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Iodine in PDB 3lmu: Crystal Strucutre of Dtd From Plasmodium Falciparum

Protein crystallography data

The structure of Crystal Strucutre of Dtd From Plasmodium Falciparum, PDB code: 3lmu was solved by Y.Manickam, T.K.Bhatt, S.Khan, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.96 / 3.30
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 77.180, 77.180, 214.520, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 25.6

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Iodine atom in the Crystal Strucutre of Dtd From Plasmodium Falciparum (pdb code 3lmu). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 26 binding sites of Iodine where determined in the Crystal Strucutre of Dtd From Plasmodium Falciparum, PDB code: 3lmu:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 26 in 3lmu

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Iodine binding site 1 out of 26 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I165

b:48.9
occ:1.00
OH A:TYR116 3.2 42.5 1.0
N A:SER87 3.3 38.0 1.0
N A:GLY135 3.6 37.3 1.0
CZ A:TYR116 3.6 41.0 1.0
CA A:GLY135 3.7 41.9 1.0
C A:GLY135 3.8 46.4 1.0
CA A:VAL86 3.8 29.9 1.0
O A:GLY135 3.9 46.0 1.0
CE2 A:TYR116 4.0 44.3 1.0
CB A:SER87 4.0 52.1 1.0
O A:ILE85 4.0 37.9 1.0
C A:VAL86 4.1 34.7 1.0
N A:PHE137 4.1 44.0 1.0
CA A:PHE137 4.2 46.5 1.0
CA A:SER87 4.3 40.1 1.0
N A:LYS136 4.3 44.5 1.0
CE1 A:TYR116 4.4 36.6 1.0
C A:LYS136 4.4 41.3 1.0
CG1 A:VAL86 4.6 30.5 1.0
CE A:MET141 4.6 38.1 1.0
CB A:VAL86 4.6 27.9 1.0
SD A:MET141 4.7 27.7 1.0
C A:ILE134 4.8 36.2 1.0
N A:VAL86 4.8 31.5 1.0
CB A:PHE137 4.8 41.1 1.0
CG2 A:VAL86 4.8 33.3 1.0
C A:ILE85 4.8 34.9 1.0
O A:LYS136 4.8 39.0 1.0
CB A:ILE134 4.8 42.0 1.0
O A:SER87 4.9 46.0 1.0
CA A:LYS136 4.9 42.9 1.0
CD1 A:PHE137 4.9 49.1 1.0
CD2 A:TYR116 5.0 45.1 1.0

Iodine binding site 2 out of 26 in 3lmu

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Iodine binding site 2 out of 26 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I165

b:73.5
occ:1.00
N B:SER87 3.4 37.8 1.0
OH B:TYR116 3.5 42.7 1.0
C B:GLY135 3.7 47.4 1.0
CA B:GLY135 3.8 42.9 1.0
N B:GLY135 3.8 37.2 1.0
N B:PHE137 3.8 46.4 1.0
CZ B:TYR116 3.9 43.6 1.0
CA B:PHE137 3.9 45.1 1.0
CB B:SER87 3.9 52.6 1.0
O B:GLY135 4.0 45.9 1.0
CA B:VAL86 4.1 30.8 1.0
C B:LYS136 4.2 43.3 1.0
N B:LYS136 4.2 46.3 1.0
CE2 B:TYR116 4.2 45.7 1.0
C B:VAL86 4.2 34.7 1.0
CA B:SER87 4.3 41.7 1.0
CE B:MET141 4.4 36.7 1.0
O B:ILE85 4.4 40.0 1.0
CB B:PHE137 4.5 41.1 1.0
CE1 B:TYR116 4.5 40.5 1.0
O B:LYS136 4.6 39.4 1.0
CG1 B:VAL86 4.6 32.5 1.0
SD B:MET141 4.6 28.9 1.0
CD1 B:PHE137 4.7 49.5 1.0
O B:SER87 4.7 46.5 1.0
CA B:LYS136 4.7 43.8 1.0
CB B:VAL86 4.8 28.8 1.0
CG B:PHE137 4.9 43.3 1.0
CG2 B:VAL86 4.9 32.5 1.0

