Magnesium in PDB 5wmb: Structure of the 10S (-)-Cis-Bp-Dg Modified REV1 Ternary Complex (the Bp Residue Is Disordered)

Protein crystallography data

The structure of Structure of the 10S (-)-Cis-Bp-Dg Modified REV1 Ternary Complex (the Bp Residue Is Disordered), PDB code: 5wmb was solved by O.Rechkoblit, A.Kolbanovsky, H.Landes, N.E.Geacintov, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.83 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.307, 65.476, 131.657, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the 10S (-)-Cis-Bp-Dg Modified REV1 Ternary Complex (the Bp Residue Is Disordered) (pdb code 5wmb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the 10S (-)-Cis-Bp-Dg Modified REV1 Ternary Complex (the Bp Residue Is Disordered), PDB code: 5wmb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5wmb

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Magnesium binding site 1 out of 4 in the Structure of the 10S (-)-Cis-Bp-Dg Modified REV1 Ternary Complex (the Bp Residue Is Disordered)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the 10S (-)-Cis-Bp-Dg Modified REV1 Ternary Complex (the Bp Residue Is Disordered) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:34.5
occ:1.00
 O A:HOH934 1.9 46.9 1.0
O A:VAL553 2.2 29.9 1.0
O A:ASP548 2.2 27.7 1.0
O P:HOH204 2.2 32.8 1.0
OP1 P:DA11 2.7 34.8 0.7
O A:LEU550 2.9 33.7 1.0
OP2 P:DA11 3.0 33.2 0.7
OP1 P:DA11 3.0 33.9 0.3
C A:ASP548 3.2 26.0 1.0
C A:VAL553 3.3 30.7 1.0
P P:DA11 3.3 34.9 0.7
OP2 P:DA11 3.3 32.3 0.3
P P:DA11 3.6 34.1 0.3
CA A:ASP548 3.9 27.2 1.0
N A:VAL553 3.9 28.0 1.0
C A:LEU550 4.0 35.3 1.0
CA A:VAL553 4.1 28.5 1.0
CB A:ASP548 4.1 29.5 1.0
N A:GLY554 4.2 31.4 1.0
N A:ASP549 4.2 25.0 1.0
C A:ASP549 4.4 28.2 1.0
O5' P:DA11 4.4 34.3 0.7
CB A:VAL553 4.4 28.4 1.0
CA A:GLY554 4.4 30.9 1.0
CA A:ASP549 4.5 26.9 1.0
O3' P:DT10 4.5 32.8 1.0
NH2 A:ARG518 4.5 58.8 1.0
N A:LEU550 4.5 30.6 1.0
O A:ASP549 4.7 28.5 1.0
CA A:PRO551 4.7 36.1 1.0
N A:GLY552 4.7 31.2 1.0
N A:PRO551 4.8 35.5 1.0
CA A:LEU550 4.9 33.3 1.0
O5' P:DA11 4.9 33.6 0.3

Magnesium binding site 2 out of 4 in 5wmb

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Magnesium binding site 2 out of 4 in the Structure of the 10S (-)-Cis-Bp-Dg Modified REV1 Ternary Complex (the Bp Residue Is Disordered)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the 10S (-)-Cis-Bp-Dg Modified REV1 Ternary Complex (the Bp Residue Is Disordered) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:35.2
occ:1.00
 OD1 A:ASP467 2.2 23.8 1.0
O2A A:DCP804 2.4 21.6 1.0
OE2 A:GLU468 2.6 33.5 1.0
OD2 A:ASP467 2.8 21.9 1.0
CG A:ASP467 2.8 22.7 1.0
OD2 A:ASP362 3.0 29.6 1.0
C3' P:DDG12 3.1 43.2 0.6
MG A:MG802 3.3 22.0 1.0
PA A:DCP804 3.6 23.3 1.0
C3' P:DDG12 3.6 40.8 0.4
O A:HOH1004 3.7 43.1 1.0
MG A:MG803 3.7 35.8 1.0
C5' A:DCP804 3.7 23.8 1.0
CB A:GLU468 3.7 26.2 1.0
CD A:GLU468 3.7 30.4 1.0
OG A:SER465 3.8 23.4 0.5
CG A:ASP362 3.8 32.1 1.0
O5' A:DCP804 3.9 22.9 1.0
CB A:ASP362 3.9 29.4 1.0
C4' P:DDG12 4.0 44.5 0.6
C2' P:DDG12 4.0 41.1 0.4
CG A:GLU468 4.2 27.1 1.0
C2' P:DDG12 4.3 42.6 0.6
CB A:ASP467 4.3 22.6 1.0
O A:ASP467 4.3 20.7 1.0
C5' P:DDG12 4.3 44.1 0.6
O1A A:DCP804 4.4 23.8 1.0
C A:ASP467 4.4 23.9 1.0
C4' P:DDG12 4.4 40.2 0.4
O1B A:DCP804 4.7 23.2 1.0
OE1 A:GLU468 4.8 30.8 1.0
N A:GLU468 4.8 23.0 1.0
CA A:GLU468 4.8 25.0 1.0
CB A:SER465 4.8 23.5 0.5
CA A:ASP467 4.9 23.5 1.0
O3G A:DCP804 4.9 28.5 1.0
CB A:SER465 4.9 23.4 0.5
O3A A:DCP804 4.9 23.4 1.0

