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: Tue Apr 4 19:18:00 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy