Atomistry » Calcium » PDB 7xvv-7yq7 » 7y7s
Atomistry »
  Calcium »
    PDB 7xvv-7yq7 »
      7y7s »

Calcium in PDB 7y7s: Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp

Enzymatic activity of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp

All present enzymatic activity of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp:
2.7.7.48;

Protein crystallography data

The structure of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp, PDB code: 7y7s was solved by R.X.Cui, J.H.Gan, J.B.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.10 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.954, 120.412, 114.993, 90, 109.71, 90
R / Rfree (%) 20.8 / 24.5

Other elements in 7y7s:

The structure of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp (pdb code 7y7s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp, PDB code: 7y7s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 7y7s

Go back to Calcium Binding Sites List in 7y7s
Calcium binding site 1 out of 7 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1501

b:46.7
occ:1.00
 O3' D:C7 2.3 48.1 1.0
OD1 A:ASP1007 2.3 43.9 1.0
O2A A:ZAN1504 2.4 40.0 1.0
OD1 A:ASP1011 2.4 49.6 1.0
OD1 A:ASP1009 2.5 45.4 1.0
O A:HOH1631 2.5 46.5 1.0
OD2 A:ASP1007 2.6 48.2 1.0
CG A:ASP1007 2.8 43.0 1.0
OD2 A:ASP1009 3.1 43.0 1.0
CG A:ASP1009 3.1 45.0 1.0
CG A:ASP1011 3.3 46.4 1.0
PA A:ZAN1504 3.4 53.0 1.0
OD2 A:ASP1011 3.6 44.6 1.0
C3' D:C7 3.6 53.9 1.0
O5' A:ZAN1504 3.6 53.7 1.0
CA A:CA1502 3.7 50.6 1.0
O A:HOH1620 3.9 43.7 1.0
O2' D:C7 3.9 52.0 1.0
O1A A:ZAN1504 3.9 46.6 1.0
C4' D:C7 4.3 50.9 1.0
C2' D:C7 4.3 53.3 1.0
CB A:ASP1007 4.3 39.6 1.0
O2B A:ZAN1504 4.5 50.8 1.0
CB A:ASP1009 4.5 41.8 1.0
CB A:ASP1011 4.6 42.2 1.0
N A:ASP1007 4.7 39.7 1.0
N A:ASP1011 4.7 40.8 1.0
N A:ASP1009 4.7 42.6 1.0
N3A A:ZAN1504 4.8 49.5 1.0
C5' A:ZAN1504 4.8 42.9 1.0
C5' D:C7 4.9 38.4 1.0
CA A:ASP1007 4.9 44.7 1.0

Calcium binding site 2 out of 7 in 7y7s

Go back to Calcium Binding Sites List in 7y7s
Calcium binding site 2 out of 7 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1502

b:50.6
occ:1.00
 O2B A:ZAN1504 2.2 50.8 1.0
OD2 A:ASP1007 2.2 48.2 1.0
O3G A:ZAN1504 2.2 42.4 1.0
O A:HOH1619 2.4 51.8 1.0
O A:HOH1601 2.4 46.7 1.0
O2A A:ZAN1504 2.5 40.0 1.0
OD2 A:ASP1009 2.5 43.0 1.0
CG A:ASP1007 3.4 43.0 1.0
PB A:ZAN1504 3.5 51.5 1.0
PG A:ZAN1504 3.6 42.9 1.0
O A:HOH1620 3.7 43.7 1.0
CG A:ASP1009 3.7 45.0 1.0
CA A:CA1501 3.7 46.7 1.0
PA A:ZAN1504 3.7 53.0 1.0
O3B A:ZAN1504 4.0 55.0 1.0
N3A A:ZAN1504 4.0 49.5 1.0
O A:HOH1626 4.1 47.6 1.0
OD1 A:ASP1007 4.1 43.9 1.0
NZ A:LYS743 4.2 58.9 1.0
NZ A:LYS767 4.2 53.9 1.0
CB A:ASP1007 4.3 39.6 1.0
OD1 A:ASP1009 4.3 45.4 1.0
OD1 A:ASP709 4.4 48.2 1.0
O2G A:ZAN1504 4.5 50.5 1.0
O5' A:ZAN1504 4.5 53.7 1.0
O1G A:ZAN1504 4.6 41.8 1.0
OD2 A:ASP709 4.6 41.8 1.0
CB A:ASP1009 4.7 41.8 1.0
CG A:ASP709 4.8 40.9 1.0
O1B A:ZAN1504 4.8 58.2 1.0
O A:HOH1631 4.9 46.5 1.0
O1A A:ZAN1504 5.0 46.6 1.0

Calcium binding site 3 out of 7 in 7y7s

Go back to Calcium Binding Sites List in 7y7s
Calcium binding site 3 out of 7 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1503

b:82.6
occ:1.00
 O A:HOH1628 2.2 61.4 1.0
O A:GLY1005 2.2 62.1 1.0
O A:HOH1620 2.3 43.7 1.0
O A:HOH1625 2.6 59.1 1.0
O A:HOH1650 2.7 55.3 1.0
C A:GLY1005 3.3 53.9 1.0
CA A:GLY1005 3.9 42.5 1.0
O2B A:ZAN1504 4.3 50.8 1.0
N A:GLY1006 4.4 41.2 1.0
O3' A:ZAN1504 4.5 45.8 1.0
O A:HOH1631 4.5 46.5 1.0
O1B A:ZAN1504 4.5 58.2 1.0
O5' A:ZAN1504 4.6 53.7 1.0
CA A:GLY1006 4.8 50.1 1.0
O A:SER1004 4.9 52.8 1.0
O A:HOH1619 4.9 51.8 1.0
OD2 A:ASP1116 4.9 57.5 1.0
PB A:ZAN1504 4.9 51.5 1.0

Calcium binding site 4 out of 7 in 7y7s

Go back to Calcium Binding Sites List in 7y7s
Calcium binding site 4 out of 7 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1502

b:46.7
occ:1.00
 OD1 B:ASP1007 2.1 37.7 1.0
O2A B:ZAN1504 2.2 40.1 1.0
O3' J:C7 2.3 54.9 1.0
OD1 B:ASP1011 2.5 51.4 1.0
OD1 B:ASP1009 2.5 52.5 1.0
O B:HOH1639 2.6 43.4 1.0
CG B:ASP1007 2.8 40.5 1.0
OD2 B:ASP1007 2.9 53.2 1.0
OD2 B:ASP1009 2.9 58.3 1.0
CG B:ASP1009 3.0 61.6 1.0
PA B:ZAN1504 3.3 57.4 1.0
O5' B:ZAN1504 3.3 58.5 1.0
CG B:ASP1011 3.3 49.6 1.0
OD2 B:ASP1011 3.6 45.8 1.0
C3' J:C7 3.6 60.1 1.0
CA B:CA1503 3.8 51.0 1.0
O1A B:ZAN1504 3.8 50.8 1.0
O B:HOH1625 3.9 41.9 1.0
O2' J:C7 4.0 64.3 1.0
CB B:ASP1007 4.3 43.0 1.0
C2' J:C7 4.3 52.3 1.0
C4' J:C7 4.4 59.8 1.0
CB B:ASP1009 4.5 48.3 1.0
N B:ASP1007 4.5 45.0 1.0
C5' B:ZAN1504 4.6 56.0 1.0
O2B B:ZAN1504 4.6 63.0 1.0
CB B:ASP1011 4.7 36.9 1.0
N3A B:ZAN1504 4.7 63.0 1.0
N B:ASP1009 4.8 42.8 1.0
CA B:ASP1007 4.8 46.8 1.0
N B:ASP1011 4.8 43.8 1.0
NZ B:LYS743 5.0 57.5 1.0
C4' B:ZAN1504 5.0 55.9 1.0
O2G B:ZAN1504 5.0 69.8 1.0

