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Iodine in PDB 6wpx: Crystal Structure of Bacillus Licheniformis Lipase BLEST2 in Propetide Form

Protein crystallography data

The structure of Crystal Structure of Bacillus Licheniformis Lipase BLEST2 in Propetide Form, PDB code: 6wpx was solved by A.M.Nakamura, A.S.Godoy, M.A.S.Kadowaki, I.Polikarpov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.16 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.89, 78.315, 166.486, 90, 90, 90
R / Rfree (%) 19.6 / 22.8

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Bacillus Licheniformis Lipase BLEST2 in Propetide Form (pdb code 6wpx). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 24 binding sites of Iodine where determined in the Crystal Structure of Bacillus Licheniformis Lipase BLEST2 in Propetide Form, PDB code: 6wpx:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 24 in 6wpx

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Iodine binding site 1 out of 24 in the Crystal Structure of Bacillus Licheniformis Lipase BLEST2 in Propetide Form


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 Bacillus Licheniformis Lipase BLEST2 in Propetide Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:48.2
occ:1.00
 O A:SER426 3.4 31.3 1.0
C A:SER426 3.7 31.4 1.0
N A:LYS428 3.8 28.5 1.0
OG A:SER426 3.8 48.5 1.0
C A:LEU427 4.0 32.2 1.0
N A:LEU427 4.1 27.1 1.0
CA A:LEU427 4.1 28.4 1.0
CB A:SER426 4.1 28.6 1.0
CA A:LYS428 4.4 28.0 1.0
CA A:SER426 4.6 24.8 1.0
O A:LEU427 4.6 32.0 1.0
CB A:LYS428 4.7 30.1 1.0
O A:HOH708 4.8 23.5 1.0

Iodine binding site 2 out of 24 in 6wpx

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Iodine binding site 2 out of 24 in the Crystal Structure of Bacillus Licheniformis Lipase BLEST2 in Propetide Form


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 Bacillus Licheniformis Lipase BLEST2 in Propetide Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:45.9
occ:1.00
 CZ A:ARG111 3.6 46.4 1.0
NH2 A:ARG111 3.8 40.8 1.0
N A:PRO45 3.9 27.1 1.0
NH1 A:ARG111 3.9 21.7 1.0
NE A:ARG111 3.9 43.9 1.0
CB A:PRO43 3.9 23.7 1.0
C A:ASP44 4.0 29.1 1.0
CD A:PRO45 4.1 29.5 1.0
CA A:PRO45 4.2 27.1 1.0
CG A:PRO45 4.3 35.1 1.0
N A:ASP44 4.3 25.6 1.0
C A:PRO43 4.3 27.6 1.0
O A:ASP44 4.4 28.3 1.0
CG A:PRO43 4.4 29.9 1.0
O A:PRO43 4.5 25.9 1.0
CD A:ARG111 4.5 35.5 1.0
CA A:ASP44 4.6 25.2 1.0
CB A:PRO45 4.7 30.6 1.0
CA A:PRO43 4.8 21.7 1.0

Iodine binding site 3 out of 24 in 6wpx

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Iodine binding site 3 out of 24 in the Crystal Structure of Bacillus Licheniformis Lipase BLEST2 in Propetide Form


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 Bacillus Licheniformis Lipase BLEST2 in Propetide Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:50.0
occ:1.00
 O A:HOH606 3.3 24.9 1.0
NE2 A:HIS149 3.4 22.5 1.0
N A:PRO242 3.4 25.2 1.0
CD A:PRO242 3.6 26.9 1.0
C A:LEU241 3.6 26.2 1.0
CA A:PRO242 3.8 26.8 1.0
CE1 A:HIS149 3.8 22.7 1.0
O A:ARG240 4.0 16.8 1.0
C A:ARG240 4.0 20.0 1.0
CA A:LEU241 4.0 19.1 1.0
N A:LEU241 4.1 16.6 1.0
CB A:ARG240 4.1 14.6 1.0
CB A:PRO242 4.1 29.8 1.0
O A:LEU241 4.1 24.4 1.0
CG A:PRO242 4.4 33.7 1.0
CD2 A:HIS149 4.5 21.5 1.0
CA A:ARG240 4.7 13.8 1.0
O A:HOH793 4.9 33.6 1.0
O A:LYS237 5.0 18.3 1.0

Iodine binding site 4 out of 24 in 6wpx

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Iodine binding site 4 out of 24 in the Crystal Structure of Bacillus Licheniformis Lipase BLEST2 in Propetide Form


