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Calcium in PDB 4jv0: Ring-Opening of the -Oh-Pdg Adduct in Ternary Complexes with the Sulfolobus Solfataricus Dna Polymerase DPO4

Enzymatic activity of Ring-Opening of the -Oh-Pdg Adduct in Ternary Complexes with the Sulfolobus Solfataricus Dna Polymerase DPO4

All present enzymatic activity of Ring-Opening of the -Oh-Pdg Adduct in Ternary Complexes with the Sulfolobus Solfataricus Dna Polymerase DPO4:
2.7.7.7;

Protein crystallography data

The structure of Ring-Opening of the -Oh-Pdg Adduct in Ternary Complexes with the Sulfolobus Solfataricus Dna Polymerase DPO4, PDB code: 4jv0 was solved by S.Banerjee, G.Shanmugam, M.P.Stone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.91 / 2.95
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.826, 104.486, 52.529, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 27

Calcium Binding Sites:

The binding sites of Calcium atom in the Ring-Opening of the -Oh-Pdg Adduct in Ternary Complexes with the Sulfolobus Solfataricus Dna Polymerase DPO4 (pdb code 4jv0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ring-Opening of the -Oh-Pdg Adduct in Ternary Complexes with the Sulfolobus Solfataricus Dna Polymerase DPO4, PDB code: 4jv0:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4jv0

Go back to Calcium Binding Sites List in 4jv0
Calcium binding site 1 out of 2 in the Ring-Opening of the -Oh-Pdg Adduct in Ternary Complexes with the Sulfolobus Solfataricus Dna Polymerase DPO4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ring-Opening of the -Oh-Pdg Adduct in Ternary Complexes with the Sulfolobus Solfataricus Dna Polymerase DPO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:68.1
occ:1.00
O A:PHE8 2.7 61.3 1.0
OD2 A:ASP105 2.7 65.3 1.0
O1G A:DTP1000 2.8 76.2 1.0
O1A A:DTP1000 2.8 72.8 1.0
OD1 A:ASP7 2.9 65.5 1.0
O2B A:DTP1000 2.9 68.1 1.0
O2G A:DTP1000 3.2 75.6 1.0
CG A:ASP7 3.3 64.1 1.0
PG A:DTP1000 3.4 87.2 1.0
C A:PHE8 3.5 60.0 1.0
OD2 A:ASP7 3.5 71.1 1.0
PB A:DTP1000 3.6 76.6 1.0
O A:HOH1122 3.7 65.8 1.0
O3B A:DTP1000 3.7 79.2 1.0
O3A A:DTP1000 3.8 76.2 1.0
O A:ASP7 3.8 66.3 1.0
CG A:ASP105 3.8 65.2 1.0
PA A:DTP1000 3.9 77.9 1.0
C A:ASP7 3.9 59.7 1.0
N A:PHE8 4.1 53.5 1.0
CA A:ASP9 4.1 61.1 1.0
N A:ASP9 4.2 60.2 1.0
CB A:ASP7 4.3 61.4 1.0
CA A:PHE8 4.4 55.8 1.0
OD1 A:ASP105 4.4 63.2 1.0
N A:TYR10 4.4 62.3 1.0
NZ A:LYS159 4.5 81.4 1.0
C A:ASP9 4.5 61.7 1.0
CA A:ASP7 4.5 58.0 1.0
OD1 A:ASP9 4.7 66.2 1.0
C5' A:DTP1000 4.8 58.6 1.0
O3G A:DTP1000 4.8 88.4 1.0
O2A A:DTP1000 4.8 79.8 1.0
O5' A:DTP1000 4.9 60.1 1.0
CB A:ASP105 4.9 56.5 1.0

Calcium binding site 2 out of 2 in 4jv0

Go back to Calcium Binding Sites List in 4jv0
Calcium binding site 2 out of 2 in the Ring-Opening of the -Oh-Pdg Adduct in Ternary Complexes with the Sulfolobus Solfataricus Dna Polymerase DPO4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ring-Opening of the -Oh-Pdg Adduct in Ternary Complexes with the Sulfolobus Solfataricus Dna Polymerase DPO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:75.3
occ:1.00
O A:ILE186 2.9 65.2 1.0
O A:ALA181 2.9 70.2 1.0
O C:HOH101 3.0 60.9 1.0
O A:HOH1101 3.0 54.2 1.0
O A:HOH1102 3.1 72.5 1.0
CA A:GLY187 4.0 67.1 1.0
C A:ILE186 4.0 61.4 1.0
C A:ALA181 4.0 72.7 1.0
OP2 C:DC31 4.2 61.6 1.0
C A:GLY187 4.4 66.3 1.0
N A:GLY187 4.5 64.2 1.0
CA A:ALA181 4.7 74.5 1.0
O A:GLY187 4.8 69.2 1.0
CB A:ALA181 4.8 75.9 1.0
N A:ASN188 4.8 70.1 1.0
OP1 C:DC31 4.8 65.8 1.0
OD1 A:ASN188 4.9 88.2 1.0

Reference:

G.Shanmugam, I.G.Minko, S.Banerjee, P.P.Christov, I.D.Kozekov, C.J.Rizzo, R.S.Lloyd, M.Egli, M.P.Stone. Ring-Opening of the Gamma-Oh-Pdg Adduct Promotes Error-Free Bypass By the Sulfolobus Solfataricus Dna Polymerase DPO4. Chem.Res.Toxicol. V. 26 1348 2013.
ISSN: ISSN 0893-228X
PubMed: 23947567
DOI: 10.1021/TX400200B
Page generated: Sat Dec 12 04:53:40 2020

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