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Iodine in PDB 5a3d: Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa)

Protein crystallography data

The structure of Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa), PDB code: 5a3d was solved by J.Kuper, S.C.Koch, K.L.Gasteiger, N.Wichlein, S.Schneider, C.Kisker, T.Carell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.73 / 1.80
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 53.727, 53.727, 130.551, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 24.1

Other elements in 5a3d:

The structure of Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa) (pdb code 5a3d). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa), PDB code: 5a3d:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 5a3d

Go back to Iodine Binding Sites List in 5a3d
Iodine binding site 1 out of 6 in the Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I2

b:55.5
occ:0.55
I5 D:5IU2 0.0 55.5 0.6
C5 C:DC2 2.1 40.4 0.5
C5 D:5IU2 2.1 45.8 0.6
C4 C:DC2 2.9 40.2 0.5
C4 D:5IU2 3.0 45.5 0.6
N4 C:DC2 3.0 41.0 0.5
C6 C:DC2 3.0 39.6 0.5
C6 D:5IU2 3.1 43.5 0.6
O4 D:5IU2 3.1 45.9 0.6
OP1 C:DC2 3.6 43.4 0.5
N3 C:DC2 4.2 39.1 0.5
NE2 B:HIS258 4.2 40.0 1.0
OP2 C:DC2 4.2 42.3 0.5
N1 C:DC2 4.3 38.6 0.5
N3 D:5IU2 4.3 43.1 0.6
CE1 B:HIS258 4.3 43.4 1.0
N1 D:5IU2 4.4 40.9 0.6
OP1 D:5IU2 4.4 46.6 0.6
P C:DC2 4.4 42.5 0.5
O D:HOH2001 4.6 42.8 1.0
C2 C:DC2 4.7 38.3 0.5
C7 C:DT3 4.9 39.2 0.5
C2 D:5IU2 4.9 41.4 0.6
CD2 B:HIS258 5.0 38.4 1.0

Iodine binding site 2 out of 6 in 5a3d

Go back to Iodine Binding Sites List in 5a3d
Iodine binding site 2 out of 6 in the Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I2

b:53.5
occ:0.45
I5 D:5IU2 0.0 53.5 0.5
C5 D:5IU2 2.1 51.6 0.5
C5 C:DC2 2.1 34.1 0.6
C4 D:5IU2 3.0 51.5 0.5
C4 C:DC2 3.0 34.2 0.6
C6 D:5IU2 3.1 50.8 0.5
C6 C:DC2 3.1 33.1 0.6
N4 C:DC2 3.2 35.4 0.6
O4 D:5IU2 3.2 52.1 0.5
OP1 D:5IU2 3.7 50.7 0.5
OP1 C:DC2 3.9 43.0 0.6
OP2 D:5IU2 4.1 50.8 0.5
NE2 A:HIS258 4.2 41.1 1.0
N3 C:DC2 4.3 33.2 0.6
N1 C:DC2 4.3 32.1 0.6
N3 D:5IU2 4.3 50.6 0.5
CE1 A:HIS258 4.3 43.5 1.0
O C:HOH2001 4.4 40.1 1.0
N1 D:5IU2 4.4 49.8 0.5
OP2 C:DC2 4.4 42.2 0.6
P D:5IU2 4.4 50.3 0.5
P C:DC2 4.7 42.2 0.6
C2 C:DC2 4.9 32.2 0.6
C2 D:5IU2 4.9 49.9 0.5
CD2 A:HIS258 4.9 38.7 1.0

