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Iodine in PDB 7oiw: Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp

Enzymatic activity of Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp

All present enzymatic activity of Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp:
2.7.6.5;

Protein crystallography data

The structure of Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp, PDB code: 7oiw was solved by A.Garcia-Pino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.25 / 2.63
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.41, 132.54, 73.47, 90, 103.59, 90
R / Rfree (%) 21.5 / 26.1

Other elements in 7oiw:

The structure of Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Manganese (Mn) 2 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp (pdb code 7oiw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp, PDB code: 7oiw:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 7oiw

Go back to Iodine Binding Sites List in 7oiw
Iodine binding site 1 out of 12 in the Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I509

b:56.4
occ:1.00
 ND2 A:ASN53 3.7 56.0 1.0
CB A:LYS160 3.9 54.1 1.0
CA A:THR158 4.0 44.4 1.0
OD1 B:ASN212 4.0 58.8 1.0
O A:THR158 4.2 52.3 1.0
C A:THR158 4.2 44.8 1.0
N A:ALA161 4.2 54.4 1.0
CB A:ASN53 4.2 66.6 1.0
CB A:THR158 4.2 52.4 1.0
N A:LYS160 4.3 46.9 1.0
CG2 A:THR158 4.5 38.6 1.0
CG A:ASN53 4.5 58.6 1.0
ND2 B:ASN212 4.5 58.9 1.0
CB A:ALA161 4.6 54.1 1.0
CA A:LYS160 4.6 57.5 1.0
CD A:LYS160 4.6 55.8 1.0
CG A:LYS160 4.6 50.9 1.0
CG B:ASN212 4.7 63.4 1.0
O A:ARG157 4.8 53.0 1.0
C A:LYS160 4.8 53.7 1.0
N A:LEU159 5.0 50.2 1.0
CB B:PHE208 5.0 56.9 1.0

Iodine binding site 2 out of 12 in 7oiw

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Iodine binding site 2 out of 12 in the Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I510

b:123.0
occ:1.00
 CD A:PRO76 3.6 68.0 1.0
N A:PRO76 3.8 63.0 1.0
CG A:PRO76 3.8 58.8 1.0
CB A:TYR34 3.9 55.1 1.0
C A:GLY75 4.1 63.5 1.0
CA A:PRO76 4.3 64.6 1.0
CG A:TYR34 4.3 66.1 1.0
CD2 A:TYR34 4.4 70.3 1.0
CA A:GLU31 4.5 75.6 1.0
CG A:GLU31 4.5 67.9 1.0
O A:GLY75 4.5 61.5 1.0
CA A:GLY75 4.6 69.9 1.0
CB A:PRO76 4.6 61.1 1.0
CG2 A:VAL79 4.6 56.7 1.0
CG2 A:VAL105 4.8 71.9 1.0
O A:GLU31 4.9 66.0 1.0
CB A:GLU31 4.9 76.1 1.0

Iodine binding site 3 out of 12 in 7oiw

Go back to Iodine Binding Sites List in 7oiw
Iodine binding site 3 out of 12 in the Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I511

b:114.2
occ:0.85
 O A:HOH605 3.6 53.2 1.0
CB A:LEU272 3.7 71.5 1.0
N A:LEU273 3.8 68.7 1.0
N A:LEU272 3.8 75.8 1.0
O A:PHE270 4.0 73.4 1.0
CA A:LEU272 4.2 64.6 1.0
CD1 A:LEU272 4.2 73.4 1.0
O A:ILE269 4.2 86.0 1.0
CG A:LEU272 4.2 80.2 1.0
C A:PHE270 4.4 75.7 1.0
C A:LEU272 4.4 66.1 1.0
O A:LEU273 4.6 83.0 1.0
CB A:LEU273 4.6 63.1 1.0
CA A:LEU273 4.7 74.5 1.0
C A:ASP271 4.8 80.2 1.0
N A:ASP271 4.8 81.3 1.0
CE A:LYS217 4.8 83.8 1.0
CA A:PHE270 4.9 68.4 1.0
O A:PRO329 4.9 64.8 1.0

