Atomistry » Calcium » PDB 4dtm-4ec5 » 4ebd
Atomistry »
  Calcium »
    PDB 4dtm-4ec5 »
      4ebd »

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: Sat Jul 13 23:47:33 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy