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

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy