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Iodine in PDB 4itj: Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4

Enzymatic activity of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4

All present enzymatic activity of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4, PDB code: 4itj was solved by T.Xie, W.Peng, Y.Liu, C.Yan, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.24 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.841, 97.136, 128.119, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.2

Other elements in 4itj:

The structure of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4 also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Chlorine (Cl) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4 (pdb code 4itj). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4, PDB code: 4itj:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 4itj

Go back to Iodine Binding Sites List in 4itj
Iodine binding site 1 out of 9 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4


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 RIP1 Kinase in Complex with Necrostatin-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:19.2
occ:0.61
 O A:HOH571 3.5 31.0 0.7
NZ B:LYS77 3.8 19.6 1.0
CA B:SER73 4.0 14.1 1.0
CG A:GLU283 4.0 22.1 1.0
NE A:ARG286 4.0 15.5 1.0
CG A:GLU282 4.1 17.1 1.0
CD A:ARG286 4.1 23.1 1.0
CD A:GLU282 4.2 18.6 1.0
OE1 A:GLU282 4.2 14.5 1.0
N B:SER73 4.2 10.7 1.0
CB B:SER73 4.3 15.1 1.0
O A:GLU282 4.4 19.1 1.0
CA A:GLU283 4.4 21.5 1.0
C B:HIS72 4.5 13.0 1.0
C A:GLU282 4.5 16.0 1.0
N A:GLU283 4.6 19.0 1.0
CE B:LYS77 4.6 21.3 1.0
O B:HIS72 4.6 13.4 1.0
CB A:ARG286 4.7 18.9 1.0
CB A:GLU282 4.7 14.9 1.0
O B:HOH570 4.7 32.3 0.6
OE2 A:GLU282 4.8 18.2 1.0
CB A:GLU283 4.8 24.0 1.0

Iodine binding site 2 out of 9 in 4itj

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Iodine binding site 2 out of 9 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4


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 RIP1 Kinase in Complex with Necrostatin-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:22.4
occ:0.58
 O A:HOH479 3.3 28.1 1.0
CD2 A:PHE285 4.0 17.9 1.0
CA A:PHE285 4.0 21.3 1.0
O A:LYS284 4.2 24.5 1.0
N A:PHE285 4.2 20.6 1.0
O A:GLU259 4.2 22.9 1.0
C A:LYS284 4.2 27.4 1.0
CB A:GLU259 4.3 31.1 1.0
CB A:LYS284 4.3 31.2 1.0
CB A:PHE285 4.4 16.7 1.0
CB A:PHE288 4.5 24.3 1.0
CD1 A:PHE288 4.5 23.8 1.0
CE A:LYS284 4.6 41.6 1.0
CD2 A:LEU263 4.6 16.9 1.0
CG A:PHE288 4.6 25.7 1.0
CG A:GLU259 4.6 33.0 1.0
CG A:PHE285 4.6 17.9 1.0
C A:GLU259 4.7 19.7 1.0
CB A:LEU263 4.8 18.5 1.0
CE2 A:PHE285 4.9 19.7 1.0
CA A:LYS284 5.0 27.7 1.0

Iodine binding site 3 out of 9 in 4itj

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Iodine binding site 3 out of 9 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4


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 RIP1 Kinase in Complex with Necrostatin-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:38.3
occ:0.34
 CD1 A:ILE43 3.5 41.7 1.0
O A:HOH648 3.7 27.6 0.6
CE A:MET92 3.8 23.9 1.0
O A:HOH587 3.9 43.0 1.0
O A:HOH645 4.0 43.9 0.9
CG2 A:ILE43 4.1 34.6 1.0
CD1 A:LEU145 4.2 19.4 1.0
CD1 A:LEU157 4.3 21.1 1.0
CG1 A:ILE43 4.4 40.4 1.0
CD2 A:LEU157 4.6 24.0 1.0
CB A:ILE43 4.7 36.5 1.0
CG1 A:VAL31 4.8 45.4 1.0

Iodine binding site 4 out of 9 in 4itj

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Iodine binding site 4 out of 9 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4


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 RIP1 Kinase in Complex with Necrostatin-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:21.1
occ:0.58
 N A:ILE232 3.7 32.1 1.0
CG1 A:ILE232 4.0 38.1 1.0
CA A:ALA231 4.0 35.0 1.0
CA A:LEU237 4.0 22.1 1.0
CD1 A:ILE232 4.1 40.9 1.0
N A:LEU237 4.1 24.1 1.0
CB A:ALA231 4.2 34.2 1.0
C A:GLN236 4.3 25.7 1.0
O A:GLN236 4.3 24.1 1.0
C A:ALA231 4.4 36.8 1.0
CB A:LEU237 4.4 23.3 1.0
CB A:ILE232 4.5 41.7 1.0
CD1 A:LEU237 4.5 22.9 1.0
CB A:ALA240 4.5 23.4 1.0
CB A:GLN236 4.6 36.2 1.0
CA A:ILE232 4.7 44.3 1.0
O A:HOH505 4.9 35.1 1.0

