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Nickel 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:

Magnesium (Mg) 8 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 10 binding sites of Nickel where determined in the The Structural Basis For the Coordination of Y-Family Translesion Dna Polymerases By REV1, PDB code: 4ba9:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 10 in 4ba9

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Nickel binding site 1 out of 10 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 Nickel with other atoms in the Ni 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:Ni2244

b:48.9
occ:1.00
 NE2 A:HIS203 2.0 38.0 1.0
NE2 A:HIS205 2.0 56.2 1.0
N B:GLY201 2.0 44.6 1.0
O A:HOH2005 2.1 46.7 1.0
O B:GLY201 2.2 46.4 1.0
C B:GLY201 2.9 47.8 1.0
CA B:GLY201 2.9 44.0 1.0
CD2 A:HIS205 3.0 57.0 1.0
CD2 A:HIS203 3.0 38.0 1.0
CE1 A:HIS203 3.0 37.6 1.0
CE1 A:HIS205 3.1 55.8 1.0
O B:HOH2003 3.9 46.8 1.0
CG A:HIS205 4.1 55.3 1.0
CG A:HIS203 4.1 37.5 1.0
ND1 A:HIS203 4.2 38.2 1.0
ND1 A:HIS205 4.2 56.5 1.0
N B:PRO202 4.2 42.5 1.0
ND1 B:HIS203 4.5 37.5 1.0
O B:PRO202 4.8 43.5 1.0
O B:HOH2001 4.9 51.6 1.0
C B:PRO202 4.9 43.4 1.0
CA B:PRO202 5.0 41.3 1.0
O B:HOH2002 5.0 56.3 1.0

Nickel binding site 2 out of 10 in 4ba9

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Nickel binding site 2 out of 10 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 Nickel with other atoms in the Ni 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
A:Ni2245

b:57.3
occ:1.00
 OD2 D:ASP211 1.7 46.1 1.0
OD2 A:ASP211 1.8 66.0 1.0
OE2 D:GLU1185 1.9 52.9 1.0
OE2 A:GLU1185 1.9 46.3 1.0
CG D:ASP211 2.7 40.7 1.0
CG A:ASP211 2.7 55.5 1.0
CD D:GLU1185 3.0 68.4 1.0
CD A:GLU1185 3.0 66.2 1.0
OD1 D:ASP211 3.1 39.0 1.0
OD1 A:ASP211 3.1 49.9 1.0
OE1 D:GLU1185 3.3 53.0 1.0
OE1 A:GLU1185 3.3 68.2 1.0
O A:HOH2018 3.9 62.3 1.0
CB D:ASP211 4.0 46.3 1.0
O A:HOH2014 4.1 61.7 1.0
CB A:ASP211 4.1 55.3 1.0
NE2 D:GLN1189 4.2 41.8 1.0
NE2 A:GLN1189 4.2 42.0 1.0
CG D:GLU1185 4.3 55.3 1.0
CG A:GLU1185 4.3 51.2 1.0
O A:HOH2009 4.4 53.2 1.0
CB D:SER208 4.4 45.6 1.0
OG D:SER208 4.5 44.6 1.0
CB A:SER208 4.5 68.2 1.0
OG A:SER208 4.6 74.5 1.0

Nickel binding site 3 out of 10 in 4ba9

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Nickel binding site 3 out of 10 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 Nickel with other atoms in the Ni 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:Ni2245

b:47.6
occ:1.00
 NE2 B:HIS203 2.0 37.8 1.0
N A:GLY201 2.0 34.4 1.0
NE2 B:HIS205 2.1 53.2 1.0
O A:GLY201 2.2 44.5 1.0
C A:GLY201 2.9 42.8 1.0
CA A:GLY201 2.9 34.7 1.0
CE1 B:HIS203 3.0 37.2 1.0
CD2 B:HIS203 3.0 38.5 1.0
CE1 B:HIS205 3.0 52.8 1.0
CD2 B:HIS205 3.1 53.4 1.0
O A:HOH2001 3.7 44.0 1.0
ND1 B:HIS203 4.1 37.5 1.0
CG B:HIS203 4.1 36.6 1.0
ND1 B:HIS205 4.2 52.9 1.0
CG B:HIS205 4.2 51.1 1.0
N A:PRO202 4.2 39.9 1.0
ND1 A:HIS203 4.3 38.2 1.0
O A:PRO202 4.8 44.0 1.0
C A:PRO202 4.9 43.9 1.0
CA A:PRO202 4.9 39.1 1.0
CB A:HIS203 5.0 35.4 1.0

