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Iodine in PDB 4b43: Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A

Protein crystallography data

The structure of Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A, PDB code: 4b43 was solved by A.Simonetti, A.Urzhumtsev, B.P.Klaholz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.283 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.787, 61.971, 162.578, 90.00, 90.00, 90.00
R / Rfree (%) 19.39 / 23.55

Other elements in 4b43:

The structure of Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A (pdb code 4b43). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A, PDB code: 4b43:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 4b43

Go back to Iodine Binding Sites List in 4b43
Iodine binding site 1 out of 7 in the Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1366

b:59.5
occ:0.84
 O A:HOH2143 2.8 41.1 1.0
ND2 A:ASN180 3.7 39.0 1.0
O A:HOH2063 3.8 50.8 1.0
CG2 A:THR88 4.1 37.7 1.0
CB A:ALA217 4.1 38.2 1.0
CE A:LYS181 4.1 46.3 1.0
N A:LYS218 4.2 46.7 1.0
CB A:THR88 4.2 40.3 1.0
CA A:GLY85 4.2 31.7 1.0
CG A:LYS181 4.2 44.9 1.0
OG1 A:THR88 4.4 44.6 1.0
CB A:LYS218 4.5 53.0 1.0
CG A:ASN180 4.5 34.5 1.0
OD1 A:ASN180 4.6 35.3 1.0
CA A:LYS218 4.7 48.9 1.0
CD A:LYS181 4.8 44.4 1.0
C A:ALA217 4.8 44.7 1.0
CA A:ALA217 4.8 41.1 1.0
N A:ALA217 4.8 35.2 1.0
O A:GLY85 4.9 32.6 1.0
O A:HIS84 5.0 33.2 1.0

Iodine binding site 2 out of 7 in 4b43

Go back to Iodine Binding Sites List in 4b43
Iodine binding site 2 out of 7 in the Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1367

b:85.2
occ:0.58
 O A:HOH2063 3.4 50.8 1.0
CB A:ASP183 3.4 77.5 1.0
N A:ASP183 3.6 71.0 1.0
OG A:SER216 3.7 41.2 1.0
O A:HOH2143 3.8 41.1 1.0
CA A:ASP183 3.8 74.2 1.0
CA A:LYS181 3.9 45.2 1.0
C A:ASP183 4.0 73.6 1.0
N A:LEU184 4.0 69.9 1.0
C A:LYS181 4.0 45.5 1.0
CD2 A:LEU184 4.2 51.1 1.0
OD2 A:ASP183 4.3 90.2 1.0
CB A:SER216 4.3 41.6 1.0
CG A:ASP183 4.3 84.9 1.0
O A:LYS181 4.3 50.8 1.0
N A:ILE182 4.4 50.3 1.0
O A:ASP183 4.6 75.4 1.0
CD A:LYS218 4.6 64.9 1.0
CG A:LEU184 4.6 55.2 1.0
CB A:LYS181 4.6 45.5 1.0
CB A:LYS218 4.7 53.0 1.0
C A:ILE182 4.8 63.9 1.0
N A:LYS181 4.9 38.1 1.0
CA A:LEU184 5.0 64.1 1.0

Iodine binding site 3 out of 7 in 4b43

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Iodine binding site 3 out of 7 in the Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1368

b:62.9
occ:0.69
 O A:HOH2162 2.8 46.4 1.0
CE A:LYS193 3.2 47.4 1.0
NZ A:LYS193 3.4 43.9 1.0
CD A:PRO214 4.0 41.2 1.0
CG A:PRO214 4.0 43.5 1.0
CB A:PRO214 4.1 41.8 1.0
CB A:PRO189 4.3 40.4 1.0
CD1 A:ILE179 4.3 34.6 1.0
CG1 A:VAL212 4.4 25.2 1.0
N A:PRO214 4.5 38.8 1.0
O A:HOH2159 4.6 40.8 1.0
CD A:LYS193 4.7 42.8 1.0
CA A:PRO214 4.8 34.5 1.0

Iodine binding site 4 out of 7 in 4b43

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Iodine binding site 4 out of 7 in the Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1369

b:42.0
occ:0.59
 O A:HOH2134 2.7 37.2 1.0
O A:HOH2136 3.0 58.4 1.0
CD A:ARG199 3.8 33.1 1.0
CG A:GLU162 3.8 31.1 1.0
CG A:ARG199 3.9 31.8 1.0
O A:HOH2135 4.1 44.7 1.0
CB A:ARG199 4.1 31.7 1.0
CB A:GLU162 4.2 24.1 1.0
CD1 A:ILE165 4.2 21.1 1.0
CE2 A:PHE201 4.3 29.9 1.0
CG2 A:ILE165 4.3 25.1 1.0
NE A:ARG199 4.3 35.1 1.0
CA A:GLU162 4.4 20.8 1.0
O A:HOH2056 4.5 46.4 1.0
CB A:ILE165 4.6 22.9 1.0
CD A:GLU162 4.7 44.0 1.0
O A:GLU162 4.7 26.4 1.0
OE2 A:GLU162 4.8 45.2 1.0

