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Iodine in PDB 4u5w: Crystal Structure of Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains

Enzymatic activity of Crystal Structure of Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains

All present enzymatic activity of Crystal Structure of Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains:
2.7.10.2;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains, PDB code: 4u5w was solved by J.J.Alvarado, J.I.Yeh, T.E.Smithgall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.38 / 1.86
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.489, 57.265, 72.111, 112.28, 96.09, 106.00
R / Rfree (%) 16.9 / 19.5

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains (pdb code 4u5w). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains, PDB code: 4u5w:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 4u5w

Go back to Iodine Binding Sites List in 4u5w
Iodine binding site 1 out of 6 in the Crystal Structure of Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains


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 Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:32.2
occ:0.21
 OG1 D:THR219 2.8 27.8 1.0
O D:HOH435 2.9 30.8 1.0
CD A:PRO82 3.4 22.3 1.0
N A:PRO82 3.5 16.2 1.0
I D:IOD302 3.5 36.2 0.3
CB D:THR219 3.6 23.6 1.0
CB A:PRO82 3.8 20.8 1.0
C A:ARG81 3.9 19.5 1.0
CA A:PRO82 4.0 17.7 1.0
CG A:PRO82 4.0 22.4 1.0
CD1 D:LEU207 4.0 35.5 1.0
CG2 D:THR219 4.0 22.0 1.0
CA A:ARG81 4.1 14.7 1.0
O D:HOH430 4.3 18.8 0.7
O D:HOH444 4.3 32.5 0.9
O D:HOH517 4.4 52.8 1.0
O D:HOH458 4.5 24.4 0.6
N A:ARG81 4.6 15.5 1.0
O A:ARG81 4.6 16.9 1.0
O A:HOH476 4.6 26.3 0.8
O A:HOH443 4.9 21.7 0.9
C A:LEU80 4.9 15.7 1.0
CA D:THR219 5.0 18.7 1.0

Iodine binding site 2 out of 6 in 4u5w

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Iodine binding site 2 out of 6 in the Crystal Structure of Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains


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 Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I301

b:53.4
occ:0.44
 CB B:GLN224 3.6 58.0 1.0
O B:HOH462 3.6 35.4 1.0
N B:GLN224 3.8 48.9 1.0
CD1 B:LEU143 3.9 58.3 1.0
CA B:GLN224 4.3 51.6 1.0
CB B:LEU143 4.3 53.0 1.0
CB B:THR222 4.4 63.7 1.0
CA B:LEU143 4.4 44.3 1.0
N B:LEU223 4.6 50.2 1.0
OG1 B:THR222 4.7 55.3 1.0
OE2 B:GLU146 4.7 71.9 1.0
O B:HOH430 4.7 40.9 0.9
CG B:LEU143 4.7 53.2 1.0
C B:LEU223 4.8 47.1 1.0
CG B:GLN224 4.8 65.6 1.0
CG B:GLU146 4.8 60.8 1.0
N B:LEU143 4.9 44.6 1.0
CH2 B:TRP148 4.9 56.1 1.0
CZ2 B:TRP148 4.9 55.2 1.0
CB B:LEU223 4.9 47.6 1.0
CA B:LEU223 5.0 47.7 1.0

Iodine binding site 3 out of 6 in 4u5w

Go back to Iodine Binding Sites List in 4u5w
Iodine binding site 3 out of 6 in the Crystal Structure of Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains


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 Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I302

b:86.2
occ:0.54
 CD1 B:TRP148 3.7 47.6 1.0
CD B:PRO244 3.9 55.4 1.0
CG B:PRO244 4.0 53.4 1.0
CD B:LYS231 4.3 56.3 1.0
CZ B:PHE172 4.3 43.1 1.0
NE1 B:TRP148 4.4 53.2 1.0
CG1 B:VAL227 4.6 46.3 1.0
CG B:TRP148 4.7 46.3 1.0
CE1 B:PHE172 4.8 43.3 1.0