Nickel binding site 4 out of 10 in 4ba9

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Nickel binding site 4 out of 10 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 Nickel with other atoms in the Ni 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
B:Ni2246

b:44.4
occ:1.00
 OE2 B:GLU1185 1.7 68.5 1.0
OD2 C:ASP211 1.8 83.9 1.0
OE2 C:GLU1185 1.9 33.8 1.0
OD2 B:ASP211 1.9 31.0 1.0
CG C:ASP211 2.7 74.3 1.0
CD B:GLU1185 2.8 71.6 1.0
CG B:ASP211 2.8 44.9 1.0
OD1 C:ASP211 3.0 74.7 1.0
CD C:GLU1185 3.0 47.5 1.0
OD1 B:ASP211 3.1 51.0 1.0
OE1 B:GLU1185 3.2 71.3 1.0
OE1 C:GLU1185 3.4 53.4 1.0
NE2 B:GLN1189 4.0 35.5 1.0
NE2 C:GLN1189 4.1 63.7 1.0
CG B:GLU1185 4.1 52.1 1.0
CB C:ASP211 4.1 56.8 1.0
CB B:ASP211 4.2 43.5 1.0
CG C:GLU1185 4.2 39.3 1.0
O B:HOH2006 4.3 49.7 1.0
O B:HOH2024 4.3 43.3 1.0
CB B:SER208 4.5 46.3 1.0
OG B:SER208 4.6 46.5 1.0
OG C:SER208 4.6 59.6 1.0
CB C:SER208 4.6 60.1 1.0
O C:HOH2016 4.9 49.1 1.0

Nickel binding site 5 out of 10 in 4ba9

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Nickel binding site 5 out of 10 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 Nickel with other atoms in the Ni 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:Ni2244

b:57.3
occ:1.00
 NE2 C:HIS205 1.9 68.1 1.0
N D:GLY201 1.9 42.2 1.0
O D:HOH2001 1.9 39.2 1.0
NE2 C:HIS203 2.1 41.6 1.0
O D:GLY201 2.2 46.4 1.0
O C:HOH2004 2.4 55.5 1.0
CE1 C:HIS205 2.8 68.0 1.0
CA D:GLY201 2.9 42.0 1.0
C D:GLY201 2.9 46.1 1.0
CD2 C:HIS205 2.9 68.5 1.0
CD2 C:HIS203 3.1 42.5 1.0
CE1 C:HIS203 3.2 41.2 1.0
ND1 C:HIS205 4.0 68.9 1.0
CG C:HIS205 4.0 67.3 1.0
O D:HOH2002 4.1 46.1 1.0
N D:PRO202 4.2 42.2 1.0
CG C:HIS203 4.2 41.8 1.0
O C:HOH2003 4.3 52.8 1.0
ND1 C:HIS203 4.3 42.7 1.0
ND1 D:HIS203 4.4 47.2 1.0
O D:PRO202 4.7 50.1 1.0
C D:PRO202 4.8 49.1 1.0
CA D:PRO202 4.9 42.1 1.0
CB D:HIS203 5.0 42.6 1.0

Nickel binding site 6 out of 10 in 4ba9

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Nickel binding site 6 out of 10 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 Nickel with other atoms in the Ni 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
D:Ni2245

b:52.2
occ:1.00
 N C:GLY201 1.9 37.5 1.0
NE2 D:HIS205 2.0 47.1 1.0
O D:HOH2004 2.0 40.1 1.0
OXT E:GLN1242 2.1 66.9 1.0
NE2 D:HIS203 2.1 46.3 1.0
O C:GLY201 2.2 45.7 1.0
C C:GLY201 2.9 45.5 1.0
CA C:GLY201 2.9 38.3 1.0
CE1 D:HIS205 2.9 47.3 1.0
CD2 D:HIS205 3.1 47.9 1.0
CD2 D:HIS203 3.1 46.9 1.0
CE1 D:HIS203 3.1 46.2 1.0
C E:GLN1242 3.2 60.9 1.0
O E:GLN1242 3.7 64.4 1.0
ND1 D:HIS205 4.1 48.7 1.0
CG D:HIS205 4.2 47.5 1.0
N C:PRO202 4.2 43.9 1.0
CG D:HIS203 4.2 45.3 1.0
ND1 D:HIS203 4.2 47.2 1.0
O C:HOH2001 4.2 45.6 1.0
ND1 C:HIS203 4.3 42.7 1.0
O D:HOH2003 4.3 43.1 1.0
CA E:GLN1242 4.4 47.1 1.0
O C:PRO202 4.7 48.2 1.0
C C:PRO202 4.8 48.1 1.0
CA C:PRO202 4.9 44.1 1.0
O E:GLN1241 4.9 51.8 1.0
CG C:HIS203 4.9 41.8 1.0
CB C:HIS203 4.9 39.8 1.0

