Iodine in PDB 7skx: Ab Initio Structure of Proteinase K From Electron-Counted Microed Data

Enzymatic activity of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data

All present enzymatic activity of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data:
3.4.21.64;

Other elements in 7skx:

The structure of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data also contains other interesting chemical elements:

Calcium (Ca) 5 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data (pdb code 7skx). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data, PDB code: 7skx:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 7skx

Go back to Iodine Binding Sites List in 7skx
Iodine binding site 1 out of 6 in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I301

b:42.6
occ:0.77
 I3 C:I3C301 0.0 42.6 0.8
C6 C:I3C301 2.1 40.0 0.8
HN1A C:I3C301 2.6 34.0 0.8
C5 C:I3C301 3.0 38.4 0.8
C1 C:I3C301 3.0 43.0 0.8
N13 C:I3C301 3.1 33.6 0.8
HG C:SER219 3.2 16.9 0.0
C7 C:I3C301 3.3 32.6 0.8
HB2 C:SER219 3.4 14.2 1.0
HB2 C:LEU209 3.5 9.5 1.0
O8 C:I3C301 3.6 34.5 0.8
O C:HOH403 3.7 9.6 1.0
HH22 C:ARG185 3.7 26.9 1.0
HB3 C:SER207 3.7 11.1 1.0
OG C:SER219 3.8 17.2 1.0
O C:SER207 3.8 10.1 1.0
HH21 C:ARG185 3.9 27.8 1.0
O9 C:I3C301 3.9 30.5 0.8
CB C:SER219 4.0 13.9 1.0
HN13 C:I3C301 4.0 35.0 0.8
NH2 C:ARG185 4.2 27.1 1.0
HB3 C:SER219 4.3 13.4 1.0
C4 C:I3C301 4.3 40.7 0.8
C2 C:I3C301 4.3 48.1 0.8
H C:LEU209 4.4 8.4 1.0
HD1 C:TRP8 4.4 10.3 1.0
CB C:LEU209 4.4 9.3 1.0
HD21 C:LEU209 4.5 12.6 1.0
C C:SER207 4.6 8.1 1.0
HD13 C:LEU209 4.7 9.9 1.0
CB C:SER207 4.7 10.4 1.0
HB3 C:LEU209 4.7 9.5 1.0
N C:LEU209 4.8 8.4 1.0
C3 C:I3C301 4.9 47.3 0.8
HB2 C:SER207 5.0 11.0 1.0

Iodine binding site 2 out of 6 in 7skx

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Iodine binding site 2 out of 6 in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I301

b:79.8
occ:0.77
 I2 C:I3C301 0.0 79.8 0.8
C4 C:I3C301 2.1 40.7 0.8
HN13 C:I3C301 2.7 35.0 0.8
C5 C:I3C301 3.0 38.4 0.8
C3 C:I3C301 3.1 47.3 0.8
N13 C:I3C301 3.2 33.6 0.8
C10 C:I3C301 3.3 47.0 0.8
O11 C:I3C301 3.5 63.4 0.8
HD21 C:LEU209 3.7 12.6 1.0
O12 C:I3C301 3.9 46.0 0.8
HD22 C:LEU209 4.0 11.8 1.0
HN1A C:I3C301 4.1 34.0 0.8
CD2 C:LEU209 4.3 12.4 1.0
C6 C:I3C301 4.3 40.0 0.8
C2 C:I3C301 4.4 48.1 0.8
HD13 C:LEU209 4.7 9.9 1.0
HD12 C:LEU209 4.9 9.8 1.0
HD23 C:LEU209 4.9 12.1 1.0
C1 C:I3C301 4.9 43.0 0.8

Iodine binding site 3 out of 6 in 7skx

Go back to Iodine Binding Sites List in 7skx
Iodine binding site 3 out of 6 in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I301

b:49.8
occ:0.77
 I1 C:I3C301 0.0 49.8 0.8
C2 C:I3C301 2.1 48.1 0.8
C1 C:I3C301 3.0 43.0 0.8
C3 C:I3C301 3.1 47.3 0.8
HA C:PRO7 3.1 11.3 1.0
C7 C:I3C301 3.2 32.6 0.8
O C:ALA6 3.3 12.3 1.0
C10 C:I3C301 3.3 47.0 0.8
O9 C:I3C301 3.4 30.5 0.8
O12 C:I3C301 3.5 46.0 0.8
O C:ASN5 3.6 15.8 1.0
O8 C:I3C301 3.7 34.5 0.8
C C:ALA6 3.8 11.0 1.0
O11 C:I3C301 3.9 63.4 0.8
CA C:PRO7 3.9 11.0 1.0
N C:PRO7 4.0 11.8 1.0
C C:ASN5 4.2 16.3 1.0
C6 C:I3C301 4.3 40.0 0.8
C4 C:I3C301 4.4 40.7 0.8
H C:TRP8 4.4 9.5 1.0
HB3 C:ASN5 4.6 18.7 1.0
C C:PRO7 4.7 10.6 1.0
HA C:ASN5 4.7 16.2 1.0
N C:TRP8 4.7 9.4 1.0
N C:ALA6 4.7 13.6 1.0
HD3 C:PRO7 4.8 13.0 1.0
CA C:ALA6 4.8 12.9 1.0
HD23 C:LEU209 4.8 12.1 1.0
CD C:PRO7 4.9 12.6 1.0
C5 C:I3C301 4.9 38.4 0.8
CA C:ASN5 5.0 16.4 1.0
HG3 C:PRO7 5.0 13.0 1.0
HD21 C:LEU209 5.0 12.6 1.0
HA C:ALA6 5.0 12.9 1.0

Iodine binding site 4 out of 6 in 7skx

Go back to Iodine Binding Sites List in 7skx
Iodine binding site 4 out of 6 in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I302

b:40.0
occ:0.73
 I3 C:I3C302 0.0 40.0 0.7
C6 C:I3C302 2.1 37.4 0.7
HN1A C:I3C302 2.7 26.7 0.7
C5 C:I3C302 3.0 32.4 0.7
C1 C:I3C302 3.0 51.1 0.7
N13 C:I3C302 3.2 26.7 0.7
HB3 C:SER45 3.2 14.3 1.0
C7 C:I3C302 3.3 56.9 0.7
HB3 C:ALA44 3.6 15.0 1.0
O8 C:I3C302 3.7 55.7 0.7
O9 C:I3C302 3.7 57.4 0.7
H C:SER45 3.9 12.6 1.0
HN13 C:I3C302 4.1 26.5 0.7
CB C:SER45 4.2 14.4 1.0
O C:HOH476 4.2 28.0 1.0
N C:SER45 4.3 12.7 1.0
C4 C:I3C302 4.3 32.6 0.7
O C:HOH512 4.4 25.7 1.0
C2 C:I3C302 4.4 53.3 0.7
CB C:ALA44 4.5 14.9 1.0
HA C:SER45 4.6 11.8 1.0
CA C:SER45 4.6 11.8 1.0
H C:ALA44 4.7 11.1 1.0
HB2 C:SER45 4.7 14.1 1.0
HB1 C:ALA44 4.8 14.3 1.0
OG C:SER45 4.8 16.7 1.0
HG C:SER45 4.8 16.2 0.0
C3 C:I3C302 4.9 49.7 0.7
C C:ALA44 4.9 12.2 1.0

Iodine binding site 5 out of 6 in 7skx

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Iodine binding site 5 out of 6 in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I302

b:36.0
occ:0.73
 I2 C:I3C302 0.0 36.0 0.7
C4 C:I3C302 2.1 32.6 0.7
O11 C:I3C302 2.7 73.9 0.7
HN13 C:I3C302 2.8 26.5 0.7
C5 C:I3C302 3.0 32.4 0.7
C3 C:I3C302 3.0 49.7 0.7
N13 C:I3C302 3.2 26.7 0.7
C10 C:I3C302 3.2 61.3 0.7
HG3 C:GLU43 3.3 13.0 1.0
HD2 C:ARG64 3.4 39.6 1.0
HG C:SER45 3.6 16.2 0.0
HD3 C:ARG64 3.8 41.3 1.0
O C:HOH442 4.0 23.5 1.0
CD C:ARG64 4.1 41.2 1.0
OE2 C:GLU43 4.1 20.1 1.0
HN1A C:I3C302 4.1 26.7 0.7
O C:HOH517 4.2 19.2 1.0
OG C:SER45 4.2 16.7 1.0
CG C:GLU43 4.2 12.8 1.0
CD C:GLU43 4.3 15.2 1.0
C6 C:I3C302 4.3 37.4 0.7
HG2 C:ARG64 4.4 26.5 1.0
C2 C:I3C302 4.4 53.3 0.7
O C:HOH556 4.4 43.7 1.0
O12 C:I3C302 4.5 66.0 0.7
HG2 C:GLU43 4.5 13.1 1.0
CG C:ARG64 4.8 27.0 1.0
O C:HOH520 4.8 45.2 1.0
C1 C:I3C302 4.9 51.1 0.7

Iodine binding site 6 out of 6 in 7skx

Go back to Iodine Binding Sites List in 7skx
Iodine binding site 6 out of 6 in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I302

b:89.6
occ:0.73
 I1 C:I3C302 0.0 89.6 0.7
C2 C:I3C302 2.1 53.3 0.7
O12 C:I3C302 2.7 66.0 0.7
C1 C:I3C302 3.1 51.1 0.7
C3 C:I3C302 3.1 49.7 0.7
C7 C:I3C302 3.2 56.9 0.7
C10 C:I3C302 3.3 61.3 0.7
O C:HOH601 3.3 38.6 1.0
O9 C:I3C302 3.6 57.4 0.7
O8 C:I3C302 3.7 55.7 0.7
O C:HOH520 3.8 45.2 1.0
O C:HOH444 4.2 38.5 1.0
C6 C:I3C302 4.4 37.4 0.7
C4 C:I3C302 4.4 32.6 0.7
O11 C:I3C302 4.5 73.9 0.7
O C:HOH556 4.8 43.7 1.0
C5 C:I3C302 5.0 32.4 0.7

Reference:

M.W.Martynowycz, M.T.B.Clabbers, J.Hattne, T.Gonen. Ab Initio Phasing Macromolecular Structures Using Electron-Counted Microed Data. Nat.Methods V. 19 724 2022.
ISSN: ESSN 1548-7105
PubMed: 35637302
DOI: 10.1038/S41592-022-01485-4
Page generated: Wed Apr 5 09:22:54 2023

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