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 Bacillus Licheniformis Lipase BLEST2 in Propetide Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:57.5
occ:1.00
 N A:GLY55 3.4 17.5 1.0
CE2 A:TYR118 3.6 16.4 1.0
CB A:ALA62 3.6 23.1 1.0
CD2 A:TYR118 3.7 15.4 1.0
CA A:GLY58 3.7 23.1 1.0
CB A:HIS54 3.9 13.9 1.0
CA A:GLY55 4.0 16.7 1.0
O A:GLY55 4.0 16.8 1.0
C A:GLY55 4.1 19.7 1.0
C A:HIS54 4.4 19.5 1.0
N A:GLY58 4.4 24.4 1.0
O A:LEU56 4.4 20.5 1.0
CA A:HIS54 4.4 14.3 1.0
N A:SER59 4.6 19.6 1.0
C A:GLY58 4.6 24.2 1.0
ND1 A:HIS54 4.7 17.0 1.0
O A:SER59 4.8 23.0 1.0
CG A:HIS54 4.8 16.5 1.0
N A:LEU56 4.8 16.1 1.0
CZ A:TYR118 4.9 18.5 1.0
CA A:ALA62 5.0 22.5 1.0

Iodine binding site 5 out of 24 in 6wpx

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Iodine binding site 5 out of 24 in the Crystal Structure of Bacillus Licheniformis Lipase BLEST2 in Propetide Form


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 Bacillus Licheniformis Lipase BLEST2 in Propetide Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I505

b:57.2
occ:1.00
 CB A:ASN390 3.2 30.8 1.0
O A:HOH672 3.2 28.1 1.0
NH2 A:ARG465 3.3 21.4 1.0
NE A:ARG465 3.4 20.2 1.0
N A:TYR289 3.5 22.4 1.0
CA A:ASN390 3.6 33.6 1.0
N A:ASN390 3.8 34.1 1.0
CZ A:ARG465 3.8 22.4 1.0
O A:PHE385 3.9 25.5 1.0
O A:TYR289 4.0 18.6 1.0
CA A:SER288 4.0 26.1 1.0
CB A:SER288 4.1 29.5 1.0
O A:HOH628 4.1 35.5 1.0
O A:SER387 4.2 30.2 1.0
C A:SER288 4.2 27.5 1.0
CB A:PHE385 4.3 23.6 1.0
CD2 A:TYR289 4.3 27.8 1.0
CG A:ASN390 4.4 53.6 1.0
CA A:TYR289 4.4 20.6 1.0
OG A:SER288 4.4 43.1 1.0
CB A:TYR289 4.5 22.2 1.0
CD A:ARG465 4.6 17.2 1.0
C A:LEU389 4.6 34.6 1.0
C A:TYR289 4.7 20.6 1.0
C A:PHE385 4.7 26.4 1.0
CB A:SER387 4.8 28.4 1.0
N A:SER387 4.9 24.9 1.0
OD1 A:ASN390 4.9 48.6 1.0
CG A:TYR289 4.9 26.3 1.0

Iodine binding site 6 out of 24 in 6wpx

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Iodine binding site 6 out of 24 in the Crystal Structure of Bacillus Licheniformis Lipase BLEST2 in Propetide Form


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 Bacillus Licheniformis Lipase BLEST2 in Propetide Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I506

b:56.6
occ:1.00
 N A:LYS344 3.5 30.4 1.0
N A:ALA216 3.8 25.5 1.0
CA A:ALA343 4.0 30.2 1.0
CB A:ALA343 4.0 30.0 1.0
CB A:ALA216 4.2 26.8 1.0
C A:ALA343 4.3 34.9 1.0
CB A:LYS344 4.3 32.4 1.0
CA A:ALA216 4.3 25.7 1.0
O A:GLY214 4.4 31.1 1.0
C A:SER215 4.4 29.2 1.0
CG A:LYS344 4.5 46.4 1.0
CA A:LYS344 4.5 29.5 1.0
CA A:SER215 4.6 26.4 1.0
O A:LYS344 4.8 31.3 1.0

Iodine binding site 7 out of 24 in 6wpx

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Iodine binding site 7 out of 24 in the Crystal Structure of Bacillus Licheniformis Lipase BLEST2 in Propetide Form


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 Bacillus Licheniformis Lipase BLEST2 in Propetide Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I507

b:64.9
occ:1.00
 ND2 A:ASN160 3.2 17.8 1.0
NH2 A:ARG412 3.4 40.5 1.0
CG A:ARG412 4.0 32.8 1.0
CB A:ASN160 4.0 14.3 1.0
CD A:ARG412 4.1 31.3 1.0
CG A:ASN160 4.1 32.1 1.0
CE A:LYS424 4.1 54.0 1.0
CD A:LYS424 4.3 45.1 1.0
CB A:ARG412 4.4 26.5 1.0
CZ A:ARG412 4.5 56.3 1.0
CG A:LYS424 4.6 39.6 1.0
NE A:ARG412 4.7 33.6 1.0
O A:LYS425 4.8 23.8 1.0
CA A:ASN160 4.9 16.4 1.0
CH2 A:TRP164 5.0 30.7 1.0
NZ A:LYS424 5.0 58.2 1.0

Iodine binding site 8 out of 24 in 6wpx

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Iodine binding site 8 out of 24 in the Crystal Structure of Bacillus Licheniformis Lipase BLEST2 in Propetide Form


