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Iodine in PDB 2gs7: Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp

Enzymatic activity of Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp

All present enzymatic activity of Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp, PDB code: 2gs7 was solved by X.Zhang, J.Gureasko, K.Shen, P.A.Cole, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.601, 85.253, 78.327, 90.00, 96.36, 90.00
R / Rfree (%) 23.3 / 29.8

Other elements in 2gs7:

The structure of Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iodine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp (pdb code 2gs7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp, PDB code: 2gs7:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in 2gs7

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Iodine binding site 1 out of 11 in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp


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 the Inactive Egfr Kinase Domain in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:58.1
occ:1.00
 NE2 A:GLN825 3.1 50.4 1.0
NZ B:LYS715 3.8 42.7 1.0
CD A:PRO824 3.8 32.3 1.0
CD A:GLN825 4.0 49.7 1.0
CG A:GLN825 4.0 47.2 1.0
CE B:LYS715 4.0 41.5 1.0
OG1 A:THR823 4.1 40.4 1.0
CD B:LYS689 4.2 44.6 1.0
CG A:PRO824 4.3 33.8 1.0
CB A:PRO824 4.3 34.3 1.0
CB A:THR823 4.3 36.1 1.0
O A:HOH46 4.4 23.4 1.0
N A:GLN825 4.4 39.9 1.0
N A:PRO824 4.5 33.0 1.0
CD B:LYS715 4.5 40.7 1.0
CE B:LYS689 4.5 46.8 1.0
CB A:GLN825 4.5 43.2 1.0
CD1 B:ILE708 4.7 43.3 1.0
CD1 B:LEU706 4.7 26.3 1.0
CA A:PRO824 4.9 34.8 1.0

Iodine binding site 2 out of 11 in 2gs7

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Iodine binding site 2 out of 11 in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp


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 the Inactive Egfr Kinase Domain in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:53.0
occ:1.00
 N A:LYS855 3.7 37.7 1.0
CG A:LYS855 3.7 37.0 1.0
N A:ILE854 3.9 43.6 1.0
CB A:LYS855 4.0 37.5 1.0
CD A:LYS855 4.2 39.0 1.0
CZ3 A:TRP856 4.3 31.2 1.0
O A:VAL852 4.3 52.6 1.0
CE A:LYS855 4.4 39.1 1.0
CB A:ILE854 4.4 42.4 1.0
C A:PRO853 4.4 46.1 1.0
CA A:ILE854 4.4 40.8 1.0
CA A:LYS855 4.5 37.3 1.0
CA A:PRO853 4.5 48.1 1.0
C A:ILE854 4.6 39.7 1.0
CE3 A:TRP856 4.6 31.1 1.0
CB A:ALA896 4.8 47.1 1.0

Iodine binding site 3 out of 11 in 2gs7

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Iodine binding site 3 out of 11 in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp


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 the Inactive Egfr Kinase Domain in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:82.3
occ:1.00
 N A:VAL810 3.5 35.4 1.0
NH2 A:ARG812 3.6 40.3 1.0
NH1 A:ARG812 3.7 36.5 1.0
CA A:LEU809 3.9 40.1 1.0
CD2 A:LEU809 4.0 36.7 1.0
NZ A:LYS836 4.0 41.3 1.0
CZ A:ARG812 4.2 40.3 1.0
C A:LEU809 4.2 38.7 1.0
O A:VAL810 4.3 32.8 1.0
CB A:LEU809 4.4 39.3 1.0
CB A:VAL810 4.5 31.6 1.0
CA A:VAL810 4.5 31.8 1.0
CG2 A:VAL810 4.5 30.8 1.0
O A:ARG808 4.6 45.2 1.0
C A:VAL810 4.8 31.0 1.0
CG A:LEU809 4.8 39.0 1.0
CE A:LYS836 4.9 43.3 1.0
CD A:LYS836 4.9 42.3 1.0

Iodine binding site 4 out of 11 in 2gs7

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Iodine binding site 4 out of 11 in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp


