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Iodine in PDB 6eg7: Bbvci B2 Dimer with I3C Clusters

Protein crystallography data

The structure of Bbvci B2 Dimer with I3C Clusters, PDB code: 6eg7 was solved by B.W.Shen, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.38 / 3.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 93.888, 168.245, 106.477, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 26.2

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iodine atom in the Bbvci B2 Dimer with I3C Clusters (pdb code 6eg7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 24 binding sites of Iodine where determined in the Bbvci B2 Dimer with I3C Clusters, PDB code: 6eg7:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 24 in 6eg7

Go back to Iodine Binding Sites List in 6eg7
Iodine binding site 1 out of 24 in the Bbvci B2 Dimer with I3C Clusters


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Bbvci B2 Dimer with I3C Clusters within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:64.1
occ:1.00
 I3 A:I3C305 0.0 64.1 1.0
C6 A:I3C305 2.1 88.0 1.0
OD1 A:ASP146 2.9 30.8 1.0
C5 A:I3C305 3.1 83.1 1.0
C1 A:I3C305 3.1 97.2 1.0
N13 A:I3C305 3.3 77.2 1.0
C7 A:I3C305 3.3 86.0 1.0
O9 A:I3C305 3.7 74.8 1.0
O A:HIS145 3.7 22.5 1.0
O8 A:I3C305 3.8 78.1 1.0
CA A:ASP146 3.8 22.5 1.0
C A:HIS145 3.9 23.7 1.0
N A:ASP146 3.9 25.2 1.0
CG A:ASP146 4.0 27.6 1.0
O2 A:EDO301 4.1 20.0 1.0
OE2 A:GLU92 4.3 29.8 1.0
CB A:ASP144 4.4 28.2 1.0
O1 A:EDO301 4.4 20.0 1.0
C4 A:I3C305 4.5 84.9 1.0
C2 A:I3C305 4.5 0.9 1.0
CB A:ASP146 4.5 24.5 1.0
CB A:PRO115 4.5 13.8 1.0
C2 A:EDO301 4.6 20.0 1.0
C1 A:EDO301 4.6 20.0 1.0
N A:HIS145 4.8 24.3 1.0
CA A:HIS145 4.8 22.7 1.0
C A:ASP146 4.8 20.6 1.0
C A:ASP144 4.9 26.5 1.0
CD A:GLU92 4.9 32.0 1.0
O A:ASP146 5.0 21.5 1.0

Iodine binding site 2 out of 24 in 6eg7

Go back to Iodine Binding Sites List in 6eg7
Iodine binding site 2 out of 24 in the Bbvci B2 Dimer with I3C Clusters


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Bbvci B2 Dimer with I3C Clusters within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:83.8
occ:1.00
 I2 A:I3C305 0.0 83.8 1.0
C4 A:I3C305 2.1 84.9 1.0
C3 A:I3C305 3.1 97.5 1.0
C5 A:I3C305 3.1 83.1 1.0
N13 A:I3C305 3.3 77.2 1.0
C10 A:I3C305 3.3 91.2 1.0
O11 A:I3C305 3.6 81.6 1.0
O12 A:I3C305 3.9 82.9 1.0
CG A:LYS117 3.9 18.7 1.0
CA A:ALA116 4.0 14.7 1.0
C A:ALA116 4.1 15.5 1.0
N A:LYS117 4.2 16.1 1.0
OD1 A:ASP144 4.3 39.1 1.0
N A:ALA116 4.3 15.4 1.0
O A:HOH405 4.5 0.5 1.0
C6 A:I3C305 4.5 88.0 1.0
C2 A:I3C305 4.5 0.9 1.0
CE A:LYS117 4.6 23.8 1.0
C A:PRO115 4.6 16.2 1.0
O A:PRO115 4.6 16.1 1.0
NZ A:LYS117 4.7 26.7 1.0
O A:ALA116 4.7 15.5 1.0
CG A:ASP144 4.8 33.5 1.0
CB A:LYS117 4.9 16.2 1.0
CD A:LYS117 4.9 21.9 1.0
CA A:LYS117 5.0 15.1 1.0

Iodine binding site 3 out of 24 in 6eg7

Go back to Iodine Binding Sites List in 6eg7
Iodine binding site 3 out of 24 in the Bbvci B2 Dimer with I3C Clusters


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Bbvci B2 Dimer with I3C Clusters within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:0.1
occ:1.00
 I1 A:I3C305 0.0 0.1 1.0
C2 A:I3C305 2.1 0.9 1.0
C1 A:I3C305 3.1 97.2 1.0
C3 A:I3C305 3.1 97.5 1.0
C7 A:I3C305 3.3 86.0 1.0
C10 A:I3C305 3.3 91.2 1.0
O12 A:I3C305 3.6 82.9 1.0
O8 A:I3C305 3.7 78.1 1.0
O9 A:I3C305 3.8 74.8 1.0
O11 A:I3C305 3.9 81.6 1.0
I3 A:I3C306 4.1 0.5 1.0
C6 A:I3C305 4.5 88.0 1.0
C4 A:I3C305 4.5 84.9 1.0
NZ A:LYS15 4.9 52.6 1.0

