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Iodine in PDB 3id2: Crystal Structure of Rsep PDZ2 Domain

Protein crystallography data

The structure of Crystal Structure of Rsep PDZ2 Domain, PDB code: 3id2 was solved by X.Li, B.Wang, L.Feng, J.Wang, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.82 / 3.09
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.961, 108.961, 58.335, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 27

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Rsep PDZ2 Domain (pdb code 3id2). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Crystal Structure of Rsep PDZ2 Domain, PDB code: 3id2:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 3id2

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Iodine binding site 1 out of 10 in the Crystal Structure of Rsep PDZ2 Domain


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 Rsep PDZ2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I101

b:84.7
occ:0.52
 N A:GLU223 3.6 28.9 1.0
CE1 A:HIS220 3.6 58.2 0.5
NZ A:LYS307 3.9 0.9 1.0
CA A:ILE222 3.9 29.5 1.0
NH1 B:ARG265 4.1 51.8 1.0
CG2 A:ILE222 4.1 22.4 1.0
ND1 A:HIS220 4.1 59.6 0.5
O A:MET221 4.3 64.2 1.0
C A:ILE222 4.3 35.0 1.0
CB A:ILE222 4.4 37.5 1.0
CB A:GLU223 4.4 46.5 1.0
CG1 A:ILE222 4.5 34.5 1.0
CA A:GLU223 4.6 34.5 1.0
O A:GLU223 4.6 41.8 1.0
CD A:LYS307 4.7 95.7 1.0
CG A:GLU223 4.7 56.6 1.0
NE2 A:HIS220 4.8 61.5 0.5
OE2 A:GLU223 4.9 64.6 1.0
CE A:LYS307 4.9 0.2 1.0

Iodine binding site 2 out of 10 in 3id2

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Iodine binding site 2 out of 10 in the Crystal Structure of Rsep PDZ2 Domain


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 Rsep PDZ2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I102

b:99.7
occ:0.48
 O A:GLY280 3.3 61.7 1.0
CB A:GLU277 3.9 61.8 1.0
C A:GLY280 4.0 57.7 1.0
N A:PRO282 4.0 43.7 1.0
C A:SER281 4.0 49.5 1.0
CG A:GLU277 4.1 82.2 1.0
CB A:PRO282 4.1 32.2 1.0
CA A:PRO282 4.2 37.3 1.0
OE2 A:GLU277 4.2 94.7 1.0
O A:SER281 4.3 50.8 1.0
CA A:SER281 4.4 52.1 1.0
CG A:PRO282 4.4 31.3 1.0
CA A:GLU277 4.4 46.6 1.0
N A:SER281 4.5 56.3 1.0
CD A:PRO282 4.6 39.6 1.0
CD A:GLU277 4.7 96.6 1.0
CA A:GLY280 4.8 53.4 1.0
O A:ILE276 5.0 39.6 1.0

Iodine binding site 3 out of 10 in 3id2

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Iodine binding site 3 out of 10 in the Crystal Structure of Rsep PDZ2 Domain


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 Rsep PDZ2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I103

b:0.1
occ:0.63
 CA A:PRO293 4.0 0.9 1.0
N A:PRO293 4.1 93.1 1.0
OG A:SER291 4.2 64.7 1.0
C A:LYS292 4.3 79.4 1.0
O A:LYS292 4.4 73.7 1.0
O A:SER291 4.4 63.1 1.0
C A:SER291 4.6 63.4 1.0
CB A:SER291 4.7 60.1 1.0
CD A:PRO293 4.7 97.2 1.0
CB A:ALA298 4.7 52.8 1.0
N A:LYS292 4.8 68.2 1.0
CG A:PRO293 4.9 99.7 1.0
O A:PRO293 4.9 0.8 1.0
CB A:PRO293 5.0 0.2 1.0
CA A:LYS292 5.0 74.9 1.0
C A:PRO293 5.0 0.0 1.0

Iodine binding site 4 out of 10 in 3id2

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Iodine binding site 4 out of 10 in the Crystal Structure of Rsep PDZ2 Domain


