Iodine in PDB 5td5: Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna

Protein crystallography data

The structure of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna, PDB code: 5td5 was solved by K.Shi, S.Banerjee, K.Kurahashi, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.49 / 1.72
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 96.411, 96.411, 84.875, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 20.9

Other elements in 5td5:

The structure of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna (pdb code 5td5). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna, PDB code: 5td5:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 5td5

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Iodine binding site 1 out of 9 in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:38.4
occ:0.75
H A:TYR338 2.9 41.3 1.0
HE21 A:GLN367 2.9 65.2 1.0
HG2 A:GLU363 3.0 58.0 0.4
HA A:GLU363 3.3 44.9 0.6
HA A:GLU363 3.3 44.7 0.4
HB3 A:SER366 3.5 44.5 1.0
HG3 A:GLN367 3.5 47.7 1.0
HB2 A:TYR338 3.5 38.8 1.0
HB A:THR337 3.6 41.5 1.0
HG3 A:GLU363 3.6 61.5 0.6
N A:TYR338 3.7 34.4 1.0
HA A:THR337 3.7 36.0 1.0
NE2 A:GLN367 3.8 54.4 1.0
CG A:GLU363 3.9 48.4 0.4
HB3 A:GLU363 3.9 52.0 0.4
HB3 A:GLU363 4.0 50.9 0.6
OG A:SER366 4.0 38.8 1.0
HB3 A:TYR338 4.1 38.8 1.0
HG2 A:GLU363 4.1 61.5 0.6
CB A:SER366 4.2 37.1 1.0
CA A:GLU363 4.2 37.2 0.4
CB A:TYR338 4.2 32.4 1.0
CG A:GLU363 4.2 51.3 0.6
CA A:GLU363 4.2 37.4 0.6
CB A:GLU363 4.2 43.4 0.4
HE22 A:GLN367 4.2 65.2 1.0
O A:HOH565 4.3 39.9 1.0
CG A:GLN367 4.3 39.8 1.0
CB A:GLU363 4.3 42.4 0.6
CB A:THR337 4.3 34.6 1.0
HD23 A:LEU362 4.3 43.5 1.0
CA A:THR337 4.4 30.0 1.0
HG3 A:GLU363 4.4 58.0 0.4
HG22 A:THR337 4.4 48.8 1.0
HG2 A:GLN367 4.5 47.7 1.0
HB2 A:SER366 4.5 44.5 1.0
CD A:GLN367 4.5 48.5 1.0
C A:THR337 4.6 34.0 1.0
CA A:TYR338 4.6 29.3 1.0
O A:GLU363 4.6 34.7 0.4
O A:GLU363 4.6 32.5 0.6
HD22 A:LEU362 4.6 43.5 1.0
HD21 A:LEU362 4.7 43.5 1.0
HG A:SER366 4.8 46.6 1.0
CD2 A:LEU362 4.8 36.2 1.0
CD A:GLU363 4.8 57.7 0.4
CG2 A:THR337 4.9 40.7 1.0
C A:GLU363 4.9 34.5 0.4
C A:GLU363 4.9 33.9 0.6
H A:GLN367 4.9 38.7 1.0
HA A:TYR338 5.0 35.2 1.0

Iodine binding site 2 out of 9 in 5td5

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Iodine binding site 2 out of 9 in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:0.8
occ:0.30
O A:HOH569 3.1 38.0 1.0
HG3 A:ARG304 3.2 37.4 1.0
O A:HOH591 3.3 46.5 1.0
HB2 A:ARG304 3.4 33.9 1.0
HD3 A:ARG274 3.6 69.3 1.0
HB3 A:ARG304 3.6 33.9 1.0
HB2 A:ARG274 3.8 42.5 1.0
CB A:ARG304 3.9 28.2 1.0
CG A:ARG304 4.0 31.1 1.0
HG3 A:ARG274 4.0 54.3 1.0
HH11 A:ARG304 4.2 38.7 1.0
HG21 A:ILE272 4.2 44.5 1.0
CD A:ARG274 4.4 57.8 1.0
HG22 A:ILE272 4.4 44.5 1.0
O A:HOH585 4.4 54.0 0.8
CG A:ARG274 4.5 45.2 1.0
CB A:ARG274 4.5 35.5 1.0
HD2 A:ARG274 4.5 69.3 1.0
HG2 A:ARG304 4.6 37.4 1.0
CG2 A:ILE272 4.7 37.1 1.0
HA A:ARG274 4.7 35.7 1.0
HD2 A:ARG304 4.8 42.4 1.0
NH1 A:ARG304 4.9 32.2 1.0
HH11 A:ARG274 4.9 0.1 1.0
O A:HOH568 4.9 46.2 1.0
HG23 A:ILE272 4.9 44.5 1.0

Iodine binding site 3 out of 9 in 5td5

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Iodine binding site 3 out of 9 in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:81.1
occ:0.79
H A:ASP194 2.8 57.9 1.0
HG21 A:THR197 3.1 60.1 1.0
HG3 A:MET193 3.1 51.3 1.0
HB3 A:ASP194 3.3 71.7 1.0
HE2 A:PHE237 3.5 59.2 1.0
HA A:MET193 3.6 54.5 1.0
HB A:THR197 3.6 66.5 1.0
N A:ASP194 3.7 48.2 1.0
OG1 A:THR197 3.8 53.4 1.0
CG2 A:THR197 3.9 50.1 1.0
CB A:THR197 4.0 55.4 1.0
HE2 A:TYR215 4.0 50.2 1.0
CG A:MET193 4.0 42.7 1.0
CB A:ASP194 4.0 59.7 1.0
HB2 A:ASP194 4.0 71.7 1.0
HH A:TYR215 4.1 65.7 1.0
HG2 A:MET193 4.1 51.3 1.0
HG1 A:THR197 4.2 64.1 1.0
CE2 A:PHE237 4.2 49.4 1.0
HZ A:PHE237 4.2 62.3 1.0
CA A:MET193 4.3 45.4 1.0
HG22 A:THR197 4.4 60.1 1.0
CA A:ASP194 4.5 50.0 1.0
C A:MET193 4.5 55.4 1.0
CZ A:PHE237 4.6 52.0 1.0
HG23 A:THR197 4.6 60.1 1.0
CE2 A:TYR215 4.7 41.8 1.0
CB A:MET193 4.7 40.4 1.0
OH A:TYR215 4.7 54.7 1.0
HB2 A:MET193 4.9 48.5 1.0

Iodine binding site 4 out of 9 in 5td5

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Iodine binding site 4 out of 9 in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:79.3
occ:0.80
H A:HIS212 2.7 42.7 1.0
HD2 A:ARG211 2.7 69.3 1.0
O2 C:DT-2 3.2 0.7 1.0
HD3 A:ARG211 3.3 69.3 1.0
HB2 A:HIS212 3.3 50.3 1.0
HD2 A:HIS212 3.4 58.3 1.0
CD A:ARG211 3.4 57.8 1.0
HB3 A:ARG211 3.4 53.1 1.0
N A:HIS212 3.5 35.6 1.0
HA A:ARG211 3.6 46.1 1.0
H61 C:DA1 3.8 83.7 1.0
C2 C:DT-2 3.8 89.5 1.0
N6 C:DA1 3.8 69.8 1.0
H62 C:DA1 3.9 83.7 1.0
H3 C:DT-2 4.1 0.4 1.0
CB A:ARG211 4.1 44.3 1.0
CB A:HIS212 4.1 41.9 1.0
CA A:ARG211 4.1 38.4 1.0
CD2 A:HIS212 4.2 48.6 1.0
C6 C:DA1 4.2 67.0 1.0
N3 C:DT-2 4.2 86.2 1.0
CA A:HIS212 4.3 32.8 1.0
C A:ARG211 4.3 33.1 1.0
CG A:ARG211 4.4 55.5 1.0
NE A:ARG211 4.4 74.4 1.0
H1' C:DT-2 4.5 0.8 1.0
CG A:HIS212 4.5 40.0 1.0
O A:HOH577 4.5 54.0 1.0
H2'' C:DT-2 4.6 98.6 1.0
HG2 A:LYS213 4.6 62.4 1.0
N1 C:DT-2 4.6 84.7 1.0
N1 C:DA1 4.6 62.5 1.0
HE A:ARG211 4.7 89.3 1.0
C5 C:DA1 4.8 63.3 1.0
C A:HIS212 4.8 42.2 1.0
HG3 A:ARG211 4.8 66.6 1.0
HB3 A:HIS212 4.9 50.3 1.0
C1' C:DT-2 4.9 91.5 1.0
I C:IOD101 5.0 0.4 0.3
HB2 A:ARG211 5.0 53.1 1.0
HG3 A:LYS213 5.0 62.4 1.0
HH11 A:ARG211 5.0 91.3 1.0

