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Iodine in PDB 8ail: Bacillus Phage VMY22 P56 in Complex with Bacillus Weidmannii Ung

Enzymatic activity of Bacillus Phage VMY22 P56 in Complex with Bacillus Weidmannii Ung

All present enzymatic activity of Bacillus Phage VMY22 P56 in Complex with Bacillus Weidmannii Ung:
3.2.2.27;

Protein crystallography data

The structure of Bacillus Phage VMY22 P56 in Complex with Bacillus Weidmannii Ung, PDB code: 8ail was solved by W.Muselmani, C.Bagneris, R.Savva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.87 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.327, 97.495, 100.555, 90, 111.36, 90
R / Rfree (%) 20.4 / 23.7

Iodine Binding Sites:

The binding sites of Iodine atom in the Bacillus Phage VMY22 P56 in Complex with Bacillus Weidmannii Ung (pdb code 8ail). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Bacillus Phage VMY22 P56 in Complex with Bacillus Weidmannii Ung, PDB code: 8ail:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 8ail

Go back to Iodine Binding Sites List in 8ail
Iodine binding site 1 out of 4 in the Bacillus Phage VMY22 P56 in Complex with Bacillus Weidmannii Ung


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Bacillus Phage VMY22 P56 in Complex with Bacillus Weidmannii Ung within 5.0Å range:
probe atom residue distance (Å) B Occ
I:I303

b:49.6
occ:1.00
 H I:GLY140 2.9 25.6 1.0
HB2 I:GLU142 2.9 33.4 1.0
H I:GLU142 3.0 29.3 1.0
HA2 I:GLY138 3.2 29.3 1.0
O I:HOH412 3.2 21.1 1.0
HA2 I:GLY140 3.3 24.7 1.0
H I:HIS143 3.5 32.3 1.0
N I:GLY140 3.6 25.4 1.0
CA I:GLY140 3.7 24.8 1.0
N I:GLU142 3.8 29.1 1.0
CB I:GLU142 3.8 33.3 1.0
C I:GLY140 3.9 23.9 1.0
H I:GLY138 3.9 28.9 1.0
CA I:GLY138 4.0 28.9 1.0
H I:LYS139 4.0 30.2 1.0
O I:HOH405 4.1 25.9 1.0
H I:TRP141 4.1 23.3 1.0
N I:TRP141 4.1 22.7 1.0
N I:HIS143 4.2 32.7 1.0
CA I:GLU142 4.2 32.0 1.0
N I:LYS139 4.2 30.6 1.0
C I:GLY138 4.2 30.0 1.0
NE2 I:HIS143 4.3 36.0 1.0
CD2 I:HIS143 4.3 31.4 1.0
O I:GLY140 4.3 23.7 1.0
N I:GLY138 4.4 29.6 1.0
HE2 I:HIS143 4.4 35.9 0.0
HG3 I:GLU142 4.4 34.9 1.0
HB3 I:GLU142 4.4 33.4 1.0
HD2 I:HIS143 4.4 33.0 1.0
C I:GLU142 4.6 33.0 1.0
CE1 I:HIS143 4.6 35.5 1.0
CG I:HIS143 4.6 33.4 1.0
CG I:GLU142 4.7 35.1 1.0
HA3 I:GLY140 4.7 24.7 1.0
C I:LYS139 4.7 26.5 1.0
HA3 I:GLY138 4.8 29.3 1.0
ND1 I:HIS143 4.8 36.1 1.0
C I:TRP141 4.8 27.1 1.0
O I:HOH423 4.9 20.1 1.0
HE1 I:HIS143 5.0 35.6 1.0
O I:GLY138 5.0 30.6 1.0

Iodine binding site 2 out of 4 in 8ail

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Iodine binding site 2 out of 4 in the Bacillus Phage VMY22 P56 in Complex with Bacillus Weidmannii Ung


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Bacillus Phage VMY22 P56 in Complex with Bacillus Weidmannii Ung within 5.0Å range:
probe atom residue distance (Å) B Occ
M:I302

b:68.8
occ:1.00
 H M:GLY140 2.8 46.4 1.0
H M:GLU142 2.9 37.0 1.0
HB2 M:GLU142 3.1 45.4 1.0
HA2 M:GLY138 3.1 43.2 1.0
HA2 M:GLY140 3.2 44.4 1.0
N M:GLY140 3.5 47.4 1.0
H M:HIS143 3.5 40.7 1.0
CA M:GLY140 3.6 43.8 1.0
N M:GLU142 3.7 35.2 1.0
C M:GLY140 3.8 42.8 1.0
H M:GLY138 3.8 41.6 1.0
CA M:GLY138 3.9 42.5 1.0
O M:HOH411 3.9 34.9 1.0
H M:LYS139 3.9 47.5 1.0
CB M:GLU142 4.0 45.8 1.0
OE1 M:GLU142 4.0 54.3 1.0
H M:TRP141 4.0 41.0 1.0
N M:TRP141 4.0 41.7 1.0
N M:LYS139 4.1 47.6 1.0
C M:GLY138 4.2 47.3 1.0
O M:GLY140 4.2 42.0 1.0
N M:HIS143 4.2 41.4 1.0
CA M:GLU142 4.3 41.8 1.0
CD2 M:HIS143 4.3 37.3 1.0
N M:GLY138 4.3 41.0 1.0
HD2 M:HIS143 4.3 37.3 1.0
NE2 M:HIS143 4.3 36.5 1.0
HE2 M:HIS143 4.4 35.9 0.0
CD M:GLU142 4.5 53.7 1.0
HA3 M:GLY140 4.6 44.4 1.0
C M:LYS139 4.6 46.8 1.0
HB3 M:GLU142 4.6 45.4 1.0
C M:GLU142 4.6 40.4 1.0
CG M:GLU142 4.6 48.3 1.0
HA3 M:GLY138 4.7 43.2 1.0
CG M:HIS143 4.7 38.3 1.0
HG3 M:GLU142 4.7 48.9 1.0
C M:TRP141 4.8 36.4 1.0
CE1 M:HIS143 4.8 38.6 1.0
O M:GLY138 4.9 58.1 1.0
ND1 M:HIS143 5.0 34.9 1.0
CA M:TRP141 5.0 37.9 1.0

Iodine binding site 3 out of 4 in 8ail

Go back to Iodine Binding Sites List in 8ail
Iodine binding site 3 out of 4 in the Bacillus Phage VMY22 P56 in Complex with Bacillus Weidmannii Ung


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Bacillus Phage VMY22 P56 in Complex with Bacillus Weidmannii Ung within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:52.9
occ:1.00
 HB2 A:GLU142 2.9 29.2 1.0
H A:GLY140 2.9 26.8 1.0
H A:GLU142 3.0 25.3 1.0
HA2 A:GLY138 3.1 27.3 1.0
HA2 A:GLY140 3.2 26.5 1.0
O A:HOH413 3.5 17.2 1.0
H A:HIS143 3.6 27.6 1.0
N A:GLY140 3.6 26.3 1.0
CA A:GLY140 3.7 26.4 1.0
N A:GLU142 3.8 24.7 1.0
H A:GLY138 3.8 27.6 1.0
CB A:GLU142 3.8 29.0 1.0
C A:GLY140 3.9 26.9 1.0
CA A:GLY138 3.9 27.1 1.0
H A:LYS139 4.1 29.0 1.0
N A:TRP141 4.2 24.1 1.0
H A:TRP141 4.2 24.4 1.0
CA A:GLU142 4.2 28.0 1.0
N A:HIS143 4.2 26.8 1.0
C A:GLY138 4.2 27.6 1.0
O A:HOH402 4.2 15.3 1.0
O A:GLY140 4.3 28.4 1.0
N A:LYS139 4.3 29.1 1.0
N A:GLY138 4.3 27.4 1.0
NE2 A:HIS143 4.3 31.1 1.0
CD2 A:HIS143 4.3 30.1 1.0
HB3 A:GLU142 4.4 29.2 1.0
HG3 A:GLU142 4.4 30.9 1.0
HE2 A:HIS143 4.4 31.4 0.0
HD2 A:HIS143 4.4 30.0 1.0
C A:GLU142 4.6 28.3 1.0
CG A:GLU142 4.6 31.1 1.0
HA3 A:GLY140 4.7 26.5 1.0
HA3 A:GLY138 4.7 27.3 1.0
CG A:HIS143 4.7 28.5 1.0
CE1 A:HIS143 4.7 32.1 1.0
C A:LYS139 4.8 27.9 1.0
C A:TRP141 4.8 23.7 1.0
ND1 A:HIS143 4.9 32.2 1.0
O A:GLY138 5.0 25.6 1.0