Iodine binding site 4 out of 24 in 6eg7

Go back to Iodine Binding Sites List in 6eg7
Iodine binding site 4 out of 24 in the Bbvci B2 Dimer with I3C Clusters


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Bbvci B2 Dimer with I3C Clusters within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:0.5
occ:1.00
 I3 A:I3C306 0.0 0.5 1.0
C6 A:I3C306 2.1 81.2 1.0
C1 A:I3C306 3.1 73.5 1.0
C5 A:I3C306 3.1 72.0 1.0
N13 A:I3C306 3.3 66.8 1.0
C7 A:I3C306 3.3 62.6 1.0
O8 A:I3C306 3.6 51.7 1.0
O9 A:I3C306 3.9 61.0 1.0
I1 A:I3C305 4.1 0.1 1.0
C2 A:I3C306 4.5 73.7 1.0
C4 A:I3C306 4.5 71.9 1.0
CG1 A:VAL85 4.8 72.2 1.0

Iodine binding site 5 out of 24 in 6eg7

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Iodine binding site 5 out of 24 in the Bbvci B2 Dimer with I3C Clusters


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Bbvci B2 Dimer with I3C Clusters within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:94.8
occ:1.00
 I2 A:I3C306 0.0 94.8 1.0
C4 A:I3C306 2.1 71.9 1.0
C5 A:I3C306 3.1 72.0 1.0
C3 A:I3C306 3.1 70.4 1.0
OE1 A:GLU84 3.1 74.4 1.0
N13 A:I3C306 3.3 66.8 1.0
C10 A:I3C306 3.3 61.4 1.0
O12 A:I3C306 3.6 52.1 1.0
O A:HOH407 3.6 30.0 1.0
O11 A:I3C306 3.9 62.8 1.0
CB A:SER81 4.1 97.9 1.0
CD A:GLU84 4.4 71.0 1.0
C6 A:I3C306 4.5 81.2 1.0
C2 A:I3C306 4.5 73.7 1.0
CB A:GLU84 4.5 64.3 1.0
CG1 A:VAL85 4.6 72.2 1.0
O A:SER81 4.7 96.7 1.0
NZ A:LYS22 4.8 42.2 1.0
OG A:SER81 4.9 0.9 1.0

Iodine binding site 6 out of 24 in 6eg7

Go back to Iodine Binding Sites List in 6eg7
Iodine binding site 6 out of 24 in the Bbvci B2 Dimer with I3C Clusters


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Bbvci B2 Dimer with I3C Clusters within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:58.8
occ:1.00
 I1 A:I3C306 0.0 58.8 1.0
C2 A:I3C306 2.1 73.7 1.0
C3 A:I3C306 3.1 70.4 1.0
C1 A:I3C306 3.1 73.5 1.0
C10 A:I3C306 3.3 61.4 1.0
C7 A:I3C306 3.3 62.6 1.0
CE A:LYS22 3.3 46.7 1.0
NZ A:LYS22 3.5 42.2 1.0
O11 A:I3C306 3.6 62.8 1.0
CB A:LYS19 3.6 39.1 1.0
O9 A:I3C306 3.6 61.0 1.0
O A:LYS15 3.8 33.0 1.0
O8 A:I3C306 3.9 51.7 1.0
CA A:LYS19 3.9 34.7 1.0
N A:LYS19 3.9 36.1 1.0
O12 A:I3C306 3.9 52.1 1.0
CG1 A:VAL85 4.2 72.2 1.0
CB A:LYS15 4.2 31.6 1.0
CD A:ARG18 4.2 54.1 1.0
CA A:LYS15 4.4 31.0 1.0
C A:LYS15 4.4 31.2 1.0
CG A:ARG18 4.5 50.9 1.0
C4 A:I3C306 4.5 71.9 1.0
C6 A:I3C306 4.5 81.2 1.0
CG A:LYS19 4.5 45.5 1.0
C A:ARG18 4.6 39.8 1.0
CG A:LYS15 4.6 40.0 1.0
CB A:ARG18 4.6 44.6 1.0
CD A:LYS19 4.6 50.9 1.0
O A:VAL85 4.8 92.5 1.0
CD A:LYS22 4.8 44.3 1.0
CD1 A:LEU86 4.9 39.9 1.0

Iodine binding site 7 out of 24 in 6eg7

Go back to Iodine Binding Sites List in 6eg7
Iodine binding site 7 out of 24 in the Bbvci B2 Dimer with I3C Clusters


