Iodine in PDB 7w6b: Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis
Protein crystallography data
The structure of Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis, PDB code: 7w6b
was solved by
R.K.Yadav,
V.Krishnan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
51.93 /
2.98
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.271,
422.928,
48.391,
90,
90,
90
|
R / Rfree (%)
|
25.3 /
30.5
|
Other elements in 7w6b:
The structure of Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis also contains other interesting chemical elements:
Iodine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
15;
Binding sites:
The binding sites of Iodine atom in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis
(pdb code 7w6b). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the
Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis, PDB code: 7w6b:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iodine binding site 1 out
of 15 in 7w6b
Go back to
Iodine Binding Sites List in 7w6b
Iodine binding site 1 out
of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis
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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I902
b:64.1
occ:0.76
|
N
|
A:ILE586
|
3.7
|
20.7
|
1.0
|
CA
|
A:GLU585
|
4.2
|
21.3
|
1.0
|
CD1
|
A:ILE586
|
4.4
|
20.0
|
1.0
|
O
|
A:ILE586
|
4.4
|
21.5
|
1.0
|
CB
|
A:ILE586
|
4.5
|
20.1
|
1.0
|
O
|
A:LYS584
|
4.5
|
20.7
|
1.0
|
CG1
|
A:ILE586
|
4.5
|
20.2
|
1.0
|
C
|
A:GLU585
|
4.5
|
21.7
|
1.0
|
CA
|
A:ILE586
|
4.6
|
20.5
|
1.0
|
CE
|
A:LYS584
|
4.8
|
17.3
|
1.0
|
N
|
A:GLU585
|
4.8
|
20.6
|
1.0
|
C
|
A:LYS584
|
4.8
|
19.6
|
1.0
|
|
Iodine binding site 2 out
of 15 in 7w6b
Go back to
Iodine Binding Sites List in 7w6b
Iodine binding site 2 out
of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis
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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I903
b:66.8
occ:0.65
|
CG
|
A:ARG737
|
3.7
|
65.3
|
1.0
|
CD
|
A:ARG737
|
3.9
|
69.9
|
1.0
|
O
|
A:ILE736
|
3.9
|
41.7
|
1.0
|
CB
|
A:ASN735
|
4.1
|
45.0
|
1.0
|
NE
|
A:ARG737
|
4.1
|
80.3
|
1.0
|
C
|
A:ILE736
|
4.1
|
43.4
|
1.0
|
N
|
A:ILE736
|
4.4
|
39.0
|
1.0
|
N
|
A:ARG737
|
4.4
|
48.1
|
1.0
|
O
|
A:GLY764
|
4.4
|
39.4
|
1.0
|
CB
|
A:ARG737
|
4.5
|
60.6
|
1.0
|
O
|
A:ASN763
|
4.6
|
38.1
|
1.0
|
C
|
A:ASN735
|
4.6
|
40.3
|
1.0
|
CZ
|
A:ARG737
|
4.6
|
82.1
|
1.0
|
CA
|
A:GLY764
|
4.6
|
39.3
|
1.0
|
CA
|
A:ARG737
|
4.7
|
54.7
|
1.0
|
OD1
|
A:ASN735
|
4.7
|
51.2
|
1.0
|
CA
|
A:ASN735
|
4.7
|
41.7
|
1.0
|
CA
|
A:PRO743
|
4.7
|
56.5
|
1.0
|
C
|
A:GLY764
|
4.8
|
40.4
|
1.0
|
CA
|
A:ILE736
|
4.8
|
39.8
|
1.0
|
CB
|
A:PRO743
|
4.8
|
57.2
|
1.0
|
CG
|
A:ASN735
|
4.9
|
49.1
|
1.0
|
NH1
|
A:ARG737
|
4.9
|
82.6
|
1.0
|
|
Iodine binding site 3 out
of 15 in 7w6b
Go back to
Iodine Binding Sites List in 7w6b
Iodine binding site 3 out
of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis
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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I904
b:57.7
occ:0.61
|
N
|
A:ASP700
|
4.0
|
21.5
|
1.0
|
CG2
|
A:THR513
|
4.0
|
25.9
|
1.0
|
CB
|
A:ASP700
|
4.2
|
23.1
|
1.0
|
OG1
|
A:THR513
|
4.2
|
25.7
|
1.0
|
CB
|
A:VAL512
|
4.3
|
22.1
|
1.0
|
CG1
|
A:VAL512
|
4.3
|
21.6
|
1.0
|
OD2
|
A:ASP700
|
4.4
|
25.2
|
1.0
|
CB
|
A:LYS699
|
4.4
|
18.2
|
1.0
|
CG
|
A:ASP700
|
4.4
|
24.5
|
1.0
|
CB
|
A:THR513
|
4.7
|
25.8
|
1.0
|
CA
|
A:ASP700
|
4.7
|
21.8
|
1.0
|
CA
|
A:LYS699
|
4.8
|
19.6
|
1.0
|
N
|
A:THR513
|
4.9
|
24.9
|
1.0
|
C
|
A:LYS699
|
4.9
|
20.4
|
1.0
|
|
Iodine binding site 4 out
of 15 in 7w6b
Go back to
Iodine Binding Sites List in 7w6b
Iodine binding site 4 out
of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis
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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I905
b:66.6
occ:0.60
|
O
|
A:HOH1016
|
3.4
|
13.2
|
1.0
|
N
|
A:GLU564
|
3.5
|
41.8
|
1.0
|
CA
|
A:PHE563
|
3.7
|
34.4
|
1.0
|
O
|
A:LYS547
|
3.8
|
28.4
|
1.0
|
O
|
A:ASN562
|
4.0
|
33.6
|
1.0
|
C
|
A:PHE563
|
4.2
|
38.2
|
1.0
|
CD
|
A:ARG546
|
4.3
|
28.6
|
1.0
|
CB
|
A:ARG546
|
4.3
|
28.1
|
1.0
|
O
|
A:GLU564
|
4.4
|
45.6
|
1.0
|
CB
|
A:PHE563
|
4.5
|
34.1
|
1.0
|
CA
|
A:GLU564
|
4.6
|
45.1
|
1.0
|
CD1
|
A:PHE563
|
4.6
|
33.4
|
1.0
|
CB
|
A:GLU564
|
4.6
|
52.0
|
1.0
|
N
|
A:LYS547
|
4.7
|
28.2
|
1.0
|
N
|
A:PHE563
|
4.7
|
32.4
|
1.0
|
C
|
A:LYS547
|
4.8
|
28.2
|
1.0
|
CG
|
A:ARG546
|
4.8
|
28.3
|
1.0
|
C
|
A:ASN562
|
4.8
|
33.1
|
1.0
|
CG
|
A:GLU564
|
4.9
|
62.3
|
1.0
|
C
|
A:GLU564
|
4.9
|
44.5
|
1.0
|
|
Iodine binding site 5 out
of 15 in 7w6b
Go back to
Iodine Binding Sites List in 7w6b
Iodine binding site 5 out
of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis
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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I906
b:61.9
occ:0.82
|
CB
|
A:ASN725
|
4.0
|
67.8
|
1.0
|
CG1
|
A:VAL722
|
4.0
|
75.9
|
1.0
|
CG2
|
A:VAL719
|
4.0
|
64.8
|
1.0
|
CE2
|
A:PHE730
|
4.1
|
56.0
|
1.0
|
CB
|
A:LYS728
|
4.2
|
73.3
|
1.0
|
CG1
|
A:VAL719
|
4.2
|
61.8
|
1.0
|
CA
|
A:LYS728
|
4.2
|
75.5
|
1.0
|
CZ
|
A:PHE730
|
4.2
|
58.4
|
1.0
|
CG2
|
A:VAL722
|
4.3
|
73.6
|
1.0
|
OH
|
A:TYR799
|
4.4
|
59.3
|
1.0
|
O
|
A:LEU727
|
4.4
|
74.5
|
1.0
|
CB
|
A:VAL719
|
4.5
|
63.1
|
1.0
|
ND2
|
A:ASN725
|
4.6
|
67.3
|
1.0
|
CB
|
A:VAL722
|
4.6
|
72.5
|
1.0
|
CG
|
A:ASN725
|
4.7
|
70.2
|
1.0
|
C
|
A:LEU727
|
4.7
|
73.8
|
1.0
|
CB
|
A:LYS772
|
4.8
|
63.4
|
1.0
|
CD
|
A:LYS772
|
4.8
|
69.3
|
1.0
|
N
|
A:LYS728
|
4.9
|
69.7
|
1.0
|
|
Iodine binding site 6 out
of 15 in 7w6b
Go back to
Iodine Binding Sites List in 7w6b
Iodine binding site 6 out
of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis
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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I907
b:83.4
occ:0.96
|
N
|
A:LYS496
|
3.7
|
65.3
|
1.0
|
CA
|
A:PHE495
|
3.9
|
67.0
|
1.0
|
CG
|
A:PRO51
|
4.1
|
62.5
|
1.0
|
CB
|
A:PHE495
|
4.2
|
62.1
|
1.0
|
CB
|
A:PRO51
|
4.2
|
61.8
|
1.0
|
CD
|
A:PRO51
|
4.3
|
64.4
|
1.0
|
C
|
A:PHE495
|
4.4
|
66.8
|
1.0
|
O
|
A:LYS496
|
4.5
|
61.0
|
1.0
|
CB
|
A:LYS496
|
4.5
|
66.0
|
1.0
|
CE1
|
A:TYR59
|
4.6
|
48.5
|
1.0
|
CA
|
A:LYS496
|
4.7
|
63.1
|
1.0
|
O
|
A:THR494
|
4.7
|
70.2
|
1.0
|
CD1
|
A:TYR59
|
4.7
|
50.2
|
1.0
|
|
Iodine binding site 7 out
of 15 in 7w6b
Go back to
Iodine Binding Sites List in 7w6b
Iodine binding site 7 out
of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis
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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I908
b:54.0
occ:0.71
|
OG1
|
A:THR747
|
3.7
|
40.1
|
1.0
|
N
|
A:THR749
|
3.8
|
36.9
|
1.0
|
OG1
|
A:THR749
|
3.8
|
37.8
|
1.0
|
C
|
A:TYR748
|
3.8
|
36.4
|
1.0
|
CA
|
A:THR749
|
4.2
|
37.4
|
1.0
|
O
|
A:TYR748
|
4.2
|
35.3
|
1.0
|
CA
|
A:TYR748
|
4.2
|
37.0
|
1.0
|
CA
|
A:PRO758
|
4.2
|
38.1
|
1.0
|
CB
|
A:PRO758
|
4.2
|
38.4
|
1.0
|
O
|
A:THR747
|
4.3
|
37.3
|
1.0
|
C
|
A:THR747
|
4.4
|
38.5
|
1.0
|
N
|
A:TYR748
|
4.4
|
38.0
|
1.0
|
CB
|
A:THR749
|
4.5
|
36.5
|
1.0
|
CB
|
A:THR747
|
4.7
|
39.9
|
1.0
|
CG2
|
A:THR749
|
4.9
|
35.8
|
1.0
|
N
|
A:PRO758
|
5.0
|
39.3
|
1.0
|
|
Iodine binding site 8 out
of 15 in 7w6b
Go back to
Iodine Binding Sites List in 7w6b
Iodine binding site 8 out
of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis
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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I909
b:93.1
occ:0.54
|
NZ
|
A:LYS587
|
3.0
|
26.6
|
1.0
|
CE
|
A:LYS587
|
3.7
|
26.4
|
1.0
|
CD
|
A:LYS598
|
3.7
|
15.2
|
1.0
|
NZ
|
A:LYS598
|
3.8
|
16.2
|
1.0
|
CE
|
A:LYS598
|
4.3
|
15.7
|
1.0
|
CG1
|
A:VAL589
|
4.5
|
25.9
|
1.0
|
|
Iodine binding site 9 out
of 15 in 7w6b
Go back to
Iodine Binding Sites List in 7w6b
Iodine binding site 9 out
of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis
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 Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I910
b:68.0
occ:0.61
|
CA
|
A:THR591
|
4.0
|
35.6
|
1.0
|
N
|
A:GLU592
|
4.0
|
38.8
|
1.0
|
O
|
A:HOH1014
|
4.0
|
17.8
|
1.0
|
CB
|
A:THR591
|
4.3
|
34.7
|
1.0
|
C
|
A:THR591
|
4.3
|
37.6
|
1.0
|
O
|
A:GLY590
|
4.9
|
33.8
|
1.0
|
CB
|
A:GLU592
|
4.9
|
40.8
|
1.0
|
|
Iodine binding site 10 out
of 15 in 7w6b
Go back to
Iodine Binding Sites List in 7w6b
Iodine binding site 10 out
of 15 in the Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 10 of Crystal Structure of Pita From Pilus Islet-2 of Streptococcus Oralis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I911
b:60.4
occ:0.44
|
OD1
|
A:ASN551
|
2.2
|
29.5
|
1.0
|
O
|
A:SER525
|
2.9
|
32.2
|
1.0
|
CG
|
A:ASN551
|
3.2
|
26.3
|
1.0
|
O
|
A:VAL552
|
3.3
|
26.9
|
1.0
|
ND2
|
A:ASN551
|
3.6
|
26.2
|
1.0
|
C
|
A:VAL552
|
3.8
|
26.6
|
1.0
|
C
|
A:SER525
|
3.8
|
30.8
|
1.0
|
N
|
A:VAL552
|
3.8
|
24.7
|
1.0
|
CA
|
A:SER525
|
4.1
|
30.4
|
1.0
|
CB
|
A:SER525
|
4.1
|
31.8
|
1.0
|
N
|
A:SER553
|
4.3
|
29.7
|
1.0
|
CA
|
A:VAL552
|
4.4
|
25.3
|
1.0
|
CB
|
A:ASN551
|
4.5
|
25.2
|
1.0
|
CA
|
A:SER553
|
4.5
|
33.6
|
1.0
|
C
|
A:ASN551
|
4.7
|
24.3
|
1.0
|
CA
|
A:ASN551
|
4.7
|
24.3
|
1.0
|
OG
|
A:SER525
|
5.0
|
34.9
|
1.0
|
|
Reference:
R.K.Yadav,
V.Krishnan.
New Structural Insights Into the Pi-2 Pilus From Streptococcus Oralis, An Early Dental Plaque Colonizer. Febs J. V. 289 6342 2022.
ISSN: ISSN 1742-464X
PubMed: 35561142
DOI: 10.1111/FEBS.16527
Page generated: Mon Aug 12 02:18:17 2024
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