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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

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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

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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

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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

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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

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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

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