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Iodine in PDB 3dhx: Crystal Structure of Isolated C2 Domain of the Methionine Uptake Transporter

Protein crystallography data

The structure of Crystal Structure of Isolated C2 Domain of the Methionine Uptake Transporter, PDB code: 3dhx was solved by E.Johnson, J.T.Kaiser, A.T.Lee, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.11 / 2.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 53.277, 53.277, 150.495, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 23.8

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Isolated C2 Domain of the Methionine Uptake Transporter (pdb code 3dhx). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Crystal Structure of Isolated C2 Domain of the Methionine Uptake Transporter, PDB code: 3dhx:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 3dhx

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Iodine binding site 1 out of 12 in the Crystal Structure of Isolated C2 Domain of the Methionine Uptake Transporter


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 Isolated C2 Domain of the Methionine Uptake Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I360

b:75.5
occ:0.26
 O B:ARG43 2.7 14.2 1.0
O B:HOH443 2.9 15.9 1.0
CD A:ARG43 3.3 10.4 1.0
C B:ARG43 3.6 13.3 1.0
O A:HOH445 3.6 2.7 1.0
CA B:ARG43 3.7 13.3 1.0
O B:ALA42 3.8 11.1 1.0
OD1 B:ASN46 3.8 21.0 1.0
CB B:ASN46 3.9 11.8 1.0
CA B:ASN46 3.9 12.0 1.0
CG A:ARG43 3.9 14.9 1.0
N B:ASN46 4.1 11.5 1.0
CG B:ASN46 4.1 16.9 1.0
NE A:ARG43 4.6 14.7 1.0
CB B:ARG43 4.6 13.0 1.0
C B:ALA42 4.7 10.8 1.0
N B:ARG43 4.7 11.8 1.0
N B:ARG44 4.8 13.5 1.0
O A:HOH444 5.0 36.2 1.0
CG B:ARG43 5.0 14.6 1.0

Iodine binding site 2 out of 12 in 3dhx

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Iodine binding site 2 out of 12 in the Crystal Structure of Isolated C2 Domain of the Methionine Uptake Transporter


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 Isolated C2 Domain of the Methionine Uptake Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I154

b:40.4
occ:1.00
 CD A:PRO36 3.6 11.3 1.0
CH2 A:TRP84 3.8 13.9 1.0
CG A:PRO36 4.0 12.0 1.0
CZ2 A:TRP84 4.1 12.4 1.0
CG A:GLU40 4.2 16.8 1.0
CD2 A:LEU37 4.2 16.3 1.0
CB A:GLU40 4.4 9.9 1.0
N A:PRO36 4.4 9.2 1.0
C A:PRO36 4.7 9.8 1.0
O A:PRO36 4.7 8.4 1.0
CA A:LEU37 4.9 9.2 1.0
N A:LEU37 4.9 8.8 1.0
CZ3 A:TRP84 4.9 11.9 1.0
CE1 A:HIS88 4.9 20.6 1.0
C A:ALA35 5.0 9.8 1.0

Iodine binding site 3 out of 12 in 3dhx

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Iodine binding site 3 out of 12 in the Crystal Structure of Isolated C2 Domain of the Methionine Uptake Transporter


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 Isolated C2 Domain of the Methionine Uptake Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I247

b:19.6
occ:1.00
 O A:HOH400 3.6 17.0 1.0
CA A:GLU15 3.8 14.8 1.0
O A:ALA14 3.9 14.8 1.0
C A:ALA14 4.0 15.2 1.0
CB A:GLU15 4.1 15.3 1.0
N A:GLU15 4.1 15.0 1.0
CB A:ALA14 4.3 17.8 1.0
CG A:GLU15 4.4 12.6 1.0
OE1 A:GLU15 4.8 15.1 1.0
CD A:PRO16 4.8 19.3 1.0
O A:HOH496 4.8 55.8 1.0
CA A:ALA14 4.9 15.6 1.0

Iodine binding site 4 out of 12 in 3dhx

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Iodine binding site 4 out of 12 in the Crystal Structure of Isolated C2 Domain of the Methionine Uptake Transporter


