Atomistry » Calcium » PDB 6ojh-6p8p » 6p1h
Atomistry »
  Calcium »
    PDB 6ojh-6p8p »
      6p1h »

Calcium in PDB 6p1h: Cryo-Em Structure of Dna Polymerase Delta Holoenzyme

Enzymatic activity of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme

All present enzymatic activity of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme:
2.7.7.7;

Other elements in 6p1h:

The structure of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme (pdb code 6p1h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme, PDB code: 6p1h:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6p1h

Go back to Calcium Binding Sites List in 6p1h
Calcium binding site 1 out of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1103

b:65.0
occ:1.00
O1B A:DCP1102 2.3 64.0 1.0
OD2 A:ASP764 2.4 67.2 1.0
O A:PHE609 2.4 63.6 1.0
OD2 A:ASP608 2.6 66.8 1.0
O1G A:DCP1102 2.8 64.0 1.0
O1A A:DCP1102 3.1 64.0 1.0
CG A:ASP608 3.3 66.8 1.0
CG A:ASP764 3.5 67.2 1.0
C A:PHE609 3.5 63.6 1.0
CB A:ASP608 3.7 66.8 1.0
PB A:DCP1102 3.8 64.0 1.0
N A:PHE609 3.8 63.6 1.0
CA A:CA1104 3.9 87.0 1.0
PG A:DCP1102 3.9 64.0 1.0
O3G A:DCP1102 4.0 64.0 1.0
OD1 A:ASP764 4.2 67.2 1.0
CA A:PHE609 4.2 63.6 1.0
OD1 A:ASP608 4.3 66.8 1.0
C A:ASP608 4.4 66.8 1.0
CB A:ASP764 4.4 67.2 1.0
O3B A:DCP1102 4.4 64.0 1.0
PA A:DCP1102 4.4 64.0 1.0
N A:ASN610 4.6 63.5 1.0
CA A:ASP608 4.6 66.8 1.0
O3A A:DCP1102 4.6 64.0 1.0
O2B A:DCP1102 4.7 64.0 1.0
N A:SER611 4.7 62.1 1.0
CA A:ASN610 4.8 63.5 1.0
C5' A:DCP1102 4.8 64.0 1.0
CB A:PHE609 4.9 63.6 1.0

Calcium binding site 2 out of 5 in 6p1h

Go back to Calcium Binding Sites List in 6p1h
Calcium binding site 2 out of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1104

b:87.0
occ:1.00
O A:HOH1225 2.9 57.8 1.0
O1A A:DCP1102 3.5 64.0 1.0
OD1 A:ASP764 3.6 67.2 1.0
OD2 A:ASP608 3.8 66.8 1.0
CA A:CA1103 3.9 65.0 1.0
OD2 A:ASP764 3.9 67.2 1.0
CG A:ASP764 4.1 67.2 1.0
C5' P:DC30 4.1 65.4 1.0
CB A:ASP608 4.1 66.8 1.0
OG A:SER765 4.3 67.6 1.0
CB A:SER765 4.3 67.6 1.0
CG A:ASP608 4.4 66.8 1.0
C3' P:DC30 4.4 65.4 1.0
OE2 A:GLU802 4.5 69.5 1.0
O5' P:DC30 4.6 65.4 1.0
C4' P:DC30 4.6 65.4 1.0
PA A:DCP1102 4.8 64.0 1.0
O2A A:DCP1102 4.9 64.0 1.0

Calcium binding site 3 out of 5 in 6p1h

Go back to Calcium Binding Sites List in 6p1h
Calcium binding site 3 out of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1105

b:90.2
occ:1.00
OE1 A:GLU800 2.3 71.0 1.0
OD1 A:ASP608 3.1 66.8 1.0
OD2 A:ASP608 3.3 66.8 1.0
OD1 A:ASN610 3.4 63.5 1.0
CD A:GLU800 3.4 71.0 1.0
CG A:ASP608 3.6 66.8 1.0
CG A:GLU802 3.8 69.5 1.0
CG A:GLU800 3.8 71.0 1.0
CB A:GLU802 4.2 69.5 1.0
CD A:GLU802 4.5 69.5 1.0
OE2 A:GLU800 4.5 71.0 1.0
O1G A:DCP1102 4.6 64.0 1.0
CG A:ASN610 4.6 63.5 1.0
O3G A:DCP1102 4.6 64.0 1.0
CA A:GLU802 4.7 69.5 1.0
OE1 A:GLU802 4.8 69.5 1.0

Calcium binding site 4 out of 5 in 6p1h

Go back to Calcium Binding Sites List in 6p1h
Calcium binding site 4 out of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1106

b:95.6
occ:1.00
OD2 A:ASP321 1.9 74.1 1.0
CG A:ASP321 2.6 74.1 1.0
OD1 A:ASP321 2.6 74.1 1.0
O A:ILE322 3.3 74.7 1.0
OD2 A:ASP520 4.0 77.5 1.0
CB A:ASP321 4.1 74.1 1.0
OE2 A:GLU323 4.2 81.8 1.0
CD A:GLU323 4.3 81.8 1.0
N A:ILE322 4.3 74.7 1.0
C A:ILE322 4.4 74.7 1.0
O A:HOH1211 4.4 77.3 1.0
CB A:ASP520 4.5 77.5 1.0
OE1 A:GLU323 4.6 81.8 1.0
CG A:ASP520 4.6 77.5 1.0
OD1 A:ASP407 4.7 77.2 1.0
CG A:GLU323 4.8 81.8 1.0
CA A:ASP321 4.8 74.1 1.0
C A:ASP321 5.0 74.1 1.0

Calcium binding site 5 out of 5 in 6p1h

Go back to Calcium Binding Sites List in 6p1h
Calcium binding site 5 out of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca101

b:0.9
occ:1.00
O T:HOH201 3.2 81.7 1.0
OP2 T:DG10 3.2 72.6 1.0
C8 T:DG10 4.0 72.6 1.0
N7 T:DG10 4.2 72.6 1.0
N7 T:DG11 4.3 78.3 1.0
P T:DG10 4.6 72.6 1.0
C2' T:DG9 4.9 68.7 1.0
O5' T:DG10 4.9 72.6 1.0
C8 T:DG11 4.9 78.3 1.0

Reference:

R.Jain, W.J.Rice, R.Malik, R.E.Johnson, L.Prakash, S.Prakash, I.Ubarretxena-Belandia, A.K.Aggarwal. Cryo-Em Structure and Dynamics of Eukaryotic Dna Polymerase Delta Holoenzyme. Nat.Struct.Mol.Biol. V. 26 955 2019.
ISSN: ESSN 1545-9985
PubMed: 31582849
DOI: 10.1038/S41594-019-0305-Z
Page generated: Tue Jul 16 12:43:16 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