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Calcium in PDB 4ebe: Conformationally Restrained North-Methanocarba-2'-Deoxyadenosine Corrects the Error-Prone Nature of Human Dna Polymerase Iota

Enzymatic activity of Conformationally Restrained North-Methanocarba-2'-Deoxyadenosine Corrects the Error-Prone Nature of Human Dna Polymerase Iota

All present enzymatic activity of Conformationally Restrained North-Methanocarba-2'-Deoxyadenosine Corrects the Error-Prone Nature of Human Dna Polymerase Iota:
2.7.7.7;

Protein crystallography data

The structure of Conformationally Restrained North-Methanocarba-2'-Deoxyadenosine Corrects the Error-Prone Nature of Human Dna Polymerase Iota, PDB code: 4ebe was solved by R.L.Eoff, A.Ketkar, S.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.17 / 2.10
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 98.233, 98.233, 202.067, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 26.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Conformationally Restrained North-Methanocarba-2'-Deoxyadenosine Corrects the Error-Prone Nature of Human Dna Polymerase Iota (pdb code 4ebe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Conformationally Restrained North-Methanocarba-2'-Deoxyadenosine Corrects the Error-Prone Nature of Human Dna Polymerase Iota, PDB code: 4ebe:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4ebe

Go back to Calcium Binding Sites List in 4ebe
Calcium binding site 1 out of 3 in the Conformationally Restrained North-Methanocarba-2'-Deoxyadenosine Corrects the Error-Prone Nature of Human Dna Polymerase Iota


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Conformationally Restrained North-Methanocarba-2'-Deoxyadenosine Corrects the Error-Prone Nature of Human Dna Polymerase Iota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:51.8
occ:1.00
 O A:HOH849 2.2 53.1 1.0
O A:HOH789 2.3 58.8 1.0
OE2 A:GLU127 2.6 28.9 1.0
O A:HOH825 2.8 39.2 1.0
OD2 A:ASP34 2.8 41.0 1.0
O A:HOH847 2.9 48.3 1.0
OD1 A:ASP34 3.1 33.7 1.0
O A:HOH848 3.3 52.3 1.0
CG A:ASP34 3.3 34.2 1.0
CD A:GLU127 3.5 31.0 1.0
CA A:CA503 3.9 43.4 1.0
CG A:GLU127 4.0 25.4 1.0
O2G A:DTP501 4.1 52.1 0.8
OE1 A:GLU127 4.4 31.2 1.0
O A:HOH788 4.5 36.4 1.0
O3A A:DTP501 4.5 51.0 0.7
O1A A:DTP501 4.5 49.5 0.7
NZ A:LYS207 4.6 31.7 1.0
C5' P:DOC7 4.6 30.7 1.0
C3' P:DOC7 4.7 33.0 1.0
CB A:ASP34 4.8 31.2 1.0
C4' P:DOC7 4.8 34.6 1.0
OD1 A:ASP126 4.8 32.5 1.0
O2A A:DTP501 4.9 47.9 0.7
PA A:DTP501 5.0 50.3 0.7
O A:HOH845 5.0 53.4 1.0

Calcium binding site 2 out of 3 in 4ebe

Go back to Calcium Binding Sites List in 4ebe
Calcium binding site 2 out of 3 in the Conformationally Restrained North-Methanocarba-2'-Deoxyadenosine Corrects the Error-Prone Nature of Human Dna Polymerase Iota


