Atomistry » Magnesium » PDB 6wwl-6x3j » 6wya
Atomistry »
  Magnesium »
    PDB 6wwl-6x3j »
      6wya »

Magnesium in PDB 6wya: Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp

Enzymatic activity of Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp

All present enzymatic activity of Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp:
2.7.7.7;

Protein crystallography data

The structure of Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp, PDB code: 6wya was solved by W.S.Choi, P.He, A.Pothukuchy, J.Gollihar, A.D.Ellington, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.78 / 2.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.960, 96.360, 112.900, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 21.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp (pdb code 6wya). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp, PDB code: 6wya:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6wya

Go back to Magnesium Binding Sites List in 6wya
Magnesium binding site 1 out of 5 in the Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:87.5
occ:1.00
 O A:HOH983 2.3 88.5 0.7
O A:HOH904 2.3 40.8 0.3
O3' C:DT20 2.7 65.3 1.0
O C:HOH113 3.0 73.3 1.0
OD2 A:ASP542 3.2 56.5 1.0
O1A A:DZ4805 3.3 77.4 1.0
OD2 A:ASP404 3.5 62.3 1.0
N3A A:DZ4805 3.6 74.4 1.0
C3' C:DT20 3.9 60.8 1.0
PA A:DZ4805 4.0 73.3 1.0
CG A:ASP542 4.0 53.4 1.0
OD1 A:ASP542 4.1 53.8 1.0
C5' A:DZ4805 4.1 70.1 1.0
OH A:TYR402 4.3 52.2 1.0
CG A:ASP404 4.5 55.8 1.0
C2' C:DT20 4.6 61.0 1.0
O5' A:DZ4805 4.6 73.6 1.0
O A:HOH994 4.7 72.1 1.0
MG A:MG802 4.8 75.9 1.0
CB A:ASP404 4.8 43.7 1.0
O A:HOH1013 4.9 39.0 1.0

Magnesium binding site 2 out of 5 in 6wya

Go back to Magnesium Binding Sites List in 6wya
Magnesium binding site 2 out of 5 in the Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:75.9
occ:1.00
 O2G A:DZ4805 2.0 80.8 1.0
O A:HOH994 2.2 72.1 1.0
O A:HOH983 2.6 88.5 0.7
O A:HOH992 2.8 71.7 1.0
PG A:DZ4805 3.5 80.8 1.0
O1B A:DZ4805 3.6 80.2 1.0
OD2 A:ASP404 3.6 62.3 1.0
O3G A:DZ4805 4.1 81.3 1.0
N3A A:DZ4805 4.2 74.4 1.0
OE2 A:GLU578 4.3 68.3 1.0
PB A:DZ4805 4.3 78.4 1.0
O1G A:DZ4805 4.4 79.2 1.0
O3B A:DZ4805 4.4 83.0 1.0
CG A:ASP404 4.5 55.8 1.0
OD1 A:ASP404 4.7 59.3 1.0
MG A:MG801 4.8 87.5 1.0

Magnesium binding site 3 out of 5 in 6wya

Go back to Magnesium Binding Sites List in 6wya
Magnesium binding site 3 out of 5 in the Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:49.0
occ:1.00
 O A:HOH917 1.9 43.8 1.0
O A:HOH955 2.4 42.7 1.0
O A:HOH1126 2.4 53.4 1.0
O A:HOH1064 2.5 63.7 1.0
OD1 A:ASP141 2.5 54.3 1.0
MG A:MG804 2.8 57.4 1.0
OD2 A:ASP141 3.0 56.4 1.0
O A:HOH1123 3.1 68.0 1.0
CG A:ASP141 3.1 53.1 1.0
O A:HOH1103 3.7 52.0 1.0
OD2 A:ASP315 4.0 85.7 1.0
O A:ILE142 4.2 62.6 1.0
OE1 A:GLU143 4.2 73.9 1.0
O A:HOH1039 4.4 53.8 1.0
OD2 A:ASP215 4.5 68.1 1.0
CB A:ASP141 4.6 48.0 1.0
O A:TYR209 4.7 55.0 1.0
OD1 A:ASP215 4.8 65.6 1.0
CG A:ASP315 4.9 78.3 1.0

Magnesium binding site 4 out of 5 in 6wya

Go back to Magnesium Binding Sites List in 6wya
Magnesium binding site 4 out of 5 in the Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:57.4
occ:1.00
 OD2 A:ASP315 2.0 85.7 1.0
OE1 A:GLU143 2.3 73.9 1.0
OD2 A:ASP141 2.6 56.4 1.0
O A:HOH1123 2.8 68.0 1.0
MG A:MG803 2.8 49.0 1.0
CD A:GLU143 3.0 74.2 1.0
OE2 A:GLU143 3.1 75.7 1.0
CG A:ASP315 3.2 78.3 1.0
O A:HOH1103 3.2 52.0 1.0
CG A:ASP141 3.6 53.1 1.0
OH A:TYR311 3.6 71.2 1.0
O A:HOH1064 3.9 63.7 1.0
OD1 A:ASP141 3.9 54.3 1.0
OD1 A:ASP315 4.0 83.6 1.0
CE2 A:TYR311 4.0 67.9 1.0
CZ A:TYR311 4.1 67.4 1.0
O A:ILE142 4.1 62.6 1.0
CB A:ASP315 4.2 67.3 1.0
O A:HOH955 4.3 42.7 1.0
CG A:GLU143 4.5 71.5 1.0
O A:HOH1126 4.6 53.4 1.0
O A:HOH917 4.7 43.8 1.0
CB A:ASP141 5.0 48.0 1.0

Magnesium binding site 5 out of 5 in 6wya

Go back to Magnesium Binding Sites List in 6wya
Magnesium binding site 5 out of 5 in the Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Rtx (Reverse Transcription Xenopolymerase) in Complex with A Dna Duplex and Dampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:74.2
occ:1.00
 O B:HOH208 2.4 52.5 1.0
O B:HOH214 2.5 64.8 1.0
O B:HOH207 2.7 70.2 1.0
O C:HOH108 2.7 73.6 1.0
O6 B:DG5 3.1 56.7 1.0
N7 B:DA4 3.4 52.0 1.0
O B:HOH209 3.5 54.0 1.0
O B:HOH203 3.8 58.9 1.0
N7 B:DG5 3.9 47.9 1.0
C6 B:DG5 4.0 49.1 1.0
C5 B:DA4 4.1 49.6 1.0
N6 B:DA4 4.1 47.0 1.0
C8 B:DA4 4.2 48.2 1.0
C5 B:DG5 4.3 47.4 1.0
C6 B:DA4 4.5 52.8 1.0
N4 C:DC18 4.7 51.1 1.0
N4 C:DC19 5.0 52.8 1.0

Reference:

W.S.Choi, P.He, A.Pothukuchy, J.Gollihar, A.D.Ellington, W.Yang. How A B Family Dna Polymerase Has Been Evolved to Copy Rna. Proc.Natl.Acad.Sci.Usa V. 117 21274 2020.
ISSN: ESSN 1091-6490
PubMed: 32817521
DOI: 10.1073/PNAS.2009415117
Page generated: Tue Oct 1 23:19:43 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