Calcium binding site 5 out of 7 in 7y7s

Go back to Calcium Binding Sites List in 7y7s
Calcium binding site 5 out of 7 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1503

b:51.0
occ:1.00
 O2G B:ZAN1504 2.0 69.8 1.0
O B:HOH1644 2.3 60.7 1.0
OD2 B:ASP1007 2.3 53.2 1.0
O B:HOH1611 2.3 46.5 1.0
OD2 B:ASP1009 2.4 58.3 1.0
O2B B:ZAN1504 2.5 63.0 1.0
O2A B:ZAN1504 2.6 40.1 1.0
CG B:ASP1007 3.2 40.5 1.0
PG B:ZAN1504 3.4 54.0 1.0
CG B:ASP1009 3.6 61.6 1.0
PB B:ZAN1504 3.6 59.2 1.0
OD1 B:ASP1007 3.8 37.7 1.0
CA B:CA1502 3.8 46.7 1.0
O3B B:ZAN1504 3.8 72.8 1.0
PA B:ZAN1504 3.8 57.4 1.0
O B:HOH1625 4.0 41.9 1.0
N3A B:ZAN1504 4.0 63.0 1.0
O B:HOH1638 4.1 51.8 1.0
O1G B:ZAN1504 4.1 50.6 1.0
CB B:ASP1007 4.1 43.0 1.0
NZ B:LYS743 4.2 57.5 1.0
NZ B:LYS767 4.3 51.5 1.0
OD1 B:ASP1009 4.4 52.5 1.0
O3G B:ZAN1504 4.5 42.6 1.0
CB B:ASP1009 4.6 48.3 1.0
OD1 B:ASP709 4.6 55.6 1.0
O5' B:ZAN1504 4.7 58.5 1.0
O B:HOH1639 4.9 43.4 1.0
O1A B:ZAN1504 4.9 50.8 1.0
OD2 B:ASP709 5.0 63.8 1.0
CG B:ASP709 5.0 55.6 1.0
O1B B:ZAN1504 5.0 71.3 1.0

Calcium binding site 6 out of 7 in 7y7s

Go back to Calcium Binding Sites List in 7y7s
Calcium binding site 6 out of 7 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:91.2
occ:1.00
 O C:HOH205 2.2 75.5 1.0
O C:HOH209 2.3 95.2 1.0
O C:HOH207 2.6 110.5 1.0
O C:HOH201 2.7 63.6 1.0
O C:HOH206 2.9 57.3 1.0
N7 C:DG4 3.2 55.4 1.0
O6 C:DG4 3.6 47.3 1.0
C5 C:DG4 4.0 59.5 1.0
O C:HOH202 4.0 63.7 1.0
C6 C:DG4 4.1 55.5 1.0
C8 C:DG4 4.2 57.0 1.0
O6 C:DG5 4.2 68.6 1.0
N7 C:DG5 4.4 52.7 1.0

Calcium binding site 7 out of 7 in 7y7s

Go back to Calcium Binding Sites List in 7y7s
Calcium binding site 7 out of 7 in the Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Qde-1 in Complex with Dna Template, Rna Primer and Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca101

b:109.9
occ:1.00
 O I:HOH203 2.2 75.0 1.0
O I:HOH202 2.3 101.1 1.0
O I:HOH205 2.4 71.8 1.0
O I:HOH206 2.5 103.3 1.0
O I:HOH201 2.9 72.4 1.0
N7 I:DG8 4.1 64.2 1.0
O6 I:DG8 4.4 52.4 1.0
O6 I:DG9 4.4 73.6 1.0
C5 I:DG8 4.9 60.2 1.0
O4 I:DT7 4.9 65.6 1.0
N7 I:DG9 5.0 66.5 1.0

Reference:

R.Cui, H.Li, J.Zhao, X.Li, J.Gan, J.Ma. Structural Insights Into the Dual Activities of the Two-Barrel Rna Polymerase Qde-1. Nucleic Acids Res. V. 50 10169 2022.
ISSN: ESSN 1362-4962
PubMed: 36039765
DOI: 10.1093/NAR/GKAC727
Page generated: Fri Jul 19 06:11:44 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy