Atomistry » Manganese » PDB 3auz-3c5m » 3c2k
Atomistry »
  Manganese »
    PDB 3auz-3c5m »
      3c2k »

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

Go back to Manganese Binding Sites List in 3c2k
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

Go back to Manganese Binding Sites List in 3c2k
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 Oct 5 15:59:41 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy