP256 4.2 20.2 1.0
CB A:ASP190 4.2 19.4 1.0
C5' P:DC10 4.3 22.4 1.0
C4' P:DC10 4.3 23.8 1.0
O5' P:C7R11 4.3 20.1 1.0
CB A:ASP192 4.4 17.4 1.0
SP2 P:C7R11 4.5 21.8 1.0
C5' P:C7R11 4.5 17.1 1.0
O A:HOH721 4.5 37.2 1.0
NH2 A:ARG254 4.6 20.5 1.0
O A:MET191 4.7 18.6 1.0
O12 A:PPV401 4.8 32.4 0.9
OP1 P:DC10 4.8 22.6 1.0
N A:ASP256 4.8 19.4 1.0
CA A:ASP192 4.9 17.4 1.0
C A:MET191 4.9 19.6 1.0
CA A:ASP256 4.9 21.1 1.0
O5' P:DC10 5.0 22.0 1.0
O11 A:PPV401 5.0 35.1 0.9

Manganese binding site 3 out of 4 in 5u9h

Go back to Manganese Binding Sites List in 5u9h
Manganese binding site 3 out of 4 in the Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:23.7
occ:1.00
 OP1 P:C7R11 2.1 21.5 1.0
OD1 A:ASP190 2.1 22.2 1.0
OD2 A:ASP192 2.2 20.5 1.0
O11 A:PPV401 2.3 35.1 0.9
O12 A:PPV401 2.3 32.4 0.9
O A:HOH509 2.4 27.0 1.0
O32 A:PPV401 2.9 33.6 0.9
P2 A:PPV401 3.1 26.6 0.9
CG A:ASP192 3.1 17.1 1.0
CG A:ASP190 3.3 22.0 1.0
MN A:MN402 3.4 23.8 1.0
OD1 A:ASP192 3.4 18.7 1.0
P1 A:PPV401 3.6 38.1 0.9
P P:C7R11 3.6 28.0 1.0
OPP A:PPV401 3.8 29.0 0.9
OD2 A:ASP190 3.9 28.4 1.0
O5' P:C7R11 4.0 20.1 1.0
C5' P:C7R11 4.0 17.1 1.0
N A:ASP190 4.2 18.1 1.0
O A:ASP190 4.2 21.6 1.0
O31 A:PPV401 4.3 31.2 0.9
O A:HOH721 4.3 37.2 1.0
O A:HOH551 4.3 27.2 1.0
C A:ASP190 4.4 19.3 1.0
CB A:ASP190 4.4 19.4 1.0
O A:HOH581 4.4 22.2 1.0
O22 A:PPV401 4.4 20.7 0.9
CB A:ASP192 4.5 17.4 1.0
CA A:ASP190 4.5 18.2 1.0
O3' P:DC10 4.6 26.5 1.0
O21 A:PPV401 4.7 46.8 0.9
SP2 P:C7R11 4.8 21.8 1.0
CA A:GLY179 4.8 22.4 1.0
N A:ASP192 5.0 20.5 1.0
N A:MET191 5.0 18.6 1.0

Manganese binding site 4 out of 4 in 5u9h

Go back to Manganese Binding Sites List in 5u9h
Manganese binding site 4 out of 4 in the Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dna Polymerase Beta Product Complex with Inserted Sp-Isomer of Dctp- Alpha-S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:30.0
occ:1.00
 O A:HOH716 2.0 37.4 1.0
OD2 A:ASP145 2.2 27.6 1.0
O A:HOH651 2.2 33.5 1.0
O A:HOH686 2.2 41.6 1.0
ND1 A:HIS252 2.4 28.7 1.0
CE1 A:HIS252 3.1 25.3 1.0
CG A:ASP145 3.2 31.3 1.0
CG A:HIS252 3.5 26.0 1.0
OD1 A:ASP145 3.7 31.7 1.0
N A:HIS252 3.9 22.4 1.0
CB A:HIS252 4.0 22.1 1.0
CD1 A:TYR142 4.2 26.6 1.0
NE2 A:HIS252 4.3 27.3 1.0
CE1 A:TYR142 4.3 26.3 1.0
CB A:ASP145 4.5 22.8 1.0
CD2 A:HIS252 4.5 28.4 1.0
CA A:HIS252 4.6 20.2 1.0
C A:PRO251 4.8 25.1 1.0
CA A:PRO251 4.9 24.2 1.0
O A:TYR250 4.9 24.3 1.0
NE2 A:GLN240 5.0 27.3 1.0

Reference:

L.Perera, B.D.Freudenthal, W.A.Beard, L.G.Pedersen, S.H.Wilson. Revealing the Role of the Product Metal in Dna Polymerase Beta Catalysis. Nucleic Acids Res. V. 45 2736 2017.
ISSN: ESSN 1362-4962
PubMed: 28108654
DOI: 10.1093/NAR/GKW1363
Page generated: Sat Aug 16 19:17:50 2025

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