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 the Inactive Egfr Kinase Domain in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I409

b:0.1
occ:1.00
 ND2 A:ASN747 3.6 43.4 1.0
CG A:PRO748 4.3 39.5 1.0
CD A:LYS799 4.4 31.4 1.0
CD2 A:HIS749 4.4 42.6 1.0
CB A:LYS799 4.5 29.5 1.0
CG A:ASN747 4.5 42.8 1.0
OD1 A:ASN747 4.6 42.8 1.0
CD A:PRO748 4.7 39.0 1.0
CG A:LYS799 4.7 30.2 1.0
NE2 A:HIS749 4.8 44.8 1.0

Iodine binding site 5 out of 11 in 2gs7

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Iodine binding site 5 out of 11 in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp


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 the Inactive Egfr Kinase Domain in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I410

b:93.6
occ:1.00
 N A:TYR891 3.5 45.9 1.0
CA A:TYR891 3.7 46.6 1.0
N A:ASP892 4.0 50.7 1.0
CD A:PRO910 4.1 36.8 1.0
CH2 A:TRP881 4.3 31.1 1.0
CG A:PRO910 4.3 37.5 1.0
CZ2 A:TRP881 4.3 33.6 1.0
O A:LYS889 4.3 45.2 1.0
C A:TYR891 4.3 48.8 1.0
O A:HOH148 4.5 50.6 1.0
CD2 A:LEU909 4.6 32.8 1.0
C A:PRO890 4.7 45.0 1.0
CB A:TYR891 5.0 46.5 1.0

Iodine binding site 6 out of 11 in 2gs7

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Iodine binding site 6 out of 11 in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp


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 the Inactive Egfr Kinase Domain in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I401

b:62.8
occ:1.00
 NE2 B:GLN825 3.5 50.9 1.0
NZ A:LYS715 3.5 49.1 1.0
CD B:PRO824 3.7 34.4 1.0
CD A:LYS689 3.7 49.3 1.0
OG1 B:THR823 4.1 34.0 1.0
CD B:GLN825 4.1 49.7 1.0
CG B:GLN825 4.2 46.4 1.0
CB B:PRO824 4.2 34.1 1.0
CG B:PRO824 4.2 35.4 1.0
CE A:LYS689 4.3 51.3 1.0
N B:PRO824 4.3 34.3 1.0
CB B:THR823 4.4 33.5 1.0
N B:GLN825 4.4 39.9 1.0
O B:HOH2 4.6 27.9 1.0
CB B:GLN825 4.7 41.4 1.0
CE A:LYS715 4.7 46.8 1.0
CD1 A:LEU706 4.7 28.4 1.0
CA B:PRO824 4.8 36.0 1.0
CD1 A:ILE708 4.8 35.4 1.0

Iodine binding site 7 out of 11 in 2gs7

Go back to Iodine Binding Sites List in 2gs7
Iodine binding site 7 out of 11 in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp


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 the Inactive Egfr Kinase Domain in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I404

b:58.9
occ:1.00
 CG B:LYS855 3.7 42.9 1.0
N B:LYS855 3.8 40.3 1.0
NZ B:LYS851 3.9 62.7 1.0
N B:ILE854 3.9 43.9 1.0
CB B:LYS855 4.1 40.8 1.0
CD B:LYS855 4.1 45.2 1.0
CB B:ILE854 4.3 42.5 1.0
CZ3 B:TRP856 4.5 31.2 1.0
CE B:LYS855 4.5 46.6 1.0
CA B:ILE854 4.5 42.7 1.0
O B:VAL852 4.6 50.6 1.0
C B:PRO853 4.6 44.8 1.0
CA B:LYS855 4.6 39.7 1.0
CA B:PRO853 4.6 46.9 1.0
C B:ILE854 4.7 41.6 1.0
CE3 B:TRP856 4.9 32.0 1.0
CB B:ALA896 4.9 49.0 1.0