Iodine binding site 4 out of 6 in 4u5w

Go back to Iodine Binding Sites List in 4u5w
Iodine binding site 4 out of 6 in the Crystal Structure of Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains


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 Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I301

b:48.4
occ:0.39
 O C:HOH522 3.1 49.0 1.0
CD2 C:LEU80 3.6 45.2 1.0
N C:PRO82 3.7 24.5 1.0
CD C:PRO82 3.7 23.9 1.0
CG C:LEU80 3.8 39.6 1.0
C C:ARG81 3.9 23.7 1.0
CA C:PRO82 4.1 21.5 1.0
CB C:PRO82 4.1 29.2 1.0
CA C:ARG81 4.2 24.9 1.0
CG C:PRO82 4.4 32.0 1.0
N C:ARG81 4.5 21.2 1.0
O C:ARG81 4.5 20.4 1.0
O C:HOH452 4.7 22.2 0.8
C C:LEU80 4.8 22.5 1.0
CD1 C:LEU80 4.8 42.0 1.0
CB C:LEU80 4.8 25.9 1.0
O C:LEU80 4.9 21.6 1.0

Iodine binding site 5 out of 6 in 4u5w

Go back to Iodine Binding Sites List in 4u5w
Iodine binding site 5 out of 6 in the Crystal Structure of Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains


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 Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I301

b:34.0
occ:0.50
 NZ D:LYS231 3.7 42.6 1.0
O D:HOH488 3.8 32.3 0.5
CG D:PRO244 3.8 31.3 1.0
CD1 D:TRP148 3.9 25.8 1.0
CD D:PRO244 3.9 30.0 1.0
CZ D:PHE172 4.3 17.4 1.0
CB D:TRP148 4.5 25.1 1.0
CD D:LYS231 4.5 32.6 1.0
CE D:LYS231 4.6 40.1 1.0
CG1 D:VAL227 4.6 16.9 1.0
CG D:TRP148 4.6 25.6 1.0
CE1 D:PHE172 4.8 20.9 1.0
NE1 D:TRP148 5.0 31.9 1.0
CB D:GLU147 5.0 50.7 1.0

Iodine binding site 6 out of 6 in 4u5w

Go back to Iodine Binding Sites List in 4u5w
Iodine binding site 6 out of 6 in the Crystal Structure of Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains


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 Hiv-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I302

b:36.2
occ:0.31
 O A:HOH443 3.0 21.7 0.9
O D:HOH424 3.0 22.7 1.0
ND2 D:ASN209 3.1 25.8 1.0
I A:IOD304 3.5 32.2 0.2
CD1 D:LEU207 3.7 35.5 1.0
O D:HOH517 3.8 52.8 1.0
CG D:ASN209 4.0 27.3 1.0
CB A:PHE125 4.0 13.9 1.0
OD1 D:ASN209 4.1 26.4 1.0
O A:HOH505 4.3 46.5 0.8
CG2 D:THR219 4.5 22.0 1.0
O A:ARG81 4.5 16.9 1.0
CD2 A:LEU80 4.6 31.1 1.0
CB A:LEU80 4.7 18.0 1.0
C A:ARG81 4.7 19.5 1.0
O A:HOH477 4.8 29.7 0.8
CD1 A:LEU80 4.8 23.4 1.0
CG A:PHE125 4.9 18.1 1.0
CA A:PRO82 4.9 17.7 1.0
N A:PHE125 4.9 12.9 1.0
CB D:THR219 4.9 23.6 1.0
N A:PRO82 5.0 16.2 1.0
CG A:LEU80 5.0 24.0 1.0

Reference:

J.J.Alvarado, S.Tarafdar, J.I.Yeh, T.E.Smithgall. Interaction with the Src Homology (SH3-SH2) Region of the Src-Family Kinase Hck Structures the Hiv-1 Nef Dimer For Kinase Activation and Effector Recruitment. J.Biol.Chem. V. 289 28539 2014.
ISSN: ESSN 1083-351X
PubMed: 25122770
DOI: 10.1074/JBC.M114.600031
Page generated: Sun Aug 11 19:58:08 2024

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