Magnesium in PDB 6x71: REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp

Protein crystallography data

The structure of REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp, PDB code: 6x71 was solved by T.M.Weaver, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.63 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.269, 73.713, 117.221, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp (pdb code 6x71). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp, PDB code: 6x71:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6x71

Go back to Magnesium Binding Sites List in 6x71
Magnesium binding site 1 out of 4 in the REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg102

b:21.4
occ:0.50
O3' P:DG12 2.1 23.2 0.5
OP1 P:DC13 2.2 20.1 0.3
OD1 A:ASP362 2.2 28.4 1.0
O1A P:DCP106 2.2 20.7 0.7
O3' P:DG12 2.3 23.1 0.5
OD1 A:ASP467 2.4 22.6 1.0
OE2 A:GLU468 2.5 30.4 1.0
P P:DC13 2.6 19.9 0.3
O A:HOH1170 2.9 35.3 1.0
CG A:ASP467 3.1 20.7 1.0
OD2 A:ASP467 3.2 20.7 1.0
CG A:ASP362 3.3 20.1 1.0
C3' P:DG12 3.3 22.9 0.5
C3' P:DG12 3.3 23.1 0.5
PA P:DCP106 3.4 18.1 0.7
MG P:MG103 3.4 16.9 0.9
CD A:GLU468 3.5 27.3 1.0
CB A:GLU468 3.6 25.8 1.0
C4' P:DG12 3.7 22.7 0.5
OP2 P:DC13 3.7 22.8 0.3
O5' P:DCP106 3.7 18.8 0.7
OD2 A:ASP362 3.8 28.3 1.0
O5' P:DC13 3.8 18.9 0.3
C5' P:DCP106 3.8 17.9 0.7
OG A:SER465 3.8 24.8 1.0
O2A P:DCP106 3.9 23.5 0.7
C5' P:DC13 4.0 17.5 0.3
C5' P:DG12 4.1 25.5 0.5
CG A:GLU468 4.1 23.5 1.0
C2' P:DG12 4.3 19.8 0.5
O A:ASP467 4.4 14.1 1.0
C2' P:DG12 4.4 25.4 0.5
MG P:MG104 4.4 33.5 0.5
C4' P:DG12 4.4 26.2 0.5
C A:ASP467 4.5 15.0 1.0
OE1 A:GLU468 4.5 26.0 1.0
CB A:ASP467 4.6 16.8 1.0
CB A:ASP362 4.6 17.6 1.0
CA A:GLU468 4.7 16.0 1.0
O2 P:POP107 4.8 21.5 0.1
N A:GLU468 4.8 16.4 1.0
O2B P:DCP106 4.8 15.1 0.7
O3A P:DCP106 4.8 21.9 0.7
O6 P:POP107 4.8 20.3 0.1
C5' P:DG12 4.9 27.4 0.5
O3G P:DCP106 4.9 20.1 0.7
O3 P:POP107 4.9 15.6 0.1
O5' P:DG12 4.9 27.1 0.5
CB A:SER465 4.9 19.3 1.0
O5' P:DG12 5.0 26.7 0.5
CA A:ASP467 5.0 19.8 1.0

Magnesium binding site 2 out of 4 in 6x71

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Magnesium binding site 2 out of 4 in the REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg103

b:16.9
occ:0.95
OD2 A:ASP362 2.1 28.3 1.0
OP1 P:DC13 2.1 20.1 0.3
O2B P:DCP106 2.1 15.1 0.7
O1A P:DCP106 2.2 20.7 0.7
O3 P:POP107 2.2 15.6 0.1
O6 P:POP107 2.3 20.3 0.1
O A:PHE363 2.3 16.4 1.0
O3G P:DCP106 2.4 20.1 0.7
OD2 A:ASP467 2.4 20.7 1.0
CG A:ASP362 2.8 20.1 1.0
OD1 A:ASP362 3.0 28.4 1.0
P1 P:POP107 3.3 20.2 0.1
PB P:DCP106 3.3 20.3 0.7
PA P:DCP106 3.4 18.1 0.7
MG P:MG102 3.4 21.4 0.5
O2 P:POP107 3.4 21.5 0.1
P P:DC13 3.5 19.9 0.3
P2 P:POP107 3.5 21.6 0.1
C A:PHE363 3.5 20.0 1.0
CG A:ASP467 3.5 20.7 1.0
PG P:DCP106 3.5 21.6 0.7
O3A P:DCP106 3.6 21.9 0.7
O P:POP107 3.8 20.6 0.1
O3B P:DCP106 3.8 20.7 0.7
OD1 A:ASP467 4.0 22.6 1.0
C5' P:DCP106 4.0 17.9 0.7
N A:PHE363 4.0 14.3 1.0
MG P:MG104 4.1 33.5 0.5
NZ A:LYS525 4.1 23.3 1.0
O4 P:POP107 4.2 20.2 0.1
O1G P:DCP106 4.2 20.1 0.7
CB A:ASP362 4.2 17.6 1.0
CA A:PHE363 4.2 14.3 1.0
OP2 P:DC13 4.3 22.8 0.3
O5' P:DCP106 4.3 18.8 0.7
O5' P:DC13 4.3 18.9 0.3
C5' P:DC13 4.4 17.5 0.3
C A:ASP362 4.4 15.3 1.0
O A:HOH1170 4.4 35.3 1.0
O3' P:DG12 4.5 23.2 0.5
CB A:PHE363 4.5 14.3 1.0
O2A P:DCP106 4.5 23.5 0.7
CB A:PHE366 4.5 14.2 1.0
N A:ASP364 4.6 16.5 1.0
N A:CYS365 4.6 17.9 1.0
N A:PHE366 4.6 14.8 1.0
O1 P:POP107 4.6 17.5 0.1
O1B P:DCP106 4.6 17.3 0.7
CE A:LYS525 4.7 24.4 1.0
O5 P:POP107 4.7 22.1 0.1
CA A:ASP364 4.8 14.2 1.0
CA A:ASP362 4.8 17.2 1.0
O2G P:DCP106 4.8 22.1 0.7
CB A:ASP467 4.8 16.8 1.0
O A:ASP467 4.8 14.1 1.0
C A:ASP364 4.8 15.8 1.0
O A:ASP362 4.9 20.6 1.0

