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Calcium in PDB 4ebc: 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: 4ebc 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) 48.90 / 2.90
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 97.797, 97.797, 203.628, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 25.3

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

Calcium binding site 1 out of 3 in 4ebc

Go back to Calcium Binding Sites List in 4ebc
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:49.7
occ:1.00
 O A:LEU35 2.5 40.8 1.0
OD2 A:ASP126 2.6 58.7 1.0
OD1 A:ASP34 2.6 55.0 1.0
OAC A:0OH501 3.1 53.7 1.0
OAG A:0OH501 3.1 61.5 1.0
OAI A:0OH501 3.2 52.2 1.0
OAT A:0OH501 3.3 67.8 1.0
OAS A:0OH501 3.4 64.3 1.0
PBE A:0OH501 3.5 62.4 1.0
CG A:ASP34 3.6 53.2 1.0
C A:LEU35 3.6 39.5 1.0
PBD A:0OH501 3.7 57.8 1.0
PBC A:0OH501 3.7 60.7 1.0
CG A:ASP126 3.7 59.5 1.0
OD2 A:ASP34 3.9 58.7 1.0
N A:LEU35 3.9 42.5 1.0
CA A:CA504 4.0 0.8 1.0
OAB A:0OH501 4.2 62.1 1.0
CA A:LEU35 4.3 38.8 1.0
C A:ASP34 4.3 46.2 1.0
CB A:ASP126 4.3 58.4 1.0
OAR A:0OH501 4.4 57.7 1.0
CAL A:0OH501 4.4 52.1 1.0
N A:ASP36 4.6 44.9 1.0
OD1 A:ASP126 4.7 60.4 1.0
N A:CYS37 4.7 49.3 1.0
O A:ASP34 4.8 50.2 1.0
O A:HOH603 4.8 63.0 1.0
CB A:ASP34 4.8 49.1 1.0
CA A:ASP36 4.8 47.5 1.0
C A:ASP36 4.8 53.1 1.0
N A:PHE38 4.8 59.9 1.0
CA A:ASP34 4.9 44.0 1.0
O A:HOH645 4.9 62.5 1.0
O A:HOH606 5.0 49.6 1.0
CB A:LEU35 5.0 41.7 1.0
OAD A:0OH501 5.0 62.2 1.0

Calcium binding site 2 out of 3 in 4ebc

Go back to Calcium Binding Sites List in 4ebc
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:83.8
occ:1.00
 O A:HOH647 2.3 68.0 1.0
O A:LYS237 2.8 67.0 1.0
O P:HOH105 2.8 66.0 1.0
O A:HOH619 3.0 59.9 1.0
O P:HOH107 3.1 74.5 1.0
OP1 P:DC6 3.5 76.1 1.0
O A:ILE239 3.7 69.6 1.0
O A:ILE242 3.8 74.4 1.0
C A:LYS237 3.9 61.9 1.0
C A:ILE239 4.0 65.7 1.0
C A:GLU238 4.1 70.6 1.0
CA A:PRO240 4.2 71.1 1.0
N A:PRO240 4.2 70.4 1.0
O A:GLU238 4.2 68.9 1.0
CA A:GLU238 4.3 74.7 1.0
N A:ILE239 4.3 61.5 1.0
OP2 P:DOC7 4.3 59.5 1.0
N A:GLU238 4.5 75.1 1.0
P P:DC6 4.6 72.7 1.0
CA A:ILE239 4.8 59.4 1.0
O P:HOH102 4.9 65.9 1.0
OP2 P:DC6 4.9 61.5 1.0
C A:ILE242 4.9 75.2 1.0
CD A:PRO240 4.9 66.7 1.0

Calcium binding site 3 out of 3 in 4ebc

Go back to Calcium Binding Sites List in 4ebc
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:0.8
occ:1.00
 O A:HOH603 2.1 63.0 1.0
OD2 A:ASP34 2.4 58.7 1.0
OE2 A:GLU127 2.7 61.5 1.0
OAC A:0OH501 3.0 53.7 1.0
CG A:ASP34 3.4 53.2 1.0
OD1 A:ASP34 3.6 55.0 1.0
CD A:GLU127 3.8 59.8 1.0
CA A:CA502 4.0 49.7 1.0
OAG A:0OH501 4.1 61.5 1.0
PBD A:0OH501 4.1 57.8 1.0
O A:HOH645 4.2 62.5 1.0
O A:HOH644 4.3 76.9 1.0
OAH A:0OH501 4.3 53.6 1.0
OAT A:0OH501 4.5 67.8 1.0
CG A:GLU127 4.6 50.2 1.0
OD2 A:ASP126 4.6 58.7 1.0
CB A:ASP34 4.7 49.1 1.0
OE1 A:GLU127 4.7 55.8 1.0
C3' P:DOC7 4.8 63.9 1.0
C5' P:DOC7 4.8 62.7 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: Sat Jul 13 23:47:16 2024

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