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Calcium in PDB 4ebd: 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: 4ebd 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) 48.89 / 2.57
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 97.776, 97.776, 202.739, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 26.3

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 4ebd). 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: 4ebd:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4ebd

Go back to Calcium Binding Sites List in 4ebd
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:68.2
occ:1.00
 OD2 A:ASP34 2.9 44.9 1.0
OE2 A:GLU127 2.9 43.5 1.0
O A:HOH651 3.0 54.3 1.0
O A:HOH662 3.0 52.9 1.0
O A:HOH707 3.0 57.3 1.0
O A:HOH656 3.2 52.5 1.0
OD1 A:ASP34 3.3 36.4 1.0
O A:HOH652 3.3 51.9 1.0
CG A:ASP34 3.5 39.3 1.0
H3'2 P:DOC7 3.8 47.9 1.0
CA A:CA503 3.8 42.5 1.0
OAC A:0OJ501 3.9 61.9 1.0
CD A:GLU127 3.9 41.7 1.0
H5'' P:DOC7 4.0 41.3 1.0
O A:HOH722 4.3 50.2 1.0
OAH A:0OJ501 4.3 56.9 1.0
CG A:GLU127 4.5 36.0 1.0
PBD A:0OJ501 4.6 63.4 1.0
C3' P:DOC7 4.7 47.9 1.0
O A:HOH659 4.7 46.0 1.0
OAT A:0OJ501 4.7 59.9 1.0
OE1 A:GLU127 4.7 41.7 1.0
O A:HOH635 4.7 39.4 1.0
NZ A:LYS207 4.7 33.0 1.0
H4' P:DOC7 4.7 47.0 1.0
OD1 A:ASP126 4.8 43.8 1.0
OAF A:0OJ501 4.8 44.2 1.0
C5' P:DOC7 4.9 41.3 1.0
O A:HOH703 4.9 50.4 1.0
CB A:ASP34 5.0 35.5 1.0
H3'1 P:DOC7 5.0 47.9 1.0
C4' P:DOC7 5.0 47.0 1.0

Calcium binding site 2 out of 3 in 4ebd

Go back to Calcium Binding Sites List in 4ebd
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:42.5
occ:1.00
 OAF A:0OJ501 2.7 44.2 1.0
OD1 A:ASP34 2.7 36.4 1.0
O A:LEU35 2.8 36.8 1.0
OAI A:0OJ501 2.8 40.1 1.0
OAC A:0OJ501 3.1 61.9 1.0
O A:HOH722 3.2 50.2 1.0
OAT A:0OJ501 3.2 59.9 1.0
OD1 A:ASP126 3.2 43.8 1.0
OD2 A:ASP126 3.3 53.6 1.0
CG A:ASP126 3.4 40.5 1.0
PBE A:0OJ501 3.5 45.4 1.0
O A:HOH662 3.6 52.9 1.0
CG A:ASP34 3.8 39.3 1.0
PBD A:0OJ501 3.8 63.4 1.0
PBC A:0OJ501 3.8 46.0 1.0
CA A:CA502 3.8 68.2 1.0
C A:LEU35 3.9 32.3 1.0
OAS A:0OJ501 4.0 52.5 1.0
N A:LEU35 4.1 31.4 1.0
OD2 A:ASP34 4.3 44.9 1.0
OAB A:0OJ501 4.4 44.1 1.0
CB A:ASP126 4.4 42.0 1.0
C A:ASP34 4.5 35.2 1.0
CA A:LEU35 4.6 28.4 1.0
H5 A:0OJ501 4.6 51.4 0.5
OAH A:0OJ501 4.8 56.9 1.0
CB A:ASP34 4.8 35.5 1.0
O A:ASP126 4.9 34.9 1.0
OAD A:0OJ501 4.9 53.1 1.0
CA A:ASP34 4.9 33.7 1.0
N A:CYS37 4.9 38.7 1.0
N A:ASP36 4.9 33.8 1.0
O A:HOH645 5.0 41.0 1.0
OAR A:0OJ501 5.0 56.7 1.0

Calcium binding site 3 out of 3 in 4ebd

Go back to Calcium Binding Sites List in 4ebd
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:65.9
occ:1.00
 OP1 P:DC6 2.9 47.8 1.0
O A:LYS237 2.9 65.8 1.0
O A:ILE242 3.0 53.4 1.0
O A:HOH708 3.0 52.2 1.0
O A:HOH702 3.1 52.0 1.0
O A:ILE239 3.2 43.0 1.0
O A:HOH655 3.2 65.5 1.0
O A:HOH661 3.4 57.5 1.0
C A:ILE239 3.8 41.0 1.0
P P:DC6 3.9 44.6 1.0
C A:LYS237 3.9 59.7 1.0
CA A:PRO240 3.9 44.7 1.0
C A:ILE242 4.0 51.5 1.0
OP2 P:DC6 4.0 40.5 1.0
N A:PRO240 4.2 43.2 1.0
C A:GLU238 4.3 47.4 1.0
N A:GLY241 4.4 44.3 1.0
N A:ILE239 4.4 37.6 1.0
N A:ILE242 4.5 46.5 1.0
CA A:GLU238 4.6 50.1 1.0
O A:GLU238 4.6 45.3 1.0
N A:GLU238 4.7 52.2 1.0
C A:PRO240 4.7 44.1 1.0
CA A:GLY243 4.8 55.8 1.0
N A:GLY243 4.8 56.9 1.0
CA A:ILE242 4.8 48.5 1.0
CA A:ILE239 4.8 37.5 1.0
O5' P:DC6 4.8 39.9 1.0
CA A:LYS237 4.9 59.7 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: Tue Jul 8 19:41:30 2025

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