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Magnesium in PDB 4ba9: The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1

Protein crystallography data

The structure of The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1, PDB code: 4ba9 was solved by C.G.Grummitt, M.L.Kilkenny, A.Frey, S.M.Roe, A.W.Oliver, J.E.Sale, L.H.Pearl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.82 / 2.73
Space group H 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.750, 105.750, 424.270, 90.00, 90.00, 120.00
R / Rfree (%) 21.44 / 25.01

Other elements in 4ba9:

The structure of The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1 also contains other interesting chemical elements:

Nickel (Ni) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1 (pdb code 4ba9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1, PDB code: 4ba9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4ba9

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Magnesium binding site 1 out of 8 in the The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2243

b:67.3
occ:1.00
 OD1 A:ASP1234 2.3 88.2 1.0
O A:HOH2025 2.9 41.4 1.0
CG A:ASP1234 3.0 85.6 1.0
OD2 A:ASP1234 3.1 92.5 1.0
CB A:ASP1230 4.2 64.2 1.0
OD1 A:ASP1230 4.3 87.2 1.0
CG A:ASP1230 4.4 83.7 1.0
O A:ASP1230 4.4 64.9 1.0
CB A:ASP1234 4.5 67.2 1.0
CA A:ASP1230 4.5 61.7 1.0
CD2 A:LEU1233 4.6 73.3 1.0
C A:ASP1230 4.8 64.5 1.0

Magnesium binding site 2 out of 8 in 4ba9

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Magnesium binding site 2 out of 8 in the The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2243

b:59.5
occ:1.00
 O B:HOH2044 2.3 46.7 1.0
OD1 B:ASP1234 2.3 59.0 1.0
O B:HOH2042 2.3 76.5 1.0
O B:HOH2045 2.8 82.8 1.0
OD2 B:ASP1234 2.9 70.1 1.0
CG B:ASP1234 2.9 60.3 1.0
O E:HOH2007 4.1 69.3 1.0
CB B:ASP1234 4.4 47.4 1.0
CB B:ASP1230 4.5 45.3 1.0
O B:ASP1230 4.6 46.7 1.0
OD1 B:ASP1230 4.7 64.6 1.0
CG B:ASP1230 4.7 63.1 1.0
CD1 E:LEU1203 4.7 96.2 1.0
CA B:ASP1230 4.8 41.6 1.0
O E:LYS1201 5.0 91.2 1.0

Magnesium binding site 3 out of 8 in 4ba9

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Magnesium binding site 3 out of 8 in the The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2244

b:57.7
occ:1.00
 O B:HOH2047 2.2 72.1 1.0
O B:HOH2018 2.5 58.1 1.0
OD2 D:ASP1181 2.7 73.3 1.0
OD1 D:ASP1181 3.0 62.8 1.0
O B:HOH2019 3.2 63.3 1.0
CG D:ASP1181 3.2 65.6 1.0
OD2 B:ASP1181 3.3 79.0 1.0
OD1 B:ASP1181 3.3 61.6 1.0
CG B:ASP1181 3.7 62.2 1.0
O B:HOH2034 4.2 46.1 1.0
O B:PRO1182 4.5 39.4 1.0
O D:PRO1182 4.5 53.2 1.0
CB D:ASP1181 4.7 57.5 1.0
CE B:MET1183 4.9 41.8 1.0

Magnesium binding site 4 out of 8 in 4ba9

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Magnesium binding site 4 out of 8 in the The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2243

b:63.1
occ:1.00
 OD2 C:ASP1234 2.1 92.0 1.0
O C:HOH2017 2.2 56.1 1.0
CG C:ASP1234 3.0 83.0 1.0
OD1 C:ASP1234 3.3 84.8 1.0
CB C:ASP1230 4.3 60.1 1.0
CB C:ASP1234 4.4 62.0 1.0
CG C:ASP1230 4.7 80.2 1.0
O C:ASP1230 4.9 58.8 1.0

Magnesium binding site 5 out of 8 in 4ba9

Go back to Magnesium Binding Sites List in 4ba9
Magnesium binding site 5 out of 8 in the The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2243

b:79.3
occ:1.00
 OD1 D:ASP1234 2.3 72.3 1.0
O D:HOH2033 2.8 53.0 1.0
CG D:ASP1234 3.3 70.9 1.0
OD2 D:ASP1234 3.6 79.5 1.0
CD2 D:LEU1233 4.0 58.8 1.0
OD1 D:ASP1230 4.3 69.1 1.0
O D:ASP1230 4.4 46.8 1.0
CB D:ASP1230 4.4 49.5 1.0
CA D:ASP1230 4.5 46.0 1.0
CG D:ASP1230 4.5 68.3 1.0
OE1 D:GLN1237 4.6 0.8 1.0
CB D:ASP1234 4.7 50.9 1.0
CG D:LEU1233 4.7 53.7 1.0
C D:ASP1230 4.9 47.1 1.0
N D:ASP1234 4.9 49.7 1.0

Magnesium binding site 6 out of 8 in 4ba9

Go back to Magnesium Binding Sites List in 4ba9
Magnesium binding site 6 out of 8 in the The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg2243

b:74.8
occ:1.00
 OD2 E:ASP1181 3.0 89.7 1.0
OD1 E:ASP1181 3.4 76.1 1.0
CG E:ASP1181 3.6 77.9 1.0
CE E:MET1183 4.5 53.2 0.5
O E:PRO1182 4.6 54.4 1.0

Magnesium binding site 7 out of 8 in 4ba9

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Magnesium binding site 7 out of 8 in the The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg2244

b:64.5
occ:1.00
 O E:HOH2010 1.9 54.1 1.0
OD2 E:ASP1234 1.9 76.5 1.0
O E:HOH2012 2.2 85.6 1.0
CG E:ASP1234 2.9 71.5 1.0
OD1 E:ASP1234 3.1 76.0 1.0
CB E:ASP1230 4.0 64.3 1.0
CB E:ASP1234 4.3 52.2 1.0
O E:HOH2009 4.5 74.0 1.0
CG E:ASP1230 4.5 91.5 1.0
O E:ASP1230 4.6 63.1 1.0
C E:ASP1230 4.7 60.7 1.0
CA E:ASP1230 4.8 60.6 1.0
OD2 E:ASP1230 4.9 0.4 1.0

Magnesium binding site 8 out of 8 in 4ba9

Go back to Magnesium Binding Sites List in 4ba9
Magnesium binding site 8 out of 8 in the The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2243

b:61.0
occ:1.00
 O F:HOH2012 2.5 59.0 1.0
O F:HOH2011 2.5 69.1 1.0
OD2 F:ASP1234 2.6 84.0 1.0
OD1 F:ASP1234 2.9 78.0 1.0
CG F:ASP1234 3.1 76.2 1.0
O F:HOH2016 3.2 76.1 1.0
CB F:ASP1230 3.9 61.6 1.0
CG F:ASP1230 4.1 81.2 1.0
OD1 F:ASP1230 4.4 85.0 1.0
CA F:ASP1230 4.6 59.2 1.0
OD2 F:ASP1230 4.6 90.5 1.0
O F:ASP1230 4.6 62.5 1.0
CB F:ASP1234 4.6 60.4 1.0
C F:ASP1230 4.8 62.4 1.0

Reference:

C.G.Grummitt, M.L.Kilkenny, A.Frey, S.M.Roe, A.W.Oliver, J.E.Sale, L.H.Pearl. The Structural Basis For the Coordination of Y- Family Translesion Dna Polymerases By REV1 To Be Published.
Page generated: Mon Dec 14 09:11:23 2020

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