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 Bacillus Licheniformis Lipase BLEST2 in Propetide Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I508

b:54.8
occ:1.00
 OG A:SER127 3.2 30.2 1.0
CA A:GLN92 3.7 28.5 1.0
CB A:GLN92 3.7 30.9 1.0
CD2 A:HIS131 4.0 32.4 1.0
CG A:GLN92 4.0 50.0 1.0
CB A:HIS131 4.0 30.5 1.0
CE1 A:HIS132 4.1 33.8 1.0
CG A:HIS131 4.1 32.6 1.0
CB A:SER127 4.1 25.7 1.0
N A:GLN92 4.1 28.2 1.0
CE1 A:PHE187 4.2 29.0 1.0
CG A:MET91 4.4 25.3 1.0
O A:MET91 4.5 28.8 1.0
C A:MET91 4.5 29.0 1.0
CD A:GLN92 4.5 69.2 1.0
NE2 A:GLN92 4.7 65.1 1.0
ND1 A:HIS132 4.8 35.3 1.0
CD1 A:PHE187 4.8 29.2 1.0
NE2 A:HIS131 4.9 32.2 1.0
CA A:SER127 4.9 23.9 1.0
C A:GLN92 5.0 30.7 1.0

Iodine binding site 9 out of 24 in 6wpx

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Iodine binding site 9 out of 24 in the Crystal Structure of Bacillus Licheniformis Lipase BLEST2 in Propetide Form


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 Bacillus Licheniformis Lipase BLEST2 in Propetide Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I509

b:72.2
occ:1.00
 OH A:TYR177 3.1 27.9 1.0
N A:ASN418 3.4 38.7 1.0
CE1 A:TYR472 3.7 36.3 1.0
CZ A:TYR177 3.9 30.4 1.0
CE1 A:TYR177 3.9 27.3 1.0
CA A:ASN418 4.0 38.3 1.0
C A:GLU417 4.4 40.2 1.0
N A:MET446 4.4 28.2 1.0
CA A:GLU417 4.4 35.7 1.0
CD1 A:TYR472 4.5 32.9 1.0
CA A:GLY445 4.6 36.5 1.0
OH A:TYR472 4.6 51.6 1.0
CE2 A:PHE183 4.6 32.9 1.0
O A:TYR416 4.6 32.9 1.0
N A:GLY419 4.6 36.5 1.0
CZ A:TYR472 4.7 44.9 1.0
CG A:MET446 4.7 27.6 1.0
C A:GLY445 4.8 34.9 1.0
CB A:MET446 4.9 24.9 1.0
C A:ASN418 4.9 41.8 1.0
OD1 A:ASN418 4.9 60.8 1.0
CD2 A:PHE183 5.0 29.9 1.0

Iodine binding site 10 out of 24 in 6wpx

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Iodine binding site 10 out of 24 in the Crystal Structure of Bacillus Licheniformis Lipase BLEST2 in Propetide Form


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 Bacillus Licheniformis Lipase BLEST2 in Propetide Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I510

b:71.1
occ:1.00
 OG A:SER413 3.3 30.0 1.0
O A:GLU423 3.5 28.7 1.0
N A:ARG415 3.7 28.4 1.0
CB A:ARG415 3.8 28.1 1.0
CG A:GLU423 3.8 38.4 1.0
CG A:LYS425 3.9 52.8 1.0
CD A:LYS425 3.9 63.7 1.0
C A:GLU423 4.0 29.6 1.0
C A:ILE414 4.0 31.2 1.0
C A:SER413 4.0 27.9 1.0
CB A:SER413 4.1 25.5 1.0
O A:SER413 4.1 26.6 1.0
N A:ILE414 4.1 25.1 1.0
CA A:ILE414 4.2 26.3 1.0
CE A:LYS425 4.2 74.3 1.0
CB A:GLU423 4.3 29.9 1.0
N A:LYS425 4.3 25.0 1.0
CB A:LYS425 4.3 30.1 1.0
CA A:ARG415 4.3 29.0 1.0
CD A:GLU423 4.4 57.9 1.0
N A:LYS424 4.4 24.5 1.0
CA A:LYS424 4.5 23.0 1.0
C A:LYS424 4.6 27.4 1.0
OE2 A:GLU423 4.7 55.8 1.0
CA A:SER413 4.7 22.2 1.0
O A:ILE414 4.7 29.3 1.0
CA A:GLU423 4.8 27.6 1.0
NZ A:LYS425 4.9 83.2 1.0
CA A:LYS425 5.0 25.7 1.0
CE2 A:TYR447 5.0 34.7 1.0
CD2 A:TYR447 5.0 32.4 1.0

Reference:

A.M.Nakamura, A.S.Godoy, M.A.S.Kadowaki, I.Polikarpov. The First Structure of Bacillus Licheniformis Lipase BLEST2 in Its Propeptide and Mature Form Revealing Molecular Details of Inhibition By Its C-Terminal Domains To Be Published.
Page generated: Mon Aug 12 00:31:25 2024

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