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Conformationally Restrained North-Methanocarba-2'-Deoxyadenosine Corrects the Error-Prone Nature of Human Dna Polymerase Iota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:43.4
occ:1.00
 O2G A:DTP501 1.9 52.1 0.8
O A:LEU35 2.5 30.1 1.0
OD1 A:ASP34 2.7 33.7 1.0
O1B A:DTP501 2.7 35.3 0.7
O A:HOH825 2.7 39.2 1.0
O A:HOH849 2.8 53.1 1.0
OD2 A:ASP126 3.0 47.0 1.0
O3A A:DTP501 3.1 51.0 0.7
PG A:DTP501 3.2 44.0 0.8
PB A:DTP501 3.3 45.8 0.7
O A:HOH835 3.4 42.4 1.0
C A:LEU35 3.6 28.2 1.0
O A:HOH848 3.7 52.3 1.0
O3B A:DTP501 3.7 45.8 0.7
CG A:ASP34 3.8 34.2 1.0
CG A:ASP126 3.8 36.5 1.0
O3G A:DTP501 3.8 48.9 0.8
CA A:CA502 3.9 51.8 1.0
N A:LEU35 4.0 30.1 1.0
OD1 A:ASP126 4.1 32.5 1.0
C A:ASP34 4.3 28.9 1.0
OD2 A:ASP34 4.3 41.0 1.0
CA A:LEU35 4.4 29.1 1.0
PA A:DTP501 4.4 50.3 0.7
O1G A:DTP501 4.4 48.5 0.8
N A:CYS37 4.5 35.3 1.0
O2A A:DTP501 4.5 47.9 0.7
N A:ASP36 4.6 35.3 1.0
CA A:ASP36 4.6 33.9 1.0
O A:ASP34 4.7 30.7 1.0
O2B A:DTP501 4.7 41.1 0.7
C A:ASP36 4.7 37.3 1.0
CB A:ASP34 4.8 31.2 1.0
O A:HOH807 4.9 43.6 1.0
CA A:ASP34 4.9 26.9 1.0
CB A:ASP126 4.9 31.0 1.0
CB A:LEU35 5.0 32.4 1.0

Calcium binding site 3 out of 3 in 4ebe

Go back to Calcium Binding Sites List in 4ebe
Calcium binding site 3 out of 3 in the Conformationally Restrained North-Methanocarba-2'-Deoxyadenosine Corrects the Error-Prone Nature of Human Dna Polymerase Iota


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Conformationally Restrained North-Methanocarba-2'-Deoxyadenosine Corrects the Error-Prone Nature of Human Dna Polymerase Iota within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:69.0
occ:1.00
 OP1 P:DC6 2.9 41.3 1.0
O A:LYS237 3.0 47.0 1.0
O P:HOH113 3.0 53.4 1.0
O A:ILE242 3.0 46.2 1.0
O A:ILE239 3.0 35.4 1.0
O A:HOH809 3.0 57.3 1.0
O A:HOH751 3.0 53.9 1.0
O A:HOH808 3.1 50.0 1.0
O P:HOH110 3.3 48.2 1.0
C A:ILE239 3.6 38.7 1.0
C A:ILE242 3.9 46.0 1.0
CA A:PRO240 3.9 43.7 1.0
P P:DC6 4.0 39.8 1.0
C A:LYS237 4.0 51.4 1.0
N A:PRO240 4.0 38.3 1.0
OP2 P:DC6 4.2 36.3 1.0
N A:ILE242 4.2 43.9 1.0
N A:GLY241 4.3 45.5 1.0
C A:GLU238 4.3 41.6 1.0
N A:ILE239 4.3 28.9 1.0
CA A:ILE242 4.6 43.0 1.0
C A:PRO240 4.6 45.0 1.0
O A:GLU238 4.6 44.3 1.0
CA A:ILE239 4.6 34.8 1.0
CA A:GLU238 4.6 42.8 1.0
N A:GLU238 4.8 44.5 1.0
N A:GLY243 4.8 48.3 1.0
CB A:ILE242 4.8 45.3 1.0
CA A:LYS237 4.9 51.6 1.0
O5' P:DC6 4.9 35.6 1.0
CA A:GLY243 5.0 39.9 1.0

Reference:

A.Ketkar, M.K.Zafar, S.Banerjee, V.E.Marquez, M.Egli, R.L.Eoff. A Nucleotide-Analogue-Induced Gain of Function Corrects the Error-Prone Nature of Human Dna Polymerase Iota. J.Am.Chem.Soc. V. 134 10698 2012.
ISSN: ISSN 0002-7863
PubMed: 22632140
DOI: 10.1021/JA304176Q
Page generated: Sat Jul 13 23:48:29 2024

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