Iodine binding site 3 out of 26 in 3lmu

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Iodine binding site 3 out of 26 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I166

b:80.3
occ:1.00
ND2 B:ASN147 3.6 40.0 1.0
ND2 A:ASN147 3.8 44.0 1.0
OD1 B:ASN147 3.9 51.0 1.0
NE2 B:GLN6 4.0 46.5 1.0
CG1 B:VAL145 4.1 41.5 1.0
NE2 A:GLN6 4.1 44.9 1.0
CB B:VAL145 4.2 36.4 1.0
CG B:GLN6 4.2 35.8 1.0
CG B:ASN147 4.2 40.2 1.0
CG1 A:VAL145 4.3 40.3 1.0
OD1 A:ASN147 4.3 55.5 1.0
CG2 B:VAL145 4.3 33.6 1.0
CB A:VAL145 4.3 38.0 1.0
CD B:GLN6 4.4 45.3 1.0
CG A:GLN6 4.4 32.6 1.0
CG2 A:VAL145 4.4 36.8 1.0
CE2 A:PHE40 4.5 32.4 1.0
CG A:ASN147 4.5 45.4 1.0
CE2 B:PHE40 4.5 32.7 1.0
CD A:GLN6 4.6 41.9 1.0
CZ A:PHE40 4.7 34.1 1.0
CZ B:PHE40 4.7 31.9 1.0
CB B:GLN6 4.9 33.4 1.0

Iodine binding site 4 out of 26 in 3lmu

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Iodine binding site 4 out of 26 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I167

b:85.0
occ:0.53
OD1 B:ASN99 3.4 22.9 1.0
CB A:ARG57 3.6 31.4 1.0
ND2 B:ASN99 3.6 35.7 1.0
CG B:ASN99 3.8 31.2 1.0
C A:ARG57 4.3 32.7 1.0
CA A:ARG57 4.5 35.5 1.0
O A:ARG57 4.5 31.6 1.0
N A:LYS58 4.6 36.5 1.0
CB A:ASN61 4.6 34.5 1.0
CG A:ASN61 4.8 42.2 1.0
ND2 A:ASN61 4.8 43.4 1.0

Iodine binding site 5 out of 26 in 3lmu

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Iodine binding site 5 out of 26 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I168

b:74.6
occ:0.56
OG B:SER87 3.1 62.3 1.0
N B:ILE43 3.8 52.2 1.0
CB B:PHE89 3.9 41.5 1.0
CB B:ILE43 4.0 42.9 1.0
CA B:PHE89 4.1 43.4 1.0
N B:PHE89 4.2 42.6 1.0
O B:ILE43 4.4 60.1 1.0
CA B:ILE43 4.4 52.0 1.0
O B:LEU41 4.4 47.3 1.0
CB B:ALA112 4.4 55.0 1.0
CB B:SER87 4.5 52.6 1.0
C B:GLN88 4.6 42.6 1.0
N B:GLN88 4.6 36.3 1.0
C B:GLY42 4.8 49.0 1.0
CA B:GLY42 4.8 44.7 1.0
CZ B:PHE137 4.8 49.9 1.0
C B:ILE43 4.9 56.5 1.0
O B:GLN88 4.9 43.3 1.0

Iodine binding site 6 out of 26 in 3lmu

Go back to Iodine Binding Sites List in 3lmu
Iodine binding site 6 out of 26 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I169

b:76.1
occ:0.42
CE2 B:PHE115 3.9 64.6 1.0
CD2 B:PHE115 4.1 61.6 1.0
CB B:TRP49 4.2 50.2 1.0
N B:TRP49 4.5 58.5 1.0
CA B:TRP49 4.8 52.4 1.0

