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Calcium in PDB 4jv1: Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Dgtp

Enzymatic activity of Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Dgtp

All present enzymatic activity of Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Dgtp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Dgtp, PDB code: 4jv1 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) 41.87 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.274, 102.183, 52.727, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 26.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Dgtp (pdb code 4jv1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Dgtp, PDB code: 4jv1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4jv1

Go back to Calcium Binding Sites List in 4jv1
Calcium binding site 1 out of 4 in the Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Dgtp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:50.8
occ:1.00
O A:PHE8 2.6 35.5 1.0
OD1 A:ASP7 2.6 52.2 1.0
O2A A:DGT401 2.7 48.3 1.0
OD2 A:ASP105 2.7 51.4 1.0
O2B A:DGT401 2.7 44.7 1.0
O2G A:DGT401 3.0 64.6 1.0
O A:HOH501 3.2 48.4 1.0
CG A:ASP7 3.4 47.6 1.0
O3G A:DGT401 3.4 48.6 1.0
PG A:DGT401 3.5 48.1 0.7
C A:PHE8 3.6 40.8 1.0
PB A:DGT401 3.7 47.9 1.0
OD2 A:ASP7 3.8 55.8 1.0
CA A:CA403 3.8 66.6 1.0
CG A:ASP105 3.8 48.2 1.0
O3B A:DGT401 3.9 49.7 1.0
PA A:DGT401 3.9 57.9 1.0
N A:PHE8 4.0 37.8 1.0
O3A A:DGT401 4.1 49.4 0.4
C A:ASP7 4.2 43.9 1.0
N A:TYR10 4.3 42.7 1.0
NZ A:LYS159 4.3 56.0 1.0
CA A:PHE8 4.4 44.5 1.0
CB A:ASP7 4.4 43.8 1.0
C5' A:DGT401 4.5 48.7 1.0
CA A:ASP9 4.5 43.5 1.0
OD1 A:ASP105 4.5 47.0 1.0
N A:ASP9 4.5 46.3 1.0
O A:ASP7 4.6 41.1 1.0
O5' A:DGT401 4.6 51.2 1.0
C A:ASP9 4.6 44.2 1.0
CA A:ASP7 4.7 40.7 1.0
N A:PHE11 4.7 41.0 1.0
CB A:ASP105 4.9 40.3 1.0
O A:ASP105 4.9 42.4 1.0
O1G A:DGT401 5.0 51.2 0.6

Calcium binding site 2 out of 4 in 4jv1

Go back to Calcium Binding Sites List in 4jv1
Calcium binding site 2 out of 4 in the Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Dgtp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:66.6
occ:1.00
O2A A:DGT401 2.7 48.3 1.0
OD1 A:ASP7 3.0 52.2 1.0
OD1 A:ASP105 3.1 47.0 1.0
O A:HOH502 3.2 53.9 1.0
OD2 A:ASP7 3.2 55.8 1.0
OE2 A:GLU106 3.2 68.2 1.0
CG A:GLU106 3.3 47.2 1.0
CG A:ASP7 3.4 47.6 1.0
OD2 A:ASP105 3.6 51.4 1.0
CD A:GLU106 3.6 52.1 1.0
O A:HOH558 3.7 56.6 1.0
CG A:ASP105 3.7 48.2 1.0
PA A:DGT401 3.7 57.9 1.0
CA A:CA402 3.8 50.8 1.0
O5' A:DGT401 4.0 51.2 1.0
O1A A:DGT401 4.0 56.7 1.0
C5' A:DGT401 4.4 48.7 1.0
O2G A:DGT401 4.7 64.6 1.0
CB A:GLU106 4.7 46.4 1.0
OE1 A:GLU106 4.7 50.0 1.0
O A:ASP105 4.8 42.4 1.0
OG A:SER103 4.8 50.4 1.0
O3' C:DC513 4.8 67.8 1.0
CB A:ASP7 4.8 43.8 1.0
NZ A:LYS159 4.9 56.0 1.0
NZ A:LYS152 4.9 58.9 1.0

Calcium binding site 3 out of 4 in 4jv1

Go back to Calcium Binding Sites List in 4jv1
Calcium binding site 3 out of 4 in the Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Dgtp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:80.9
occ:1.00
O A:ALA181 2.9 54.3 1.0
O A:ILE186 3.0 41.0 1.0
O A:HOH506 3.0 56.6 1.0
O C:HOH701 3.2 46.0 1.0
C A:ALA181 3.9 51.5 1.0
C A:ILE186 4.1 46.5 1.0
CA A:GLY187 4.2 47.8 1.0
OP2 C:DC513 4.4 46.3 1.0
CB A:ALA181 4.4 51.7 1.0
C A:GLY187 4.5 47.0 1.0
CA A:ALA181 4.6 51.3 1.0
OP1 C:DC513 4.6 48.8 1.0
N A:GLY187 4.7 47.1 1.0
O A:HOH507 4.7 62.4 1.0
O A:GLY187 4.7 45.2 1.0
N A:ASP182 4.9 48.8 1.0

Calcium binding site 4 out of 4 in 4jv1

Go back to Calcium Binding Sites List in 4jv1
Calcium binding site 4 out of 4 in the Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Dgtp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:97.5
occ:1.00
O C:HOH713 3.2 65.2 1.0
O6 C:DG504 4.2 54.8 1.0
N7 C:DG503 4.2 58.8 1.0
C8 C:DG503 4.7 62.6 1.0
N7 C:DG504 4.8 66.5 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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