Iodine binding site 4 out of 12 in 7oiw

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Iodine binding site 4 out of 12 in the Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I512

b:108.9
occ:0.50
 NE1 A:TRP296 3.3 55.7 1.0
NH2 A:ARG231 3.7 59.1 1.0
CG A:PRO325 3.8 69.4 1.0
CA A:PRO325 3.9 72.6 1.0
CB A:PRO325 4.0 69.4 1.0
CD1 A:TRP296 4.1 48.3 1.0
N A:PRO325 4.1 72.0 1.0
CD A:ARG231 4.1 70.8 1.0
CE2 A:TRP296 4.3 58.6 1.0
CD A:PRO325 4.3 64.7 1.0
CZ2 A:TRP296 4.6 52.8 1.0
CZ A:ARG231 4.6 62.1 1.0
C A:GLY324 4.7 62.9 1.0
NE A:ARG231 4.8 74.3 1.0

Iodine binding site 5 out of 12 in 7oiw

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Iodine binding site 5 out of 12 in the Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I504

b:86.5
occ:0.65
 O B:HOH623 3.1 60.8 1.0
CD2 B:TYR34 3.6 74.7 1.0
CD B:PRO76 3.6 57.8 1.0
CG2 B:VAL105 3.8 59.8 1.0
CB B:TYR34 3.8 63.8 1.0
N B:PRO76 3.8 60.1 1.0
CG B:PRO76 4.0 56.8 1.0
C B:GLY75 4.0 55.5 1.0
CA B:GLU31 4.1 56.0 1.0
CG B:GLU31 4.2 60.5 1.0
CG B:TYR34 4.2 71.4 1.0
ND2 B:ASN102 4.3 111.8 1.0
CA B:GLY75 4.3 64.8 1.0
CA B:PRO76 4.4 56.5 1.0
O B:GLY75 4.5 54.4 1.0
CB B:GLU31 4.5 68.8 1.0
O B:GLU31 4.6 66.2 1.0
CE2 B:TYR34 4.6 88.5 1.0
CB B:PRO76 4.8 51.9 1.0
CG2 B:VAL79 4.8 54.5 1.0
CG B:ASN102 4.8 97.1 1.0
C B:GLU31 4.9 57.8 1.0

Iodine binding site 6 out of 12 in 7oiw

Go back to Iodine Binding Sites List in 7oiw
Iodine binding site 6 out of 12 in the Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I505

b:66.3
occ:0.70
 NE B:ARG51 3.5 66.2 1.0
ND2 B:ASN53 3.6 56.1 1.0
CE1 B:HIS154 3.7 44.1 1.0
OD1 B:ASN53 3.9 61.3 1.0
NH1 B:ARG51 4.0 55.3 1.0
CG2 B:THR158 4.1 42.2 1.0
CB B:LEU55 4.1 59.2 1.0
CZ B:ARG51 4.2 67.0 1.0
CB B:MET59 4.2 50.7 1.0
N B:HIS60 4.2 48.6 1.0
NE2 B:HIS154 4.2 42.2 1.0
CG B:ASN53 4.2 60.3 1.0
CG B:ARG51 4.2 66.8 1.0
CG B:LEU55 4.3 49.4 1.0
CD2 B:LEU55 4.3 72.2 1.0
CD B:ARG51 4.4 59.2 1.0
CB B:HIS60 4.4 54.7 1.0
CA B:HIS60 4.4 49.6 1.0
C B:MET59 4.6 57.3 1.0
CB B:ARG51 4.7 65.5 1.0
ND1 B:HIS154 4.8 40.7 1.0
CB B:THR158 4.8 51.4 1.0
O B:PRO56 5.0 64.9 1.0
O6 B:C1Z501 5.0 48.1 1.0

Iodine binding site 7 out of 12 in 7oiw

Go back to Iodine Binding Sites List in 7oiw
Iodine binding site 7 out of 12 in the Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I506

b:50.6
occ:0.80
 ND2 B:ASN53 3.7 56.1 1.0
CB B:LYS160 3.8 60.9 1.0
OD1 A:ASN212 3.9 59.8 1.0
CA B:THR158 3.9 47.3 1.0
N B:ALA161 4.1 58.1 1.0
O B:THR158 4.1 48.4 1.0
C B:THR158 4.1 47.8 1.0
CB B:ASN53 4.2 65.5 1.0
N B:LYS160 4.2 52.8 1.0
CB B:THR158 4.2 51.4 1.0
CB B:ALA161 4.4 54.2 1.0
CG B:ASN53 4.5 60.3 1.0
CA B:LYS160 4.5 54.7 1.0
CG2 B:THR158 4.5 42.2 1.0
CG B:LYS160 4.6 52.3 1.0
ND2 A:ASN212 4.6 73.9 1.0
CD B:LYS160 4.6 55.7 1.0
CG A:ASN212 4.7 67.0 1.0
C B:LYS160 4.7 58.9 1.0
N B:LEU159 4.9 52.1 1.0
O B:ARG157 4.9 47.9 1.0
CA B:ALA161 4.9 53.2 1.0

Iodine binding site 8 out of 12 in 7oiw

Go back to Iodine Binding Sites List in 7oiw
Iodine binding site 8 out of 12 in the Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I507

b:73.3
occ:0.50
 OE1 B:GLN312 3.4 93.4 1.0
CG B:ASN313 3.7 57.0 1.0
N B:ASN313 3.8 64.9 1.0
CB B:GLN312 3.8 70.2 1.0
ND2 B:ASN313 3.9 50.7 1.0
OD1 B:ASN313 3.9 54.6 1.0
NE2 B:HIS183 4.0 51.5 1.0
CB B:ASN313 4.0 57.3 1.0
CD B:GLN312 4.1 87.3 1.0
N B:GLN312 4.2 62.3 1.0
CE1 B:HIS183 4.2 59.5 1.0
CA B:GLN312 4.3 65.1 1.0
C B:GLN312 4.3 68.0 1.0
ND1 B:HIS184 4.5 83.5 1.0
CD2 B:HIS183 4.5 51.3 1.0
CG B:GLN312 4.5 71.3 1.0
O B:HIS183 4.5 65.0 1.0
CA B:ASN313 4.5 55.4 1.0
CA B:HIS184 4.7 61.2 1.0
ND1 B:HIS183 4.8 49.2 1.0
CB B:LYS311 4.9 55.2 1.0

Iodine binding site 9 out of 12 in 7oiw

Go back to Iodine Binding Sites List in 7oiw
Iodine binding site 9 out of 12 in the Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I508

b:318.8
occ:1.00
 CD B:PRO56 4.1 58.9 1.0
CB A:LYS216 4.1 70.7 1.0
CG B:PRO56 4.1 60.5 1.0
CE B:MET59 4.4 92.7 1.0
CD1 B:LEU55 4.5 60.1 1.0
CG B:MET59 4.5 66.7 1.0
CA A:LYS216 4.6 76.5 1.0
SD B:MET59 4.6 106.2 1.0

Iodine binding site 10 out of 12 in 7oiw

Go back to Iodine Binding Sites List in 7oiw
Iodine binding site 10 out of 12 in the Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of S. Aureus Rel Catalytic Domains in Complex with Pppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I509

b:134.5
occ:0.65
 NH1 B:ARG276 3.2 73.0 1.0
CD B:ARG276 3.9 65.7 1.0
CZ B:ARG276 4.1 73.5 1.0
CB B:ASN246 4.1 71.6 1.0
ND2 B:ASN246 4.1 78.3 1.0
NE B:ARG276 4.4 66.2 1.0
CE1 B:HIS340 4.5 59.0 1.0
CB B:ARG276 4.5 51.7 1.0
CD1 B:ILE278 4.5 47.1 1.0
CG B:ASN246 4.6 75.5 1.0
CG B:ARG276 4.7 59.7 1.0
NE2 B:HIS340 4.9 59.8 1.0
CG B:ARG248 4.9 81.8 1.0

Reference:

A.Garcia-Pino, A.Garcia-Pino. N/A N/A.
Page generated: Mon Aug 12 01:51:50 2024

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