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Iodine in PDB 3w4s: Myo-Inositol Kinase From Thermococcus Kodakarensis

Protein crystallography data

The structure of Myo-Inositol Kinase From Thermococcus Kodakarensis, PDB code: 3w4s was solved by M.Fujihashi, Y.Miyamoto, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.94 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.306, 78.338, 83.875, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Iodine atom in the Myo-Inositol Kinase From Thermococcus Kodakarensis (pdb code 3w4s). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 30 binding sites of Iodine where determined in the Myo-Inositol Kinase From Thermococcus Kodakarensis, PDB code: 3w4s:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 30 in 3w4s

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Iodine binding site 1 out of 30 in the Myo-Inositol Kinase From Thermococcus Kodakarensis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Myo-Inositol Kinase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:17.3
occ:1.00
 NH2 B:ARG11 3.6 18.9 1.0
NH2 A:ARG11 3.7 17.3 1.0
N A:PRO51 3.8 15.9 1.0
N B:PRO51 3.8 18.3 1.0
C A:LEU50 3.8 15.9 1.0
C B:LEU50 3.9 17.2 1.0
CD B:PRO51 4.0 18.7 1.0
O A:HOH676 4.1 33.8 1.0
CD A:PRO51 4.1 16.0 1.0
NH1 B:ARG11 4.1 18.5 1.0
CA B:LEU50 4.2 16.5 1.0
O A:LEU50 4.2 16.4 1.0
CA A:LEU50 4.2 15.8 1.0
CB B:ASN49 4.3 17.5 1.0
CA A:PRO51 4.3 16.9 1.0
CG B:PRO51 4.3 19.3 1.0
O B:LEU50 4.3 17.4 1.0
CB A:ASN49 4.3 19.4 1.0
N B:LEU50 4.3 16.5 1.0
CZ B:ARG11 4.4 18.0 1.0
O B:HOH478 4.4 24.1 1.0
N A:LEU50 4.4 16.5 1.0
CA B:PRO51 4.4 19.5 1.0
C B:ASN49 4.4 16.9 1.0
NH1 A:ARG11 4.4 17.3 1.0
O B:ASN49 4.5 16.6 1.0
CZ A:ARG11 4.5 16.4 1.0
C A:ASN49 4.5 17.1 1.0
CG A:PRO51 4.5 16.2 1.0
O A:ASN49 4.7 17.1 1.0
O B:HOH435 4.9 18.2 1.0

Iodine binding site 2 out of 30 in 3w4s

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Iodine binding site 2 out of 30 in the Myo-Inositol Kinase From Thermococcus Kodakarensis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Myo-Inositol Kinase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:22.1
occ:0.86
 O A:HOH631 3.4 28.2 1.0
O A:HOH509 3.6 18.1 1.0
CA A:GLU91 4.0 12.3 1.0
N A:GLU91 4.0 12.6 1.0
O A:LEU90 4.0 13.4 1.0
C A:LEU90 4.1 13.5 1.0
NZ B:LYS15 4.1 23.9 1.0
CG A:PRO144 4.2 21.7 1.0
CB A:PRO144 4.2 21.3 1.0
C A:GLU91 4.3 11.6 1.0
CD2 A:LEU89 4.3 13.8 1.0
N A:ARG92 4.3 11.7 1.0
CG A:LEU89 4.4 13.6 1.0
CA A:PRO144 4.4 20.9 1.0
CB A:ARG92 4.6 13.3 1.0
CE B:LYS15 4.8 24.3 1.0
N A:PRO144 4.9 20.4 1.0
O A:LEU89 4.9 14.2 1.0
CA A:LEU90 5.0 14.2 1.0
O A:GLU91 5.0 11.2 1.0

Iodine binding site 3 out of 30 in 3w4s

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Iodine binding site 3 out of 30 in the Myo-Inositol Kinase From Thermococcus Kodakarensis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Myo-Inositol Kinase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:18.6
occ:0.80
 O A:HOH533 3.4 21.0 1.0
O A:HOH636 3.4 32.6 1.0
OG A:SER123 3.5 18.6 1.0
O A:HOH583 3.8 28.9 1.0
N A:ALA124 3.9 17.1 1.0
C A:SER123 3.9 17.5 1.0
CA A:ALA124 3.9 17.1 1.0
CB A:SER123 4.0 18.6 1.0
O A:SER123 4.1 18.2 1.0
CD1 A:LEU99 4.2 18.9 1.0
CD A:LYS127 4.2 25.7 1.0
CE1 A:PHE128 4.3 23.6 1.0
O A:HOH635 4.3 27.8 1.0
CB A:LYS127 4.4 23.0 1.0
CB A:ALA124 4.4 17.3 1.0
O A:HOH581 4.5 25.4 1.0
CB A:LEU99 4.5 18.2 1.0
CD1 A:LEU120 4.5 18.4 1.0
O A:HOH640 4.6 38.3 1.0
CA A:SER123 4.6 18.3 1.0
O A:HOH540 4.6 21.3 1.0
CG A:LEU99 4.7 18.7 1.0
CD1 A:PHE128 4.8 23.5 1.0
CG A:LYS127 4.8 25.0 1.0
O A:LEU120 4.9 17.1 1.0