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 Rsep PDZ2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I104

b:93.4
occ:0.56
 O A:HIS220 3.8 57.3 0.5
NH2 B:ARG265 4.3 41.3 1.0
OD1 B:ASP266 4.4 0.7 1.0
CA B:MET262 4.4 63.1 1.0
O B:MET262 4.5 64.7 1.0
CG A:MET221 4.6 36.8 1.0
CB B:MET262 4.6 66.9 1.0
CB B:ASP266 4.7 97.0 1.0
CA A:MET221 4.7 49.1 1.0
CB B:ARG265 4.8 67.5 1.0
O A:HIS220 4.9 63.0 0.5
C A:HIS220 4.9 61.4 0.5
C B:MET262 4.9 65.1 1.0
CG B:MET262 4.9 65.2 1.0

Iodine binding site 5 out of 10 in 3id2

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Iodine binding site 5 out of 10 in the Crystal Structure of Rsep PDZ2 Domain


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 Rsep PDZ2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I105

b:0.0
occ:0.62
 CB B:ILE222 3.5 51.5 1.0
CG1 B:VAL258 3.6 55.4 1.0
CE B:MET221 4.0 0.5 1.0
N B:ILE222 4.1 61.9 1.0
CG1 B:ILE222 4.1 45.2 1.0
SD B:MET221 4.1 0.5 1.0
N B:VAL258 4.2 56.7 1.0
CB B:VAL258 4.3 52.5 1.0
CB B:TRP257 4.3 52.8 1.0
CA B:ILE222 4.3 60.6 1.0
CG2 B:ILE222 4.4 27.5 1.0
O B:ILE222 4.5 81.8 1.0
N B:TRP257 4.5 63.0 1.0
CD1 B:ILE222 4.5 38.1 1.0
CD1 B:TRP257 4.8 56.2 1.0
CG2 A:VAL258 4.8 21.5 1.0
C B:ILE222 4.8 73.6 1.0
CA B:VAL258 4.8 55.4 1.0
CA B:TRP257 4.9 60.2 1.0
CB B:MET221 4.9 88.8 1.0

Iodine binding site 6 out of 10 in 3id2

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Iodine binding site 6 out of 10 in the Crystal Structure of Rsep PDZ2 Domain


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 Rsep PDZ2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I101

b:91.1
occ:0.52
 NZ B:LYS307 3.5 0.1 1.0
CE1 B:HIS220 3.6 91.1 0.5
N B:GLU223 3.9 75.0 1.0
NH1 A:ARG265 3.9 72.8 1.0
CD B:GLU223 4.2 0.7 1.0
ND1 B:HIS220 4.2 91.3 0.5
OE2 B:GLU223 4.3 0.2 1.0
O B:MET221 4.3 84.4 1.0
CA B:ILE222 4.3 60.6 1.0
OE1 B:GLU223 4.3 0.4 1.0
CB B:GLU223 4.5 93.4 1.0
C B:ILE222 4.6 73.6 1.0
CG2 B:ILE222 4.6 27.5 1.0
NE2 B:HIS220 4.6 92.0 0.5
CD B:LYS307 4.6 92.4 1.0
CE B:LYS307 4.7 98.9 1.0
CG1 B:ILE222 4.7 45.2 1.0
CG B:GLU223 4.8 0.5 1.0
CA B:GLU223 4.8 82.7 1.0
CB B:ILE222 4.8 51.5 1.0
CZ A:ARG265 5.0 68.3 1.0

Iodine binding site 7 out of 10 in 3id2

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Iodine binding site 7 out of 10 in the Crystal Structure of Rsep PDZ2 Domain


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 Rsep PDZ2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I102

b:0.5
occ:0.48
 O B:GLY280 3.1 0.5 1.0
CG B:PRO282 3.6 0.5 1.0
CG B:GLU277 3.9 0.9 1.0
CB B:GLU277 4.0 0.4 1.0
CD B:PRO282 4.1 0.8 1.0
N B:PRO282 4.2 0.0 1.0
C B:GLY280 4.2 0.4 1.0
OE2 B:GLU277 4.2 0.5 1.0
CB B:PRO282 4.2 0.1 1.0
CD B:GLU277 4.2 0.8 1.0
CA B:PRO282 4.3 0.7 1.0
C B:SER281 4.8 0.3 1.0
CA B:GLU277 4.8 0.9 1.0
CA B:GLY280 4.8 0.7 1.0

