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Manganese in PDB 3c2k: Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site

Enzymatic activity of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site

All present enzymatic activity of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site, PDB code: 3c2k was solved by V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.39 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.790, 80.680, 55.060, 90.00, 108.38, 90.00
R / Rfree (%) 21 / 27.8

Other elements in 3c2k:

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site (pdb code 3c2k). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site, PDB code: 3c2k:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 3c2k

Go back to Manganese Binding Sites List in 3c2k
Manganese binding site 1 out of 5 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site


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 with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn339

b:19.5
occ:1.00
 OD1 A:ASP190 2.0 18.5 1.0
OD2 A:ASP192 2.0 19.8 1.0
O1A A:DUP338 2.1 13.5 1.0
O2B A:DUP338 2.1 12.2 1.0
O A:HOH460 2.2 16.8 1.0
O3G A:DUP338 2.2 14.9 1.0
CG A:ASP190 3.0 19.5 1.0
CG A:ASP192 3.0 19.9 1.0
PB A:DUP338 3.2 16.5 1.0
PA A:DUP338 3.3 19.4 1.0
PG A:DUP338 3.4 17.9 1.0
OD2 A:ASP190 3.5 17.4 1.0
OD1 A:ASP192 3.5 20.7 1.0
MN A:MN340 3.5 17.4 1.0
N3A A:DUP338 3.5 17.5 1.0
O3B A:DUP338 3.7 15.3 1.0
O A:ASP190 3.9 20.1 1.0
O A:HOH427 4.0 27.7 1.0
C5' A:DUP338 4.1 12.6 1.0
O2G A:DUP338 4.1 14.0 1.0
O5' A:DUP338 4.1 14.6 1.0
C A:ASP190 4.2 20.6 1.0
O A:HOH462 4.3 21.3 1.0
CB A:ASP192 4.3 21.0 1.0
CB A:ASP190 4.3 18.6 1.0
CA A:GLY179 4.4 21.9 1.0
N A:ASP190 4.4 20.0 1.0
O2A A:DUP338 4.5 20.4 1.0
O1G A:DUP338 4.5 21.6 1.0
O A:HOH352 4.5 4.1 1.0
N A:SER180 4.5 23.5 1.0
O1B A:DUP338 4.6 16.9 1.0
CA A:ASP190 4.6 20.5 1.0
OG A:SER180 4.6 21.6 1.0
N A:ASP192 4.7 21.2 1.0
N A:MET191 4.8 20.8 1.0
C A:MET191 5.0 22.4 1.0
O3' P:DC10 5.0 25.2 1.0

Manganese binding site 2 out of 5 in 3c2k

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Manganese binding site 2 out of 5 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site


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 with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn340

b:17.4
occ:1.00
 OD2 A:ASP256 2.0 16.6 1.0
O A:HOH352 2.1 4.1 1.0
OD1 A:ASP192 2.2 20.7 1.0
OD2 A:ASP190 2.2 17.4 1.0
O1A A:DUP338 2.4 13.5 1.0
O3' P:DC10 2.4 25.2 1.0
CG A:ASP192 3.1 19.9 1.0
CG A:ASP190 3.1 19.5 1.0
CG A:ASP256 3.2 19.7 1.0
OD2 A:ASP192 3.3 19.8 1.0
OD1 A:ASP190 3.4 18.5 1.0
PA A:DUP338 3.4 19.4 1.0
MN A:MN339 3.5 19.5 1.0
C3' P:DC10 3.6 23.5 1.0
O5' A:DUP338 3.8 14.6 1.0
O2A A:DUP338 3.8 20.4 1.0
CB A:ASP256 3.9 17.7 1.0
C4' P:DC10 4.1 23.2 1.0
C5' P:DC10 4.2 22.1 1.0
OD1 A:ASP256 4.2 15.9 1.0
C5' A:DUP338 4.2 12.6 1.0
CB A:ASP192 4.4 21.0 1.0
CB A:ASP190 4.5 18.6 1.0
O A:HOH462 4.6 21.3 1.0
OP1 P:DC10 4.7 21.5 1.0
O5' P:DC10 4.8 21.0 1.0
C2' P:DC10 4.8 23.3 1.0
O P:HOH111 4.8 22.2 1.0
NH2 A:ARG254 4.8 24.3 1.0
O3G A:DUP338 4.9 14.9 1.0
N3A A:DUP338 4.9 17.5 1.0
O A:MET191 4.9 24.2 1.0
O P:HOH138 4.9 21.6 1.0
CA A:ASP192 5.0 21.1 1.0