Iodine binding site 3 out of 6 in 5a3d

Go back to Iodine Binding Sites List in 5a3d
Iodine binding site 3 out of 6 in the Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I5

b:52.4
occ:0.55
I5 D:5IU5 0.0 52.4 0.6
C7 C:DT5 0.6 40.0 0.5
C5 C:DT5 1.8 40.5 0.5
C5 D:5IU5 2.2 47.6 0.6
C4 C:DT5 2.6 41.4 0.5
O4 C:DT5 2.8 41.8 0.5
OD2 B:ASP240 2.8 50.5 1.0
C6 C:DT5 2.9 40.4 0.5
C4 D:5IU5 3.1 48.1 0.6
O4 D:5IU5 3.2 47.9 0.6
C6 D:5IU5 3.3 46.7 0.6
C2' C:DC4 3.6 37.8 0.5
NZ B:LYS233 3.8 44.5 1.0
N3 C:DT5 3.9 42.0 0.5
C6 C:DC4 4.0 38.6 0.5
CG B:ASP240 4.0 45.1 1.0
C8 D:DA4 4.1 36.2 0.6
N1 C:DT5 4.1 41.1 0.5
O6 D:DG6 4.1 45.6 0.6
N7 D:DA4 4.2 36.6 0.6
N1 C:DC4 4.3 38.8 0.5
C1' C:DC4 4.5 38.1 0.5
N3 D:5IU5 4.5 48.5 0.6
C5 C:DC4 4.5 39.4 0.5
N9 D:DA4 4.5 36.7 0.6
C2 C:DT5 4.6 41.9 0.5
N6 C:DA6 4.6 43.4 0.5
OD1 B:ASP240 4.6 48.8 1.0
N1 D:5IU5 4.7 46.3 0.6
OP2 C:DT5 4.7 37.7 0.5
C5 D:DA4 4.8 37.7 0.6
C3' C:DC4 4.8 37.1 0.5
C2' D:DA4 4.8 36.1 0.6
N4 C:DC10 4.9 44.2 0.6
C6 D:DG6 4.9 47.0 0.6
C4 D:DA4 5.0 37.8 0.6

Iodine binding site 4 out of 6 in 5a3d

Go back to Iodine Binding Sites List in 5a3d
Iodine binding site 4 out of 6 in the Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I5

b:47.9
occ:0.45
I5 D:5IU5 0.0 47.9 0.5
C7 C:DT5 0.6 38.5 0.6
C5 C:DT5 2.0 39.6 0.6
C5 D:5IU5 2.2 48.5 0.5
C4 C:DT5 2.9 40.5 0.6
OD2 A:ASP240 3.0 52.6 1.0
C6 C:DT5 3.0 40.0 0.6
O4 C:DT5 3.1 40.6 0.6
C4 D:5IU5 3.1 49.3 0.5
C6 D:5IU5 3.2 48.2 0.5
O4 D:5IU5 3.3 49.6 0.5
NZ A:LYS233 3.8 47.6 1.0
C2' C:DC4 3.9 36.0 0.6
CG A:ASP240 4.0 46.5 1.0
C6 C:DC4 4.0 35.9 0.6
C8 D:DA4 4.0 47.3 0.5
N7 D:DA4 4.1 47.9 0.5
O6 D:DG6 4.1 50.6 0.5
N3 C:DT5 4.2 41.8 0.6
N1 C:DT5 4.3 41.5 0.6
N1 C:DC4 4.4 36.6 0.6
OD1 A:ASP240 4.5 51.3 1.0
N3 D:5IU5 4.5 49.7 0.5
C5 C:DC4 4.5 36.5 0.6
N1 D:5IU5 4.5 48.6 0.5
N9 D:DA4 4.5 47.4 0.5
C1' C:DC4 4.7 36.3 0.6
C5 D:DA4 4.7 48.4 0.5
N6 C:DA6 4.8 45.7 0.6
C2 C:DT5 4.8 42.0 0.6
C2' D:DA4 4.9 46.3 0.5
OP2 C:DT5 4.9 38.5 0.6
C4 D:DA4 4.9 48.1 0.5
C6 D:DG6 5.0 51.0 0.5
CB A:ASP240 5.0 42.2 1.0