Iodine binding site 8 out of 11 in 2gs7

Go back to Iodine Binding Sites List in 2gs7
Iodine binding site 8 out of 11 in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp


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 the Inactive Egfr Kinase Domain in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I405

b:99.1
occ:1.00
 NZ B:LYS704 3.0 15.8 1.0
O A:HOH33 3.0 26.5 1.0
CE B:LYS704 3.4 25.2 1.0
CB A:PRO770 3.6 33.9 1.0
CA A:PRO770 3.6 31.8 1.0
CA B:PRO770 3.7 34.5 1.0
CB B:PRO770 3.7 35.5 1.0
O A:PRO770 4.1 30.1 1.0
O B:PRO770 4.1 33.1 1.0
NZ A:LYS704 4.1 35.8 1.0
CD A:LYS704 4.2 37.9 1.0
C A:PRO770 4.4 29.9 1.0
C B:PRO770 4.4 32.8 1.0
CD2 A:LEU768 4.5 21.5 1.0
CD B:LYS704 4.6 28.0 1.0
N A:PRO770 4.7 32.5 1.0
N B:PRO770 4.7 35.9 1.0
CE A:LYS704 4.8 36.7 1.0
CD2 B:LEU768 4.8 30.8 1.0
CG A:LEU768 4.9 26.1 1.0
CG A:PRO770 5.0 35.1 1.0

Iodine binding site 9 out of 11 in 2gs7

Go back to Iodine Binding Sites List in 2gs7
Iodine binding site 9 out of 11 in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp


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 the Inactive Egfr Kinase Domain in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I407

b:81.0
occ:1.00
 NH1 B:ARG812 3.5 30.9 1.0
N B:VAL810 3.7 31.9 1.0
NH2 B:ARG812 3.8 33.5 1.0
CD2 B:LEU809 4.0 30.9 1.0
CZ B:ARG812 4.1 34.0 1.0
CA B:LEU809 4.2 36.9 1.0
NZ B:LYS836 4.2 50.5 1.0
O B:VAL810 4.3 27.9 1.0
O B:HOH62 4.4 45.3 1.0
CD B:LYS836 4.5 44.9 1.0
C B:LEU809 4.5 36.1 1.0
CB B:LEU809 4.5 35.6 1.0
CB B:VAL810 4.6 27.5 1.0
CA B:VAL810 4.6 27.9 1.0
CE B:LYS836 4.6 46.0 1.0
O B:ARG808 4.7 43.3 1.0
CG2 B:VAL810 4.9 25.1 1.0
C B:VAL810 4.9 27.2 1.0
CG B:LEU809 5.0 34.0 1.0

Iodine binding site 10 out of 11 in 2gs7

Go back to Iodine Binding Sites List in 2gs7
Iodine binding site 10 out of 11 in the Crystal Structure of the Inactive Egfr Kinase Domain in Complex with Amp-Pnp


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 the Inactive Egfr Kinase Domain in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I408

b:99.2
occ:1.00
 ND2 B:ASN747 3.8 36.2 1.0
CG B:PRO748 4.0 34.9 1.0
CD2 B:HIS749 4.3 35.4 1.0
OD1 B:ASN747 4.4 39.9 1.0
CB B:LYS799 4.4 35.0 1.0
CG B:ASN747 4.4 35.6 1.0
CD B:LYS799 4.5 37.0 1.0
CD B:PRO748 4.5 33.4 1.0
CG B:LYS799 4.6 34.8 1.0
NE2 B:HIS749 4.8 35.7 1.0

Reference:

X.Zhang, J.Gureasko, K.Shen, P.A.Cole, J.Kuriyan. An Allosteric Mechanism For Activation of the Kinase Domain of Epidermal Growth Factor Receptor Cell(Cambridge,Mass.) V. 125 1137 2006.
ISSN: ISSN 0092-8674
PubMed: 16777603
DOI: 10.1016/J.CELL.2006.05.013
Page generated: Sun Aug 11 13:52:29 2024

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