Iodine binding site 5 out of 9 in 5td5

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Iodine binding site 5 out of 9 in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:0.4
occ:0.30
HD2 A:ARG372 3.0 53.0 1.0
HH11 A:ARG372 3.2 42.4 1.0
O A:HOH582 3.3 53.9 1.0
HD23 A:LEU369 3.4 41.8 1.0
HB1 A:ALA368 3.5 40.6 1.0
HD3 A:ARG372 3.7 53.0 1.0
CD A:ARG372 3.8 44.2 1.0
HD21 A:LEU369 3.8 41.8 1.0
HB3 A:ALA368 3.9 40.6 1.0
HG A:LEU369 3.9 38.9 1.0
I A:IOD408 4.0 0.6 0.8
NH1 A:ARG372 4.0 35.3 1.0
CD2 A:LEU369 4.0 34.8 1.0
HA A:LEU369 4.1 37.5 1.0
CB A:ALA368 4.1 33.8 1.0
HH12 A:ARG372 4.4 42.4 1.0
CG A:LEU369 4.5 32.4 1.0
N A:LEU369 4.5 30.8 1.0
C A:ALA368 4.5 32.1 1.0
HB2 A:ARG372 4.6 41.5 1.0
HG3 A:ARG372 4.6 57.0 1.0
CL A:CL416 4.6 49.9 1.0
NE A:ARG372 4.7 37.9 1.0
O A:ALA368 4.7 30.7 1.0
H A:LEU369 4.7 37.0 1.0
CG A:ARG372 4.7 47.5 1.0
CZ A:ARG372 4.8 37.6 1.0
CA A:LEU369 4.8 31.2 1.0
HD22 A:LEU369 4.8 41.8 1.0
HB2 A:ALA368 4.9 40.6 1.0
CA A:ALA368 5.0 31.9 1.0

Iodine binding site 6 out of 9 in 5td5

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Iodine binding site 6 out of 9 in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:0.1
occ:0.30
HB2 A:ASP194 4.0 71.7 1.0
CB A:ASP194 4.9 59.7 1.0

Iodine binding site 7 out of 9 in 5td5

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Iodine binding site 7 out of 9 in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I408

b:0.6
occ:0.80
HB1 A:ALA368 3.6 40.6 1.0
I A:IOD406 4.0 0.4 0.3
CB A:ALA368 4.5 33.8 1.0
HB2 A:ALA368 4.5 40.6 1.0
HB3 A:ALA368 4.9 40.6 1.0

Iodine binding site 8 out of 9 in 5td5

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Iodine binding site 8 out of 9 in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I409

b:78.4
occ:0.80
HA2 A:GLY330 3.2 41.2 1.0
HA3 A:GLY330 4.0 41.2 1.0
CA A:GLY330 4.0 34.4 1.0
N A:GLY330 4.6 30.1 1.0
H A:GLY330 4.7 36.1 1.0

Iodine binding site 9 out of 9 in 5td5

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Iodine binding site 9 out of 9 in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I101

b:0.4
occ:0.30
H61 C:DA1 2.6 83.7 1.0
N6 C:DA1 3.4 69.8 1.0
N1 C:DA1 4.0 62.5 1.0
H62 C:DA1 4.0 83.7 1.0
C6 C:DA1 4.2 67.0 1.0
O A:HOH559 4.3 53.6 1.0
HE3 A:LYS213 4.8 71.3 1.0
I A:IOD405 5.0 79.3 0.8

Reference:

K.Shi, M.A.Carpenter, S.Banerjee, N.M.Shaban, K.Kurahashi, D.J.Salamango, J.L.Mccann, G.J.Starrett, J.V.Duffy, O.Demir, R.E.Amaro, D.A.Harki, R.S.Harris, H.Aihara. Structural Basis For Targeted Dna Cytosine Deamination and Mutagenesis By APOBEC3A and APOBEC3B. Nat. Struct. Mol. Biol. V. 24 131 2017.
ISSN: ESSN 1545-9985
PubMed: 27991903
DOI: 10.1038/NSMB.3344
Page generated: Sun Dec 13 19:41:06 2020

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