Nickel binding site 7 out of 10 in 4ba9

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Nickel binding site 7 out of 10 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 Nickel with other atoms in the Ni 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:Ni2245

b:53.2
occ:1.00
 NE2 E:HIS205 1.9 57.5 1.0
N F:GLY201 2.0 39.8 1.0
NE2 E:HIS203 2.0 48.5 1.0
O F:GLY201 2.2 46.6 1.0
CD2 E:HIS205 2.8 57.8 1.0
C F:GLY201 2.9 46.0 1.0
CA F:GLY201 3.0 39.5 1.0
CD2 E:HIS203 3.0 49.2 1.0
CE1 E:HIS205 3.0 57.6 1.0
CE1 E:HIS203 3.1 48.5 1.0
CG E:HIS205 4.0 57.0 1.0
ND1 E:HIS205 4.1 58.7 1.0
CG E:HIS203 4.1 48.3 1.0
ND1 E:HIS203 4.2 50.0 1.0
N F:PRO202 4.3 42.5 1.0
ND1 F:HIS203 4.4 41.4 1.0
O F:PRO202 4.8 41.1 1.0
C F:PRO202 4.9 41.9 1.0
CA F:PRO202 5.0 41.3 1.0
CB F:HIS203 5.0 36.8 1.0

Nickel binding site 8 out of 10 in 4ba9

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Nickel binding site 8 out of 10 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 Nickel with other atoms in the Ni 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
E:Ni2246

b:37.7
occ:0.50
 OE2 E:GLU1185 2.1 38.7 1.0
OD2 E:ASP211 2.4 60.2 1.0
CD E:GLU1185 3.2 45.1 1.0
CG E:ASP211 3.3 53.4 1.0
OD1 E:ASP211 3.5 54.5 1.0
OE1 E:GLU1185 3.6 49.4 1.0
CG E:GLU1185 4.4 35.3 1.0
NE2 E:GLN1189 4.5 44.5 1.0
CB E:ASP211 4.6 45.8 1.0

Nickel binding site 9 out of 10 in 4ba9

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Nickel binding site 9 out of 10 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 Nickel with other atoms in the Ni binding site number 9 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:Ni2244

b:59.6
occ:1.00
 NE2 F:HIS205 1.9 61.3 1.0
N E:GLY201 2.0 53.5 1.0
NE2 F:HIS203 2.1 40.1 1.0
O E:HOH2001 2.2 34.6 1.0
O E:GLY201 2.2 51.3 1.0
CE1 F:HIS205 2.9 61.3 1.0
C E:GLY201 2.9 53.4 1.0
CA E:GLY201 2.9 52.3 1.0
CD2 F:HIS205 2.9 61.5 1.0
CD2 F:HIS203 3.0 40.3 1.0
CE1 F:HIS203 3.1 40.0 1.0
ND1 F:HIS205 4.0 61.9 1.0
CG F:HIS205 4.0 59.7 1.0
CG F:HIS203 4.2 39.4 1.0
ND1 F:HIS203 4.2 41.4 1.0
N E:PRO202 4.2 50.9 1.0
ND1 E:HIS203 4.3 50.0 1.0
O E:PRO202 4.8 52.6 1.0
C E:PRO202 4.8 52.4 1.0
CB E:HIS203 4.9 45.0 1.0
CG E:HIS203 4.9 48.3 1.0
CA E:PRO202 4.9 50.8 1.0

Nickel binding site 10 out of 10 in 4ba9

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Nickel binding site 10 out of 10 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 Nickel with other atoms in the Ni binding site number 10 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:Ni2245

b:40.5
occ:0.50
 OE2 F:GLU1185 2.3 53.8 1.0
OD2 F:ASP211 2.4 65.3 1.0
CD F:GLU1185 3.3 68.5 1.0
CG F:ASP211 3.4 58.9 1.0
OD1 F:ASP211 3.6 58.6 1.0
OE1 F:GLU1185 3.6 66.7 1.0
CG F:GLU1185 4.6 48.4 1.0
NE2 F:GLN1189 4.7 43.4 1.0
CB F:ASP211 4.7 58.9 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: Wed Oct 9 18:01:32 2024

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