Iodine binding site 5 out of 7 in 4b43

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Iodine binding site 5 out of 7 in the Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1370

b:45.8
occ:0.47
 O A:HOH2120 3.1 35.8 1.0
O A:HOH2119 3.4 42.6 1.0
N A:PRO73 3.6 22.3 1.0
C A:ARG72 3.8 24.1 1.0
CD A:PRO73 3.9 20.1 1.0
CA A:PRO73 3.9 20.4 1.0
CB A:PRO73 4.1 22.7 1.0
O A:ARG72 4.2 21.2 1.0
CA A:ARG72 4.2 18.4 1.0
O A:ARG71 4.3 24.4 1.0
C A:ARG71 4.3 25.5 1.0
CB A:ARG71 4.3 28.8 1.0
O A:HOH2079 4.4 42.4 1.0
N A:ARG72 4.4 18.7 1.0
O A:HOH2081 4.5 44.5 1.0
CG A:PRO73 4.5 23.4 1.0
O A:HOH2030 4.6 52.9 1.0
O A:HOH2050 4.9 53.7 1.0
NH2 A:ARG71 4.9 38.4 1.0

Iodine binding site 6 out of 7 in 4b43

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Iodine binding site 6 out of 7 in the Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1371

b:50.3
occ:0.28
 CE A:LYS255 3.1 58.4 1.0
CG A:LYS255 3.2 44.4 1.0
CD A:LYS255 3.4 52.3 1.0
ND2 A:ASN265 3.6 16.4 1.0
O A:HOH2196 3.8 36.6 1.0
CG A:GLU253 3.9 36.1 1.0
CB A:LYS255 4.0 36.8 1.0
C A:SER254 4.0 29.5 1.0
N A:LYS255 4.0 24.4 1.0
O A:GLU253 4.0 21.9 1.0
CA A:SER254 4.0 22.0 1.0
NZ A:LYS255 4.0 64.7 1.0
CG A:ASN265 4.1 23.6 1.0
CG1 A:ILE263 4.1 39.2 1.0
C A:GLU253 4.1 23.2 1.0
N A:SER254 4.2 18.2 1.0
O A:HOH2109 4.2 30.7 0.7
OD1 A:ASN265 4.2 19.7 1.0
O A:HOH2108 4.2 39.9 1.0
O A:ILE263 4.3 28.5 1.0
CD1 A:ILE263 4.4 44.1 1.0
O A:SER254 4.5 27.7 1.0
CA A:LYS255 4.6 33.7 1.0
N A:ASN265 4.6 20.4 1.0
CB A:GLU253 4.6 30.4 1.0
C A:ILE263 4.8 24.4 1.0
CA A:ALA264 4.9 20.3 1.0
CA A:GLU253 5.0 27.0 1.0
CB A:ASN265 5.0 22.5 1.0

Iodine binding site 7 out of 7 in 4b43

Go back to Iodine Binding Sites List in 4b43
Iodine binding site 7 out of 7 in the Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Bacterial Translation Initiation Factor IF2 (1-363), Apo Form, Double Mutant K86L H130A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1372

b:52.1
occ:0.38
 O A:HOH2161 2.8 41.4 1.0
O A:HOH2142 2.9 27.2 1.0
O A:HOH2058 3.0 45.4 1.0
O A:HOH2141 3.4 34.4 1.0
CD1 A:PHE201 3.9 27.1 1.0
CA A:ALA210 4.1 26.6 1.0
CE1 A:PHE201 4.3 28.6 1.0
O A:ASP209 4.3 37.1 1.0
CB A:ALA210 4.3 27.2 1.0
CE2 A:PHE177 4.3 20.1 1.0
O A:HOH2140 4.4 42.3 1.0
O A:HOH2139 4.4 57.4 1.0
OD1 A:ASP209 4.5 62.9 1.0
CB A:LEU175 4.5 22.1 1.0
N A:ALA210 4.6 26.6 1.0
C A:ASP209 4.7 33.5 1.0
CD1 A:LEU175 4.8 26.5 1.0
O A:LEU175 4.8 27.9 1.0
CG A:LEU175 4.9 26.9 1.0
CG A:ASP209 5.0 57.1 1.0

Reference:

A.Simonetti, S.Marzi, A.Fabbretti, A.G.Myasnikov, I.Hazemann, L.Jenner, A.Urzhumtsev, C.O.Gualerzi, B.P.Klaholz. Molecular Basis of Gtp Hydrolysis By Bacterial Translation Initiation Factor IF2 To Be Published.
Page generated: Fri Aug 8 16:48:37 2025

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