Magnesium binding site 3 out of 4 in 6x71

Go back to Magnesium Binding Sites List in 6x71
Magnesium binding site 3 out of 4 in the REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg104

b:33.5
occ:0.52
O A:HOH1170 2.4 35.3 1.0
O3G P:DCP106 2.9 20.1 0.7
O A:HOH1102 2.9 27.1 1.0
O6 P:POP107 3.0 20.3 0.1
NH2 A:ARG518 3.4 38.2 0.5
OD2 A:ASP362 3.5 28.3 1.0
O1A P:DCP106 3.5 20.7 0.7
O P:HOH205 3.7 28.1 1.0
O2G P:DCP106 3.8 22.1 0.7
OP2 P:DC13 3.8 22.8 0.3
O5 P:POP107 3.8 22.1 0.1
O2A P:DCP106 3.8 23.5 0.7
CE A:LYS525 3.9 24.4 1.0
CG A:ASP362 3.9 20.1 1.0
PG P:DCP106 3.9 21.6 0.7
P2 P:POP107 3.9 21.6 0.1
OP1 P:DC13 4.0 20.1 0.3
MG P:MG103 4.1 16.9 0.9
OD1 A:ASP362 4.1 28.4 1.0
PA P:DCP106 4.1 18.1 0.7
CZ A:ARG518 4.3 36.0 0.5
P P:DC13 4.3 19.9 0.3
MG P:MG102 4.4 21.4 0.5
O2 P:POP107 4.4 21.5 0.1
O3A P:DCP106 4.5 21.9 0.7
CD A:LYS525 4.6 28.7 1.0
O P:HOH209 4.6 33.1 1.0
OP1 P:DG12 4.7 31.6 0.5
NZ A:LYS525 4.7 23.3 1.0
CB A:ASP362 4.8 17.6 1.0
CD2 A:LEU521 4.8 18.1 1.0
NH1 A:ARG518 4.8 14.8 0.5
O3' P:DG12 4.9 23.2 0.5

Magnesium binding site 4 out of 4 in 6x71

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Magnesium binding site 4 out of 4 in the REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of REV1 MG2+-Facilitated Intermediate Complex with Reactant Dctp and Product Dcmp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg105

b:33.0
occ:1.00
O A:HOH932 2.4 43.6 1.0
OP1 P:DA11 2.6 30.3 0.4
OP1 P:DA11 2.7 30.5 0.6
O A:LEU550 2.8 25.0 1.0
O A:HOH1163 2.8 42.4 1.0
O A:ASP548 2.8 24.4 1.0
O A:VAL553 3.1 23.2 1.0
P P:DA11 3.6 27.2 0.4
OP2 P:DA11 3.7 26.9 0.4
P P:DA11 3.7 27.1 0.6
C A:LEU550 3.7 27.4 1.0
OP2 P:DA11 3.8 26.8 0.6
C A:ASP548 3.8 22.7 1.0
C A:VAL553 3.9 25.8 1.0
N A:VAL553 4.0 24.2 1.0
CA A:PRO551 4.2 26.7 1.0
C A:ASP549 4.2 25.5 1.0
N A:GLY552 4.3 28.4 1.0
N A:PRO551 4.3 24.9 1.0
O A:ASP549 4.3 24.3 1.0
N A:LEU550 4.4 25.8 1.0
CA A:VAL553 4.5 26.4 1.0
CA A:ASP548 4.5 29.3 1.0
C A:PRO551 4.6 27.6 1.0
CA A:ASP549 4.6 20.1 1.0
N A:ASP549 4.7 19.6 1.0
CA A:LEU550 4.7 25.2 1.0
O5' P:DA11 4.7 26.0 0.4
O3' P:DT10 4.8 24.8 1.0
O A:HOH928 4.8 52.2 1.0
CB A:ASP548 4.8 28.9 1.0
N A:GLY554 4.9 21.4 1.0
CB A:VAL553 4.9 25.8 1.0
O5' P:DA11 4.9 25.9 0.6
C A:GLY552 5.0 25.7 1.0

Reference:

T.M.Weaver, L.M.Cortez, T.H.Khoang, M.T.Washington, P.K.Agarwal, B.D.Freudenthal. Visualizing REV1 Catalyze Protein-Template Dna Synthesis. Proc.Natl.Acad.Sci.Usa V. 117 25494 2020.
ISSN: ESSN 1091-6490
PubMed: 32999062
DOI: 10.1073/PNAS.2010484117
Page generated: Tue Dec 15 01:40:41 2020

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