Iodine binding site 7 out of 26 in 3lmu

Go back to Iodine Binding Sites List in 3lmu
Iodine binding site 7 out of 26 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I165

b:65.3
occ:0.98
N C:SER87 3.3 36.9 1.0
OH C:TYR116 3.5 44.0 1.0
N C:GLY135 3.9 37.5 1.0
CA C:GLY135 3.9 45.4 1.0
CB C:SER87 3.9 52.4 1.0
C C:GLY135 3.9 48.3 1.0
CZ C:TYR116 3.9 43.7 1.0
CA C:VAL86 4.0 31.3 1.0
N C:PHE137 4.0 47.1 1.0
CA C:PHE137 4.0 47.2 1.0
C C:VAL86 4.1 35.6 1.0
CA C:SER87 4.2 40.7 1.0
O C:GLY135 4.2 47.6 1.0
C C:LYS136 4.3 44.9 1.0
CE2 C:TYR116 4.3 43.6 1.0
N C:LYS136 4.3 42.7 1.0
CE C:MET141 4.3 39.2 1.0
O C:ILE85 4.4 38.2 1.0
CG1 C:VAL86 4.5 32.6 1.0
CE1 C:TYR116 4.5 41.2 1.0
O C:SER87 4.6 43.2 1.0
SD C:MET141 4.6 31.1 1.0
CB C:PHE137 4.7 39.6 1.0
O C:LYS136 4.7 40.2 1.0
CB C:VAL86 4.7 27.9 1.0
CD1 C:PHE137 4.8 47.6 1.0
CA C:LYS136 4.9 42.2 1.0
C C:SER87 4.9 41.2 1.0
CG2 C:VAL86 4.9 31.6 1.0

Iodine binding site 8 out of 26 in 3lmu

Go back to Iodine Binding Sites List in 3lmu
Iodine binding site 8 out of 26 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I166

b:62.3
occ:0.65
O C:PHE92 3.6 55.7 1.0
NH1 C:ARG2 3.7 52.3 1.0
CD1 C:LEU105 3.9 68.1 1.0
CD2 C:LEU105 3.9 49.6 1.0
CB C:ASN94 4.0 58.1 1.0
CA C:ASN94 4.1 48.8 1.0
C C:PHE92 4.1 40.2 1.0
N C:ASN94 4.2 50.6 1.0
CA C:PHE92 4.3 40.7 1.0
NH2 C:ARG2 4.4 65.3 1.0
C C:GLY93 4.5 51.0 1.0
CG C:LEU105 4.5 58.0 1.0
CZ C:ARG2 4.5 60.0 1.0
CD1 C:PHE92 4.5 52.3 1.0
ND2 C:ASN94 4.6 42.8 1.0
CG C:ASN94 4.6 54.6 1.0
O C:GLY93 4.7 54.1 1.0
CB C:PHE92 4.8 34.6 1.0
N C:GLY93 5.0 39.9 1.0

Iodine binding site 9 out of 26 in 3lmu

Go back to Iodine Binding Sites List in 3lmu
Iodine binding site 9 out of 26 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I167

b:75.0
occ:0.52
ND2 C:ASN99 3.3 65.8 1.0
CG C:ASN99 4.2 57.0 1.0
OD1 C:ASN99 4.3 58.4 1.0
CG D:ASN61 4.4 44.2 1.0
OD1 D:ASN61 4.4 54.7 1.0
CB D:ASN61 4.5 38.2 1.0
ND2 D:ASN61 4.8 37.6 1.0
CB D:ARG57 4.9 30.1 1.0

Iodine binding site 10 out of 26 in 3lmu

Go back to Iodine Binding Sites List in 3lmu
Iodine binding site 10 out of 26 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I168

b:55.1
occ:0.38
CB C:TRP49 3.6 53.4 1.0
CE2 C:PHE115 3.6 65.0 1.0
N C:TRP49 3.9 60.9 1.0
CD2 C:PHE115 4.1 62.4 1.0
CA C:TRP49 4.1 54.4 1.0
CG C:TRP49 4.6 52.0 1.0
C C:THR48 4.6 61.8 1.0
CE3 C:TRP49 4.7 58.4 1.0
CZ C:PHE115 4.8 59.1 1.0
CD2 C:TRP49 4.9 56.1 1.0

Reference:

M.Yogavel, S.Khan, T.K.Bhatt, A.Sharma. Structure of D-Tyrosyl-Trnatyr Deacylase Using Home-Source Cu Kalpha and Moderate-Quality Iodide-Sad Data: Structural Polymorphism and Hepes-Bound Enzyme States Acta Crystallogr.,Sect.D V. 66 584 2010.
ISSN: ISSN 0907-4449
PubMed: 20445234
DOI: 10.1107/S0907444910006062
Page generated: Sun Dec 13 19:28:15 2020

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