Iodine binding site 4 out of 4 in 8ail

Go back to Iodine Binding Sites List in 8ail
Iodine binding site 4 out of 4 in the Bacillus Phage VMY22 P56 in Complex with Bacillus Weidmannii Ung


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Bacillus Phage VMY22 P56 in Complex with Bacillus Weidmannii Ung within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I303

b:60.3
occ:1.00
 H B:GLY140 2.8 30.6 1.0
HB2 B:GLU142 3.0 36.5 1.0
H B:GLU142 3.0 33.4 1.0
HA2 B:GLY138 3.1 33.1 1.0
HA2 B:GLY140 3.3 31.2 1.0
O B:HOH409 3.4 20.0 1.0
N B:GLY140 3.5 30.8 1.0
H B:HIS143 3.5 35.8 1.0
CA B:GLY140 3.7 30.7 1.0
N B:GLU142 3.8 32.8 1.0
C B:GLY140 3.9 33.0 1.0
CA B:GLY138 3.9 32.8 1.0
CB B:GLU142 3.9 36.7 1.0
H B:GLY138 3.9 33.2 1.0
H B:LYS139 4.0 31.8 1.0
C B:GLY138 4.1 33.0 1.0
N B:LYS139 4.1 31.5 1.0
O B:HOH405 4.1 19.2 1.0
N B:TRP141 4.2 31.3 1.0
H B:TRP141 4.2 31.7 1.0
N B:HIS143 4.2 36.0 1.0
CD2 B:HIS143 4.2 40.6 1.0
CA B:GLU142 4.3 34.5 1.0
NE2 B:HIS143 4.3 39.1 1.0
O B:GLY140 4.3 35.8 1.0
HD2 B:HIS143 4.3 39.5 1.0
HE2 B:HIS143 4.3 39.4 0.0
N B:GLY138 4.4 33.7 1.0
HG3 B:GLU142 4.4 38.5 1.0
HB3 B:GLU142 4.4 36.5 1.0
C B:LYS139 4.6 29.7 1.0
C B:GLU142 4.6 33.2 1.0
HA3 B:GLY140 4.6 31.2 1.0
HA3 B:GLY138 4.6 33.0 1.0
CG B:HIS143 4.6 38.1 1.0
CE1 B:HIS143 4.7 36.1 1.0
CG B:GLU142 4.7 38.2 1.0
O B:GLY138 4.8 33.0 1.0
C B:TRP141 4.8 33.2 1.0
ND1 B:HIS143 4.9 38.5 1.0

Reference:

W.Muselmani, N.Kashif-Khan, C.Bagneris, R.Santangelo, M.A.Williams, R.Savva. A Multimodal Approach Towards Genomic Identification of Protein Inhibitors of Uracil-Dna Glycosylase Viruses V. 15 2023.
ISSN: ESSN 1999-4915
DOI: 10.3390/V15061348
Page generated: Mon Aug 12 02:28:28 2024

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