Manganese binding site 3 out of 5 in 3c2k

Go back to Manganese Binding Sites List in 3c2k
Manganese binding site 3 out of 5 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site


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 with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn341

b:33.4
occ:1.00
 OD2 A:ASP145 2.1 18.6 1.0
O A:HOH351 2.3 25.8 1.0
ND1 A:HIS252 2.4 28.5 1.0
O A:HOH355 2.5 27.2 1.0
O A:HOH357 2.6 40.4 1.0
O A:HOH376 2.8 44.5 1.0
CE1 A:HIS252 3.1 27.0 1.0
CG A:ASP145 3.1 21.8 1.0
OD1 A:ASP145 3.5 26.2 1.0
CG A:HIS252 3.6 26.2 1.0
N A:HIS252 4.0 22.4 1.0
CB A:HIS252 4.1 25.4 1.0
NE2 A:HIS252 4.3 27.7 1.0
CB A:ASP145 4.4 21.9 1.0
CD1 A:TYR142 4.4 23.7 1.0
O A:HOH500 4.5 34.6 1.0
CE1 A:TYR142 4.5 22.2 1.0
OE2 A:GLU249 4.5 52.2 1.0
CD2 A:HIS252 4.6 27.1 1.0
CA A:HIS252 4.7 22.7 1.0
C A:PRO251 4.9 22.2 1.0
NE2 A:GLN240 4.9 23.7 1.0
CA A:PRO251 4.9 22.3 1.0
O A:TYR250 5.0 23.3 1.0

Manganese binding site 4 out of 5 in 3c2k

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Manganese binding site 4 out of 5 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site


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 with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn344

b:58.0
occ:0.50
 ND1 A:HIS285 2.2 41.4 1.0
OE1 A:GLU288 2.9 52.4 1.0
CE1 A:HIS285 2.9 43.0 1.0
CG A:HIS285 3.4 40.5 1.0
CD A:GLU288 3.6 52.4 1.0
OE2 A:GLU288 3.8 52.4 1.0
CB A:HIS285 3.9 36.2 1.0
NE2 A:HIS285 4.1 41.9 1.0
CA A:HIS285 4.3 34.4 1.0
CD2 A:HIS285 4.3 41.6 1.0
CG A:GLU288 4.8 49.0 1.0
CB A:GLU288 4.8 45.6 1.0
NE1 A:TRP325 4.8 41.6 1.0

Manganese binding site 5 out of 5 in 3c2k

Go back to Manganese Binding Sites List in 3c2k
Manganese binding site 5 out of 5 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn343

b:53.7
occ:0.50
 O P:HOH63 2.5 35.4 1.0
N7 T:DG15 3.0 32.0 1.0
O6 T:DG15 3.9 28.2 1.0
C8 T:DG15 4.0 32.3 1.0
N7 T:DA14 4.0 37.4 1.0
C5 T:DG15 4.0 30.4 1.0
C8 T:DA14 4.0 40.2 1.0
N4 T:DC16 4.1 25.4 1.0
O T:HOH364 4.3 32.0 1.0
C6 T:DG15 4.3 28.4 1.0
O6 P:DG1 4.7 25.1 1.0
C5 T:DA14 4.8 35.9 1.0
N9 T:DA14 4.8 40.8 1.0

Reference:

V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Beta with Active-Site Mismatches Suggest A Transient Abasic Site Intermediate During Misincorporation. Mol.Cell V. 30 315 2008.
ISSN: ISSN 1097-2765
PubMed: 18471977
DOI: 10.1016/J.MOLCEL.2008.02.025
Page generated: Sat Aug 16 11:32:15 2025

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