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 Isolated C2 Domain of the Methionine Uptake Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I248

b:16.8
occ:1.00
 O A:HOH470 3.6 23.4 1.0
OG A:SER53 3.6 11.2 1.0
CA A:ALA54 3.9 9.3 1.0
CG A:GLN55 3.9 16.2 1.0
N A:ALA54 3.9 8.2 1.0
N A:GLN55 4.0 10.4 1.0
CG2 A:ILE66 4.0 18.0 1.0
C A:ALA54 4.0 11.1 1.0
C A:SER53 4.0 7.3 1.0
CB A:SER53 4.1 6.2 1.0
O A:SER53 4.1 5.5 1.0
O A:ILE66 4.1 9.8 1.0
CG A:LEU68 4.2 6.0 1.0
CB A:ILE66 4.4 13.8 1.0
N A:LEU68 4.4 8.1 1.0
C A:ILE66 4.5 10.7 1.0
CD1 A:LEU68 4.5 4.7 1.0
O A:HOH425 4.6 9.0 1.0
CA A:MET67 4.6 10.6 1.0
CB A:GLN55 4.6 12.7 1.0
C A:MET67 4.7 9.0 1.0
O A:ALA54 4.7 11.2 1.0
CA A:SER53 4.7 6.6 1.0
N A:MET67 4.7 10.0 1.0
CA A:GLN55 4.9 11.8 1.0
CB A:LEU68 4.9 7.7 1.0
OE1 A:GLN55 5.0 30.9 1.0
CD A:GLN55 5.0 29.7 1.0

Iodine binding site 5 out of 12 in 3dhx

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Iodine binding site 5 out of 12 in the Crystal Structure of Isolated C2 Domain of the Methionine Uptake Transporter


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 Isolated C2 Domain of the Methionine Uptake Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I262

b:38.0
occ:1.00
 O A:HOH461 2.2 33.9 1.0
ND2 A:ASN48 3.5 12.4 1.0
CG A:HIS72 3.8 10.2 1.0
ND1 A:HIS72 3.9 15.6 1.0
O B:HOH463 3.9 42.1 1.0
OD1 A:ASN50 3.9 18.5 1.0
CG B:PRO36 4.0 15.1 1.0
CB A:HIS72 4.1 12.7 1.0
ND2 A:ASN50 4.3 10.6 1.0
CD2 A:HIS72 4.3 12.9 1.0
CE1 A:HIS72 4.3 9.4 1.0
CD B:PRO36 4.4 12.2 1.0
CB A:ASN48 4.4 7.7 1.0
O B:ASP34 4.4 16.3 1.0
CG A:ASN48 4.4 9.3 1.0
CB B:PRO36 4.4 11.7 1.0
CG A:ASN50 4.5 13.7 1.0
NE2 A:HIS72 4.5 11.3 1.0

Iodine binding site 6 out of 12 in 3dhx

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Iodine binding site 6 out of 12 in the Crystal Structure of Isolated C2 Domain of the Methionine Uptake Transporter


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 Isolated C2 Domain of the Methionine Uptake Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I263

b:12.9
occ:1.00
 O A:HOH462 0.7 8.5 1.0
O A:HOH463 1.2 10.7 1.0
O A:HOH405 3.4 6.9 1.0
NZ A:LYS63 3.5 7.9 1.0
O B:HOH408 3.7 6.7 1.0
O A:HOH420 3.7 15.0 1.0
N A:LEU38 3.9 8.5 1.0
N B:ILE51 3.9 7.2 1.0
CG A:LEU38 4.1 8.9 1.0
CB A:LEU38 4.2 7.6 1.0
N A:LEU37 4.2 8.8 1.0
CD1 A:LEU38 4.2 8.3 1.0
CB B:ILE51 4.2 6.1 1.0
CD1 B:ILE51 4.2 7.5 1.0
CG1 B:ILE51 4.2 5.5 1.0
O B:ASN49 4.3 9.3 1.0
CZ A:PHE28 4.4 12.9 1.0
O A:HOH403 4.4 13.1 1.0
O A:ALA35 4.5 9.5 1.0
CE1 A:PHE28 4.5 13.4 1.0
CA A:LEU38 4.6 8.0 1.0
CA B:ILE51 4.7 6.7 1.0
CE A:LYS63 4.7 8.6 1.0
CA B:ASN50 4.7 9.8 1.0
C A:PRO36 4.8 9.8 1.0
C A:LEU37 4.8 9.6 1.0
C B:ASN50 4.8 8.7 1.0
CA A:LEU37 4.8 9.2 1.0
CB A:LEU37 4.9 11.1 1.0
CA A:PRO36 5.0 9.7 1.0

Iodine binding site 7 out of 12 in 3dhx

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Iodine binding site 7 out of 12 in the Crystal Structure of Isolated C2 Domain of the Methionine Uptake Transporter


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 Isolated C2 Domain of the Methionine Uptake Transporter within 5.0Å range:

Iodine binding site 8 out of 12 in 3dhx

Go back to Iodine Binding Sites List in 3dhx
Iodine binding site 8 out of 12 in the Crystal Structure of Isolated C2 Domain of the Methionine Uptake Transporter