Iodine binding site 4 out of 30 in 3w4s

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Iodine binding site 4 out of 30 in the Myo-Inositol Kinase From Thermococcus Kodakarensis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Myo-Inositol Kinase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:18.6
occ:0.68
 I A:IOD423 3.3 25.9 0.1
O A:HOH603 3.4 31.8 1.0
O A:HOH514 3.4 17.2 1.0
CD1 A:PHE221 3.9 17.3 1.0
CB A:PRO206 4.0 20.0 1.0
CG A:PHE221 4.1 16.6 1.0
CG2 A:THR245 4.2 15.1 1.0
CE1 A:PHE221 4.2 18.3 1.0
CG A:PRO206 4.2 20.5 1.0
CA A:ALA242 4.2 16.1 1.0
CB A:THR245 4.3 15.1 1.0
CE2 A:PHE204 4.4 22.8 1.0
CA A:PRO206 4.5 19.7 1.0
CB A:ALA242 4.5 16.1 1.0
CD2 A:PHE221 4.5 17.6 1.0
CB A:PHE221 4.5 15.6 1.0
OG1 A:THR245 4.5 14.5 1.0
CZ A:PHE221 4.6 18.1 1.0
O A:ALA242 4.6 15.8 1.0
CE2 A:PHE221 4.8 18.2 1.0
C A:ALA242 5.0 16.3 1.0

Iodine binding site 5 out of 30 in 3w4s

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Iodine binding site 5 out of 30 in the Myo-Inositol Kinase From Thermococcus Kodakarensis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Myo-Inositol Kinase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:18.7
occ:0.58
 N A:GLY210 3.8 25.7 1.0
N A:VAL211 3.8 24.6 1.0
CA A:GLY210 4.2 25.3 1.0
CG A:LYS250 4.2 29.0 1.0
CB A:VAL211 4.3 23.4 1.0
CG1 A:VAL211 4.3 22.9 1.0
NZ A:LYS250 4.3 36.0 1.0
C A:GLY210 4.4 25.3 1.0
CB A:LYS250 4.5 25.0 1.0
CA A:VAL211 4.6 23.6 1.0
CE A:LYS250 4.6 34.4 1.0
CA A:LYS250 4.7 23.1 1.0
CB A:VAL209 4.8 24.5 1.0
C A:VAL209 4.8 25.1 1.0

Iodine binding site 6 out of 30 in 3w4s

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Iodine binding site 6 out of 30 in the Myo-Inositol Kinase From Thermococcus Kodakarensis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Myo-Inositol Kinase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:26.4
occ:0.51
 CG A:GLN236 3.9 25.1 1.0
NE2 A:GLN236 4.1 28.5 1.0
O A:ALA265 4.2 24.2 1.0
C A:ALA265 4.2 24.4 1.0
CA A:MET266 4.3 28.3 1.0
CD A:LYS239 4.3 22.3 1.0
CB A:ALA265 4.3 23.1 1.0
N A:MET266 4.3 26.5 1.0
CG A:MET266 4.4 34.5 1.0
CB A:LYS239 4.4 19.8 1.0
NE A:ARG240 4.5 24.4 1.0
CD A:GLN236 4.6 27.5 1.0
CB A:GLN236 4.7 24.0 1.0
CA A:GLN236 4.7 22.1 1.0
CG A:ARG240 4.8 21.0 1.0
O A:GLN236 4.8 21.2 1.0
CB A:MET266 4.9 30.9 1.0
CA A:ALA265 4.9 23.4 1.0

Iodine binding site 7 out of 30 in 3w4s

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Iodine binding site 7 out of 30 in the Myo-Inositol Kinase From Thermococcus Kodakarensis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Myo-Inositol Kinase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:24.2
occ:0.51
 CD A:ARG86 3.9 18.6 1.0
NH1 A:ARG86 3.9 19.4 1.0
O A:ARG85 4.1 18.8 1.0
CD1 A:LEU80 4.5 22.5 1.0
C A:ARG85 4.6 18.4 1.0
O A:HOH585 4.8 28.8 1.0
NE A:ARG86 4.8 19.1 1.0
O A:HOH626 4.8 25.6 1.0
CG A:ARG86 4.9 18.7 1.0
CZ A:ARG86 4.9 18.9 1.0
CB A:ARG84 4.9 18.8 1.0
N A:ARG85 5.0 18.4 1.0
N A:ARG86 5.0 17.4 1.0