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Bbvci B2 Dimer with I3C Clusters within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:62.5
occ:1.00
 I3 A:I3C307 0.0 62.5 1.0
C6 A:I3C307 2.1 51.8 1.0
C5 A:I3C307 3.1 51.8 1.0
C1 A:I3C307 3.1 48.7 1.0
N13 A:I3C307 3.3 48.6 1.0
C7 A:I3C307 3.3 50.2 1.0
CB A:MET36 3.4 21.6 1.0
O9 A:I3C307 3.7 49.9 1.0
O8 A:I3C307 3.8 55.5 1.0
ND2 A:ASN40 4.1 22.7 1.0
CG A:MET36 4.2 23.3 1.0
C A:MET36 4.4 23.1 1.0
C4 A:I3C307 4.5 50.2 1.0
C2 A:I3C307 4.5 45.0 1.0
CA A:MET36 4.5 21.6 1.0
N A:GLU37 4.6 23.1 1.0
O A:MET36 4.7 24.1 1.0

Iodine binding site 8 out of 24 in 6eg7

Go back to Iodine Binding Sites List in 6eg7
Iodine binding site 8 out of 24 in the Bbvci B2 Dimer with I3C Clusters


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Bbvci B2 Dimer with I3C Clusters within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:73.8
occ:1.00
 I2 A:I3C307 0.0 73.8 1.0
C4 A:I3C307 2.1 50.2 1.0
C5 A:I3C307 3.1 51.8 1.0
C3 A:I3C307 3.1 46.9 1.0
O12 A:I3C307 3.2 49.5 1.0
N13 A:I3C307 3.3 48.6 1.0
C10 A:I3C307 3.3 48.4 1.0
CD A:GLU37 3.8 20.5 1.0
CG A:GLU37 3.9 20.1 1.0
OE1 A:GLU37 4.1 18.6 1.0
OE2 A:GLU37 4.2 20.8 1.0
O11 A:I3C307 4.2 57.7 1.0
C6 A:I3C307 4.5 51.8 1.0
C2 A:I3C307 4.5 45.0 1.0
CB A:GLU37 4.6 20.3 1.0

Iodine binding site 9 out of 24 in 6eg7

Go back to Iodine Binding Sites List in 6eg7
Iodine binding site 9 out of 24 in the Bbvci B2 Dimer with I3C Clusters


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Bbvci B2 Dimer with I3C Clusters within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:39.6
occ:1.00
 I1 A:I3C307 0.0 39.6 1.0
C2 A:I3C307 2.1 45.0 1.0
C3 A:I3C307 3.1 46.9 1.0
C1 A:I3C307 3.1 48.7 1.0
O11 A:I3C307 3.2 57.7 1.0
C10 A:I3C307 3.3 48.4 1.0
C7 A:I3C307 3.3 50.2 1.0
O8 A:I3C307 3.7 55.5 1.0
O9 A:I3C307 3.8 49.9 1.0
O12 A:I3C307 4.2 49.5 1.0
C6 A:I3C307 4.5 51.8 1.0
C4 A:I3C307 4.5 50.2 1.0

Iodine binding site 10 out of 24 in 6eg7

Go back to Iodine Binding Sites List in 6eg7
Iodine binding site 10 out of 24 in the Bbvci B2 Dimer with I3C Clusters


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Bbvci B2 Dimer with I3C Clusters within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I308

b:83.1
occ:1.00
 I3 A:I3C308 0.0 83.1 1.0
C6 A:I3C308 2.1 0.3 1.0
C1 A:I3C308 3.1 0.1 1.0
C5 A:I3C308 3.1 0.8 1.0
N13 A:I3C308 3.3 0.2 1.0
C7 A:I3C308 3.3 0.5 1.0
O A:HOH401 3.4 30.0 1.0
O9 A:I3C308 3.7 90.8 1.0
O8 A:I3C308 3.8 84.6 1.0
O A:GLY159 3.8 24.2 1.0
C A:GLY159 3.9 24.7 1.0
O A:GLN158 4.1 26.2 1.0
N A:HIS160 4.1 26.9 1.0
CA A:HIS160 4.4 31.3 1.0
CA A:GLY159 4.4 23.1 1.0
C2 A:I3C308 4.5 0.1 1.0
C4 A:I3C308 4.5 0.2 1.0
C A:GLN158 4.9 23.4 1.0

Reference:

B.W.Shen, L.Doyle, P.Bradley, D.F.Heiter, K.D.Lunnen, G.G.Wilson, B.L.Stoddard. Structure, Subunit Organization and Behavior of the Asymmetric Type Iit Restriction Endonuclease Bbvci. Nucleic Acids Res. V. 47 450 2019.
ISSN: ESSN 1362-4962
PubMed: 30395313
DOI: 10.1093/NAR/GKY1059
Page generated: Sun Aug 11 23:04:50 2024

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