Atomistry » Magnesium » PDB 4b3a-4be2 » 4ba9
Atomistry »
  Magnesium »
    PDB 4b3a-4be2 »
      4ba9 »

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

Go back to Magnesium Binding Sites List in 4ba9
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

Go back to Magnesium Binding Sites List in 4ba9
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

Go back to Magnesium Binding Sites List in 4ba9
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

Go back to Magnesium Binding Sites List in 4ba9
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

Go back to Magnesium Binding Sites List in 4ba9
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: Thu Aug 15 15:23:43 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