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Iodine in PDB 1xp4: Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae

Enzymatic activity of Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae

All present enzymatic activity of Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae:
3.4.16.4;

Protein crystallography data

The structure of Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae, PDB code: 1xp4 was solved by C.Morlot, L.Pernot, A.Le Gouellec, A.M.Di Guilmi, T.Vernet, O.Dideberg, A.Dessen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.84 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.608, 120.839, 177.076, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 27.8

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae (pdb code 1xp4). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 16 binding sites of Iodine where determined in the Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae, PDB code: 1xp4:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 16 in 1xp4

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Iodine binding site 1 out of 16 in the Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae


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 A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I468

b:19.6
occ:1.00
 O A:HOH480 3.3 6.5 1.0
CG A:GLN374 3.5 19.1 1.0
CG A:GLU45 3.8 23.6 1.0
N A:GLN374 3.8 14.8 1.0
NE2 A:GLN374 3.8 22.5 1.0
CA A:GLY373 4.1 13.7 1.0
CD A:GLN374 4.2 21.9 1.0
CD1 A:ILE42 4.2 12.6 1.0
CB A:ALA48 4.3 15.6 1.0
CB A:GLU45 4.3 21.5 1.0
CD1 A:TYR186 4.3 21.3 1.0
CE D:LYS369 4.3 11.6 1.0
CB A:GLN374 4.4 14.9 1.0
C A:GLY373 4.4 13.8 1.0
CD D:LYS369 4.5 12.4 1.0
CG2 A:THR49 4.5 20.3 1.0
CD1 A:ILE33 4.5 10.2 1.0
CG D:LYS369 4.5 14.3 1.0
CA A:GLN374 4.7 16.2 1.0
CE1 A:TYR186 4.8 18.7 1.0
CD A:GLU45 4.8 25.6 1.0

Iodine binding site 2 out of 16 in 1xp4

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Iodine binding site 2 out of 16 in the Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae


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 A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I469

b:39.0
occ:1.00
 CB A:ALA37 3.9 10.1 1.0
N A:ASN38 4.1 12.0 1.0
CA A:ASN38 4.3 12.8 1.0
CG A:LYS197 4.3 15.5 1.0
CB A:ASN38 4.4 16.8 1.0
C A:ALA37 4.5 13.7 1.0
CD A:ARG260 4.6 21.6 1.0
OD1 A:ASN38 4.6 24.7 1.0
CG2 A:ILE196 4.7 20.1 1.0
CG A:ASN38 4.9 20.6 1.0
CE A:LYS197 4.9 20.1 1.0
CA A:ALA37 4.9 12.9 1.0
CG A:ARG260 4.9 19.2 1.0

Iodine binding site 3 out of 16 in 1xp4

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Iodine binding site 3 out of 16 in the Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae


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 A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I470

b:66.7
occ:0.50
 O A:HOH546 3.1 32.6 1.0
O A:PRO275 3.4 21.3 1.0
CE2 A:PHE279 4.1 9.1 1.0
CD2 A:TYR223 4.1 30.0 1.0
CE2 A:TYR223 4.1 30.7 1.0
NE A:ARG278 4.2 27.6 1.0
CD1 A:TYR276 4.3 26.6 1.0
O A:HOH491 4.4 7.0 1.0
C A:PRO275 4.4 19.3 1.0
CZ A:ARG278 4.4 28.2 1.0
NH2 A:ARG278 4.5 27.2 1.0
O A:HOH597 4.5 30.2 1.0
CE1 A:TYR276 4.7 27.9 1.0
CD A:ARG278 4.8 25.0 1.0
CA A:TYR276 4.8 19.2 1.0
CZ A:PHE279 4.8 10.3 1.0
CD2 A:PHE279 4.9 10.6 1.0
N A:TYR276 5.0 19.8 1.0

Iodine binding site 4 out of 16 in 1xp4

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Iodine binding site 4 out of 16 in the Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae


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 A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I471

b:38.4
occ:0.50
 NE2 A:GLN201 3.6 21.4 1.0
O A:HOH532 4.0 37.5 1.0
CD1 A:LEU70 4.0 7.1 1.0
CE1 A:TYR67 4.1 13.7 1.0
CD1 A:TYR67 4.2 15.7 1.0
CD1 A:LEU77 4.2 12.6 1.0
CD A:GLN201 4.6 21.8 1.0
CG A:GLN201 4.6 21.6 1.0
CG A:LEU77 4.6 16.1 1.0
CD2 A:LEU77 4.6 16.5 1.0
CB A:LEU70 4.8 12.2 1.0
CB A:GLN201 4.8 16.2 1.0
CG A:LEU70 5.0 10.5 1.0

Iodine binding site 5 out of 16 in 1xp4

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Iodine binding site 5 out of 16 in the Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae


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 A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I472

b:19.8
occ:1.00
 O B:HOH492 3.5 17.1 1.0
CG B:GLN374 3.7 21.4 1.0
CG B:GLU45 3.7 20.0 1.0
NE2 B:GLN374 3.7 23.7 1.0
N B:GLN374 3.7 23.1 1.0
CB B:GLU45 4.0 20.0 1.0
CD1 B:ILE42 4.1 5.1 1.0
O B:ALA48 4.2 32.9 1.0
CA B:GLY373 4.2 21.6 1.0
CD B:GLN374 4.2 22.5 1.0
CB B:GLN374 4.2 18.8 1.0
CD B:GLU45 4.3 20.0 1.0
C B:GLY373 4.4 23.4 1.0
CD1 B:ILE33 4.5 15.2 1.0
CD1 B:TYR186 4.5 27.9 1.0
OE2 B:GLU45 4.5 20.0 1.0
CA B:GLN374 4.6 21.0 1.0
CG2 B:THR49 4.8 29.7 1.0