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 Isolated C2 Domain of the Methionine Uptake Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I256

b:12.2
occ:1.00
 NZ B:LYS63 3.3 14.5 1.0
O A:HOH408 3.6 7.3 1.0
O A:HOH394 3.7 9.5 1.0
O B:HOH417 3.8 6.5 1.0
N B:LEU38 3.9 7.5 1.0
CG B:LEU38 4.0 10.9 1.0
N A:ILE51 4.1 7.3 1.0
CD1 A:ILE51 4.1 7.2 1.0
CD1 B:LEU38 4.1 10.1 1.0
CB B:LEU38 4.1 5.8 1.0
N B:LEU37 4.2 10.5 1.0
CG1 A:ILE51 4.2 5.8 1.0
CB A:ILE51 4.2 7.4 1.0
O A:ASN49 4.3 7.8 1.0
O B:HOH400 4.4 10.2 1.0
O B:ALA35 4.5 13.1 1.0
CE B:LYS63 4.6 21.6 1.0
CB B:LEU37 4.6 11.1 1.0
CA B:LEU38 4.7 6.4 1.0
CA B:LEU37 4.7 10.6 1.0
CZ B:PHE28 4.8 16.8 1.0
CA A:ILE51 4.8 7.0 1.0
C B:LEU37 4.8 9.4 1.0
CE1 B:PHE28 4.8 19.2 1.0
C B:PRO36 4.8 11.7 1.0
CA B:PRO36 5.0 13.1 1.0
CA A:ASN50 5.0 9.3 1.0

Iodine binding site 9 out of 12 in 3dhx

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Iodine binding site 9 out of 12 in the Crystal Structure of Isolated C2 Domain of the Methionine Uptake Transporter


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 Isolated C2 Domain of the Methionine Uptake Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I265

b:0.0
occ:1.00
 O B:HOH459 1.7 75.3 1.0
O B:HOH440 2.1 73.8 1.0
O B:HOH452 3.8 53.7 1.0
CB B:GLU100 3.9 37.2 1.0
O B:HOH430 4.3 80.6 1.0
O B:HOH431 4.4 36.1 1.0
O B:GLU100 4.5 39.2 1.0
O B:HOH396 4.5 45.1 1.0
N B:GLU100 4.5 31.9 1.0
CG B:GLU100 4.6 41.6 1.0
CA B:GLU100 4.8 35.8 1.0
O B:LEU99 4.8 28.5 1.0
C B:LEU99 5.0 28.3 1.0

Iodine binding site 10 out of 12 in 3dhx

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Iodine binding site 10 out of 12 in the Crystal Structure of Isolated C2 Domain of the Methionine Uptake Transporter


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 Isolated C2 Domain of the Methionine Uptake Transporter within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I280

b:16.2
occ:1.00
 OG B:SER53 3.5 7.5 1.0
O B:HOH484 3.8 32.2 1.0
N B:ALA54 3.9 8.2 1.0
CA B:ALA54 3.9 10.7 1.0
N B:GLN55 4.0 11.5 1.0
O B:ILE66 4.0 8.0 1.0
CG B:GLN55 4.1 16.9 1.0
CB B:SER53 4.1 6.7 1.0
C B:SER53 4.1 8.3 1.0
CG2 B:ILE66 4.1 14.6 1.0
C B:ALA54 4.1 11.5 1.0
O B:SER53 4.2 9.3 1.0
CG B:LEU68 4.3 10.8 1.0
C B:ILE66 4.4 10.5 1.0
CB B:ILE66 4.4 13.4 1.0
N B:LEU68 4.5 6.8 1.0
CB B:GLN55 4.6 12.2 1.0
CD1 B:LEU68 4.6 10.2 1.0
CA B:MET67 4.7 9.2 1.0
O B:HOH482 4.7 17.1 1.0
CA B:SER53 4.8 6.4 1.0
N B:MET67 4.8 8.0 1.0
C B:MET67 4.8 8.3 1.0
CA B:GLN55 4.9 12.9 1.0
O B:ALA54 4.9 12.1 1.0

Reference:

N.S.Kadaba, J.T.Kaiser, E.Johnson, A.Lee, D.C.Rees. The High-Affinity E. Coli Methionine Abc Transporter: Structure and Allosteric Regulation. Science V. 321 250 2008.
ISSN: ISSN 0036-8075
PubMed: 18621668
DOI: 10.1126/SCIENCE.1157987
Page generated: Sun Aug 11 14:58:54 2024

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