Iodine binding site 8 out of 30 in 3w4s

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Iodine binding site 8 out of 30 in the Myo-Inositol Kinase From Thermococcus Kodakarensis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Myo-Inositol Kinase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I408

b:22.0
occ:0.46
 CG A:GLN174 3.7 35.8 1.0
C A:ILE152 4.0 17.9 1.0
CB A:PRO151 4.1 19.1 1.0
C A:PRO151 4.1 17.6 1.0
O A:PRO151 4.1 17.6 1.0
CB A:GLN174 4.1 32.8 1.0
N A:ASP153 4.2 19.8 1.0
N A:ILE152 4.2 17.0 1.0
CA A:ILE152 4.2 16.8 1.0
O A:ILE152 4.2 18.1 1.0
CA A:PRO151 4.8 18.1 1.0
CD A:GLN174 4.8 40.4 1.0
O A:HOH537 4.8 21.5 1.0
CA A:ASP153 4.8 21.9 1.0

Iodine binding site 9 out of 30 in 3w4s

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Iodine binding site 9 out of 30 in the Myo-Inositol Kinase From Thermococcus Kodakarensis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Myo-Inositol Kinase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I409

b:18.2
occ:0.45
 O A:HOH557 2.5 40.6 1.0
I A:IOD416 3.1 18.4 0.2
I A:IOD420 3.4 20.5 0.1
O A:HOH595 3.4 24.3 1.0
N A:GLY26 3.6 13.6 1.0
O A:HOH530 3.7 22.1 1.0
I A:IOD418 4.1 19.9 0.2
CG2 A:THR215 4.3 17.1 1.0
CE2 A:TYR30 4.3 14.0 1.0
CA A:GLY26 4.4 13.8 1.0
CA A:GLY25 4.4 13.1 1.0
OD2 A:ASP12 4.4 16.1 1.0
C A:GLY26 4.5 13.7 1.0
C A:GLY25 4.5 13.1 1.0
CD2 A:TYR30 4.6 13.3 1.0
O A:HOH513 4.7 17.2 1.0
N A:GLY27 4.8 13.3 1.0
O A:GLY26 4.9 13.7 1.0

Iodine binding site 10 out of 30 in 3w4s

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Iodine binding site 10 out of 30 in the Myo-Inositol Kinase From Thermococcus Kodakarensis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Myo-Inositol Kinase From Thermococcus Kodakarensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I410

b:23.3
occ:0.34
 OG1 A:THR203 3.2 25.2 1.0
CG A:GLU269 3.7 35.1 1.0
CB A:THR203 3.8 24.0 1.0
C A:THR203 3.8 22.8 1.0
O A:THR203 3.9 23.6 1.0
CD A:LYS271 3.9 34.6 1.0
N A:PHE204 4.0 23.4 1.0
CA A:PHE204 4.0 22.5 1.0
CE A:LYS271 4.0 35.7 1.0
O A:GLU269 4.1 25.3 1.0
CG A:LYS271 4.1 30.9 1.0
C A:PHE204 4.1 22.8 1.0
N A:GLU205 4.2 22.0 1.0
CB A:GLU269 4.2 29.7 1.0
C A:GLU269 4.4 25.4 1.0
N A:LYS271 4.4 24.7 1.0
CB A:LYS271 4.5 28.6 1.0
CA A:THR203 4.5 23.2 1.0
CB A:GLU205 4.6 25.7 1.0
O A:PHE204 4.6 22.3 1.0
N A:VAL270 4.7 24.4 1.0
CA A:VAL270 4.7 24.0 1.0
C A:VAL270 4.8 24.3 1.0
CD A:GLU269 4.9 37.7 1.0
CA A:GLU205 5.0 22.8 1.0
CA A:GLU269 5.0 26.4 1.0

Reference:

T.Sato, M.Fujihashi, Y.Miyamoto, K.Kuwata, E.Kusaka, H.Fujita, K.Miki, H.Atomi. An Uncharacterized Member of the Ribokinase Family in Thermococcus Kodakarensis Exhibits Myo-Inositol Kinase Activity. J.Biol.Chem. V. 288 20856 2013.
ISSN: ISSN 0021-9258
PubMed: 23737529
DOI: 10.1074/JBC.M113.457259
Page generated: Sun Aug 11 17:09:10 2024

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