Iodine binding site 5 out of 6 in 5a3d

Go back to Iodine Binding Sites List in 5a3d
Iodine binding site 5 out of 6 in the Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I10

b:86.7
occ:0.55
I5 D:5IU10 0.0 86.7 0.6
C5 C:DC10 2.0 43.8 0.5
C5 D:5IU10 2.1 72.8 0.6
C4 C:DC10 2.9 43.2 0.5
C6 C:DC10 2.9 44.2 0.5
O4 D:5IU10 2.9 65.8 0.6
C4 D:5IU10 3.0 68.8 0.6
N4 C:DC10 3.0 42.7 0.5
C6 D:5IU10 3.1 72.4 0.6
C6 C:DT9 4.1 48.5 0.5
C5 C:DT9 4.1 47.6 0.5
N3 C:DC10 4.2 43.1 0.5
C8 D:DG9 4.2 68.2 0.6
C7 C:DT9 4.2 47.4 0.5
N1 C:DC10 4.2 44.5 0.5
N3 D:5IU10 4.3 66.2 0.6
N7 D:DG9 4.3 65.6 0.6
N1 D:5IU10 4.5 69.2 0.6
N9 D:DG9 4.5 69.0 0.6
OP2 D:DG9 4.6 76.3 0.6
C2' D:DG9 4.6 72.7 0.6
C2 C:DC10 4.7 43.9 0.5
N1 C:DT9 4.7 48.9 0.5
C2' C:DT9 4.7 49.8 0.5
N6 C:DA11 4.8 44.1 0.5
C5 D:DG9 4.8 64.5 0.6
C4 C:DT9 4.8 47.2 0.5
C2 D:5IU10 4.9 67.8 0.6
C4 D:DG9 4.9 66.7 0.6

Iodine binding site 6 out of 6 in 5a3d

Go back to Iodine Binding Sites List in 5a3d
Iodine binding site 6 out of 6 in the Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesions By RAD14 (Xpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I10

b:71.2
occ:0.45
I5 D:5IU10 0.0 71.2 0.5
C5 C:DC10 1.8 46.5 0.6
C5 D:5IU10 2.2 67.5 0.5
C4 C:DC10 2.6 44.9 0.6
N4 C:DC10 2.6 44.2 0.6
C6 C:DC10 2.9 47.0 0.6
O4 D:5IU10 3.0 65.4 0.5
C4 D:5IU10 3.0 66.3 0.5
C6 D:5IU10 3.2 67.5 0.5
N7 D:DG9 3.6 59.6 0.5
C5 C:DT9 3.6 51.9 0.6
C8 D:DG9 3.7 60.6 0.5
C7 C:DT9 3.7 52.3 0.6
C6 C:DT9 3.7 53.5 0.6
N3 C:DC10 3.8 44.2 0.6
N1 C:DC10 4.1 46.7 0.6
C5 D:DG9 4.2 59.5 0.5
N9 D:DG9 4.3 61.1 0.5
C4 C:DT9 4.3 50.3 0.6
N3 D:5IU10 4.3 65.8 0.5
N1 C:DT9 4.4 53.6 0.6
C2 C:DC10 4.5 45.2 0.6
C5' D:DG9 4.5 62.2 0.5
N1 D:5IU10 4.5 66.4 0.5
C4 D:DG9 4.6 60.4 0.5
C2' C:DT9 4.7 56.8 0.6
N6 D:DA11 4.7 59.0 0.5
C2' D:DG9 4.8 62.6 0.5
O4 C:DT9 4.8 48.8 0.6
N3 C:DT9 4.8 50.4 0.6
C6 D:DG9 4.9 58.7 0.5
C2 D:5IU10 4.9 66.2 0.5
C2 C:DT9 5.0 51.8 0.6

Reference:

S.C.Koch, J.Kuper, K.L.Gasteiger, N.Simon, R.Strasser, D.Eisen, S.Geiger, S.Schneider, C.Kisker, T.Carell. Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesion By RAD14 (Xpa). Proc.Natl.Acad.Sci.Usa V. 112 8272 2015.
ISSN: ISSN 0027-8424
PubMed: 26100901
DOI: 10.1073/PNAS.1508509112
Page generated: Sun Dec 13 19:38:22 2020

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