Iodine binding site 6 out of 16 in 1xp4

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Iodine binding site 6 out of 16 in the Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae


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 A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I473

b:43.9
occ:1.00
 N B:ASN38 4.0 20.7 1.0
CB B:ALA37 4.0 18.2 1.0
CA B:ASN38 4.1 22.4 1.0
CB B:ASN38 4.1 24.9 1.0
O B:HOH570 4.2 26.7 1.0
C B:ALA37 4.4 19.7 1.0
CE B:LYS197 4.5 25.5 1.0
OD1 B:ASN38 4.6 31.8 1.0
CD B:ARG260 4.6 18.0 1.0
CG B:LYS197 4.6 21.2 1.0
O B:HOH543 4.6 32.5 1.0
CG B:ASN38 4.7 29.6 1.0
O B:ALA37 4.8 18.5 1.0
CG B:ARG260 4.9 17.9 1.0
CA B:ALA37 4.9 19.2 1.0
CG2 B:ILE196 4.9 22.1 1.0
CD B:LYS197 5.0 22.7 1.0

Iodine binding site 7 out of 16 in 1xp4

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Iodine binding site 7 out of 16 in the Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae


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 A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I474

b:9.5
occ:0.50
 CE2 B:PHE279 3.7 12.7 1.0
CA B:TYR276 3.9 40.1 1.0
CD2 B:PHE279 4.0 12.9 1.0
O B:HOH494 4.2 18.9 1.0
NH2 B:ARG278 4.2 34.8 1.0
CD1 B:TYR276 4.3 40.6 1.0
O B:PRO275 4.3 51.8 1.0
OE1 B:GLU248 4.3 38.2 1.0
C B:TYR276 4.4 37.0 1.0
NE B:ARG278 4.4 36.3 1.0
CB B:TYR276 4.4 40.0 1.0
N B:ALA277 4.7 33.8 1.0
CD2 B:TYR223 4.7 32.5 1.0
CZ B:ARG278 4.8 35.7 1.0
N B:TYR276 4.8 45.1 1.0
CE2 B:TYR223 4.9 35.2 1.0
CZ B:PHE279 4.9 12.8 1.0
CG B:TYR276 4.9 40.0 1.0
C B:PRO275 5.0 50.5 1.0
O B:TYR276 5.0 36.9 1.0

Iodine binding site 8 out of 16 in 1xp4

Go back to Iodine Binding Sites List in 1xp4
Iodine binding site 8 out of 16 in the Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae


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 A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I475

b:56.8
occ:0.50
 NE2 B:GLN201 3.8 13.5 1.0
O B:HOH496 3.9 8.5 1.0
CD1 B:LEU70 4.1 12.8 1.0
CD1 B:LEU77 4.2 13.8 1.0
CE1 B:TYR67 4.2 11.4 1.0
CD2 B:LEU77 4.5 14.9 1.0
CG B:LEU77 4.6 17.4 1.0
CD1 B:TYR67 4.6 11.9 1.0
CG B:GLN201 4.8 16.0 1.0
CD B:GLN201 4.8 16.5 1.0

Iodine binding site 9 out of 16 in 1xp4

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Iodine binding site 9 out of 16 in the Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae


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 A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I476

b:22.8
occ:1.00
 CG C:GLN374 3.5 18.0 1.0
NE2 C:GLN374 3.7 23.2 1.0
N C:GLN374 3.7 20.2 1.0
CG C:GLU45 3.8 26.9 1.0
CD1 C:ILE42 4.0 19.6 1.0
CA C:GLY373 4.1 21.4 1.0
CD C:GLN374 4.1 20.4 1.0
CB C:ALA48 4.2 19.9 1.0
CG2 C:THR49 4.3 25.2 1.0
CB C:GLU45 4.3 22.9 1.0
CB C:GLN374 4.3 17.2 1.0
C C:GLY373 4.4 21.8 1.0
CD1 C:TYR186 4.4 19.8 1.0
CD1 C:ILE33 4.6 15.1 1.0
CD C:GLU45 4.6 29.7 1.0
CA C:GLN374 4.7 20.3 1.0
OE1 C:GLU45 4.7 32.0 1.0
CE1 C:TYR186 4.9 18.7 1.0

Iodine binding site 10 out of 16 in 1xp4

Go back to Iodine Binding Sites List in 1xp4
Iodine binding site 10 out of 16 in the Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae


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 A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I477

b:38.0
occ:1.00
 CB C:ALA37 3.9 19.5 1.0
N C:ASN38 4.0 19.0 1.0
CA C:ASN38 4.1 19.5 1.0
CB C:ASN38 4.3 22.1 1.0
CG C:LYS197 4.3 19.0 1.0
C C:ALA37 4.5 20.2 1.0
CG2 C:ILE196 4.5 16.8 1.0
CD C:ARG260 4.6 19.7 1.0
CG C:ASN38 4.8 25.8 1.0
OD1 C:ASN38 4.8 29.0 1.0
CA C:ALA37 4.9 20.6 1.0
CG C:ARG260 4.9 19.1 1.0

Reference:

C.Morlot, L.Pernot, A.Le Gouellec, A.M.Di Guilmi, T.Vernet, O.Dideberg, A.Dessen. Crystal Structure of A Peptidoglycan Synthesis Regulatory Factor (PBP3) From Streptococcus Pneumoniae J.Biol.Chem. V. 280 15984 2005.
ISSN: ISSN 0021-9258
PubMed: 15596446
DOI: 10.1074/JBC.M408446200
Page generated: Sun Dec 13 19:22:21 2020

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