Iodine binding site 8 out of 10 in 3id2

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Iodine binding site 8 out of 10 in the Crystal Structure of Rsep PDZ2 Domain


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 Rsep PDZ2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I103

b:0.5
occ:0.63
 N B:PRO293 3.7 0.2 1.0
C B:LYS292 3.7 0.6 1.0
CA B:PRO293 3.7 0.9 1.0
O B:LYS292 3.8 0.4 1.0
OG B:SER291 3.8 0.5 1.0
O B:SER291 3.8 99.8 1.0
CD B:PRO293 4.2 0.7 1.0
C B:SER291 4.2 0.1 1.0
CB B:ALA298 4.4 96.4 1.0
CA B:LYS292 4.5 0.7 1.0
N B:LYS292 4.5 0.8 1.0
CG B:PRO293 4.6 0.5 1.0
CA B:ALA298 4.6 96.4 1.0
O B:PRO293 4.7 1.0 1.0
CB B:PRO293 4.7 0.9 1.0
C B:PRO293 4.8 0.2 1.0
CB B:SER291 4.8 0.8 1.0

Iodine binding site 9 out of 10 in 3id2

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Iodine binding site 9 out of 10 in the Crystal Structure of Rsep PDZ2 Domain


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 Rsep PDZ2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I310

b:0.3
occ:0.56
 O B:HIS220 2.8 85.6 0.5
O B:HIS220 3.2 89.8 0.5
C B:HIS220 3.6 91.5 0.5
C B:HIS220 3.8 92.3 0.5
CA B:MET221 3.8 84.6 1.0
NH2 A:ARG265 3.8 75.7 1.0
CE B:MET221 3.8 0.5 1.0
N B:MET221 4.0 92.9 1.0
OD1 A:ASP266 4.4 82.1 1.0
CB A:ARG265 4.5 40.7 1.0
CG B:MET221 4.5 90.5 1.0
SD B:MET221 4.6 0.5 1.0
CA B:HIS220 4.7 93.2 0.5
N B:HIS220 4.7 89.1 0.5
CB B:MET221 4.7 88.8 1.0
C B:MET221 4.8 76.2 1.0
N B:HIS220 4.8 89.4 0.5
CA B:HIS220 4.9 93.5 0.5
O B:MET221 5.0 84.4 1.0

Iodine binding site 10 out of 10 in 3id2

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Iodine binding site 10 out of 10 in the Crystal Structure of Rsep PDZ2 Domain


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 Rsep PDZ2 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I105

b:0.0
occ:0.62
 CE A:MET221 3.3 0.2 1.0
CG1 A:ILE222 3.4 34.5 1.0
N A:ILE222 3.5 29.1 1.0
CB A:MET221 3.7 38.6 1.0
CB A:ILE222 3.7 37.5 1.0
CD1 A:ILE222 4.1 30.3 1.0
CA A:ILE222 4.2 29.5 1.0
C A:MET221 4.3 48.4 1.0
CG1 B:VAL261 4.3 26.7 1.0
CA A:MET221 4.3 49.1 1.0
CG A:MET221 4.4 36.8 1.0
CD B:ARG265 4.5 59.0 1.0
SD A:MET221 4.5 46.6 1.0
NH2 B:ARG265 4.7 41.3 1.0
NE B:ARG265 4.9 54.1 1.0
CG B:MET262 4.9 65.2 1.0
CB B:VAL261 5.0 51.8 1.0

Reference:

X.Li, B.Wang, L.Feng, H.Kang, Y.Qi, J.Wang, Y.Shi. Cleavage of Rsea By Rsep Requires A Carboxyl-Terminal Hydrophobic Amino Acid Following Degs Cleavage Proc.Natl.Acad.Sci.Usa V. 106 14837 2009.
ISSN: ISSN 0027-8424
PubMed: 19706448
DOI: 10.1073/PNAS.0903289106
Page generated: Sun Aug 11 15:21:23 2024

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