Magnesium binding site 3 out of 4 in 5wmb

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Magnesium binding site 3 out of 4 in the Structure of the 10S (-)-Cis-Bp-Dg Modified REV1 Ternary Complex (the Bp Residue Is Disordered)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the 10S (-)-Cis-Bp-Dg Modified REV1 Ternary Complex (the Bp Residue Is Disordered) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:22.0
occ:1.00
 OD2 A:ASP362 2.2 29.6 1.0
O A:PHE363 2.2 23.6 1.0
OD2 A:ASP467 2.2 21.9 1.0
O2A A:DCP804 2.2 21.6 1.0
O1B A:DCP804 2.2 23.2 1.0
O3G A:DCP804 2.6 28.5 1.0
MG A:MG803 3.0 35.8 1.0
CG A:ASP362 3.2 32.1 1.0
MG A:MG801 3.3 35.2 1.0
C A:PHE363 3.4 22.5 1.0
PB A:DCP804 3.4 24.1 1.0
CG A:ASP467 3.4 22.7 1.0
PA A:DCP804 3.5 23.3 1.0
PG A:DCP804 3.7 24.7 1.0
O3A A:DCP804 3.8 23.4 1.0
OD1 A:ASP362 3.9 42.3 1.0
N A:PHE363 3.9 24.0 1.0
O3B A:DCP804 4.0 24.4 1.0
C5' A:DCP804 4.0 23.8 1.0
OD1 A:ASP467 4.0 23.8 1.0
NZ A:LYS525 4.0 37.8 1.0
CB A:ASP362 4.1 29.4 1.0
CA A:PHE363 4.1 24.4 1.0
O5' A:DCP804 4.3 22.9 1.0
O2G A:DCP804 4.3 25.1 1.0
CB A:PHE363 4.4 24.9 1.0
C A:ASP362 4.5 24.4 1.0
N A:ASP364 4.5 23.0 1.0
CB A:PHE366 4.5 20.3 1.0
N A:PHE366 4.6 21.8 1.0
CE A:LYS525 4.6 39.5 1.0
CB A:ASP467 4.6 22.6 1.0
CA A:ASP364 4.7 22.8 1.0
N A:CYS365 4.7 22.0 1.0
O1A A:DCP804 4.8 23.8 1.0
O2B A:DCP804 4.8 23.2 1.0
O A:HOH980 4.8 52.9 1.0
O A:ASP467 4.8 20.7 1.0
C A:ASP364 4.9 22.3 1.0
CA A:ASP362 4.9 26.1 1.0
O1G A:DCP804 5.0 25.9 1.0

Magnesium binding site 4 out of 4 in 5wmb

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Magnesium binding site 4 out of 4 in the Structure of the 10S (-)-Cis-Bp-Dg Modified REV1 Ternary Complex (the Bp Residue Is Disordered)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the 10S (-)-Cis-Bp-Dg Modified REV1 Ternary Complex (the Bp Residue Is Disordered) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:35.8
occ:1.00
 O3G A:DCP804 2.2 28.5 1.0
OD2 A:ASP362 2.2 29.6 1.0
O A:HOH980 2.3 52.9 1.0
O2A A:DCP804 2.5 21.6 1.0
O A:HOH1026 2.5 37.0 1.0
O A:HOH1004 2.6 43.1 1.0
MG A:MG802 3.0 22.0 1.0
CG A:ASP362 3.2 32.1 1.0
PA A:DCP804 3.4 23.3 1.0
PG A:DCP804 3.5 24.7 1.0
OD1 A:ASP362 3.6 42.3 1.0
CE A:LYS525 3.7 39.5 1.0
MG A:MG801 3.7 35.2 1.0
O1A A:DCP804 3.8 23.8 1.0
O1G A:DCP804 3.9 25.9 1.0
O3A A:DCP804 4.0 23.4 1.0
NZ A:LYS525 4.2 37.8 1.0
O1B A:DCP804 4.4 23.2 1.0
O3B A:DCP804 4.4 24.4 1.0
OE2 A:GLU468 4.5 33.5 1.0
CB A:ASP362 4.5 29.4 1.0
O A:HOH1029 4.5 52.9 1.0
CD A:LYS525 4.5 39.0 1.0
O A:PHE363 4.5 23.6 1.0
PB A:DCP804 4.6 24.1 1.0
O2G A:DCP804 4.6 25.1 1.0
OD2 A:ASP467 4.8 21.9 1.0
O5' A:DCP804 4.9 22.9 1.0

Reference:

O.Rechkoblit, A.Kolbanovskiy, H.Landes, N.E.Geacintov, A.K.Aggarwal. Mechanism of Error-Free Replication Across Benzo[A]Pyrene Stereoisomers By REV1 Dna Polymerase. Nat Commun V. 8 965 2017.
ISSN: ESSN 2041-1723
PubMed: 29042535
DOI: 10.1038/S41467-017-01013-5
Page generated: Mon Dec 14 21:21:27 2020

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