Iodine binding site 5 out of 9 in 4itj

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Iodine binding site 5 out of 9 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4


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 RIP1 Kinase in Complex with Necrostatin-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:46.3
occ:0.32
 O A:HOH433 3.0 21.1 0.9
NH1 B:ARG286 3.5 14.6 1.0
O A:HOH436 3.5 24.9 1.0
NH2 A:ARG74 3.7 23.7 1.0
O A:HOH524 3.9 33.2 1.0
O B:HOH538 3.9 27.5 0.7
CE1 A:HIS151 3.9 23.6 1.0
O B:HOH597 4.1 28.2 0.6
CD2 B:LEU290 4.3 27.6 1.0
ND1 A:HIS151 4.4 20.9 1.0
CD2 B:LEU120 4.4 16.9 1.0
NE2 A:HIS151 4.5 20.4 1.0
NH1 A:ARG74 4.5 18.4 1.0
CZ A:ARG74 4.6 19.1 1.0
O A:HOH465 4.7 23.5 0.8
OE2 A:GLU121 4.8 21.0 1.0
CZ B:ARG286 4.8 14.5 1.0
OE1 B:GLU294 4.9 38.9 1.0
O B:HOH428 5.0 28.2 1.0
O A:HOH662 5.0 25.9 0.5

Iodine binding site 6 out of 9 in 4itj

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Iodine binding site 6 out of 9 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4


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 RIP1 Kinase in Complex with Necrostatin-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I302

b:17.8
occ:0.55
 O A:HOH600 3.6 25.2 0.5
NE B:ARG286 3.8 14.4 1.0
CD B:ARG286 3.9 15.0 1.0
CA A:SER73 4.0 16.5 1.0
CB A:SER73 4.0 19.5 1.0
CA B:GLU283 4.1 16.0 1.0
O B:GLU282 4.1 17.1 1.0
CG B:GLU282 4.1 19.5 1.0
CG B:GLU283 4.2 25.9 1.0
OE1 B:GLU282 4.2 21.8 1.0
O B:HOH576 4.3 54.1 1.0
CD B:GLU282 4.3 25.6 1.0
C B:GLU282 4.4 16.3 1.0
NZ A:LYS77 4.4 31.3 1.0
N B:GLU283 4.4 13.7 1.0
CB B:ARG286 4.4 16.8 1.0
N A:SER73 4.5 15.3 1.0
CE A:LYS77 4.5 42.6 1.0
O B:HOH593 4.7 32.5 0.7
CB B:GLU283 4.7 17.7 1.0
CG B:ARG286 4.8 14.3 1.0
CB B:GLU282 4.8 13.4 1.0
O A:HOH588 5.0 27.8 0.6
CZ B:ARG286 5.0 14.5 1.0
O A:HOH538 5.0 39.8 0.7

Iodine binding site 7 out of 9 in 4itj

Go back to Iodine Binding Sites List in 4itj
Iodine binding site 7 out of 9 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4


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 RIP1 Kinase in Complex with Necrostatin-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I303

b:20.7
occ:0.55
 O B:HOH619 3.3 51.3 1.0
O B:HOH704 3.4 28.4 1.0
CA B:PHE285 4.0 17.0 1.0
O B:LYS284 4.1 22.5 1.0
CD2 B:PHE285 4.1 17.7 1.0
C B:LYS284 4.1 25.4 1.0
N B:PHE285 4.2 19.1 1.0
CB B:LYS284 4.3 31.2 1.0
CB B:GLU259 4.4 25.9 1.0
O B:GLU259 4.4 19.8 1.0
CB B:PHE285 4.4 16.0 1.0
CB B:PHE288 4.4 18.5 1.0
CG B:PHE288 4.6 18.4 1.0
CD1 B:PHE288 4.6 21.7 1.0
CD2 B:LEU263 4.7 15.7 1.0
CG B:PHE285 4.7 15.9 1.0
O B:HOH452 4.8 24.0 0.9
C B:GLU259 4.9 18.6 1.0
CB B:LEU263 4.9 14.0 1.0
CA B:LYS284 4.9 27.6 1.0

Iodine binding site 8 out of 9 in 4itj

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Iodine binding site 8 out of 9 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4


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 RIP1 Kinase in Complex with Necrostatin-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I304

b:32.6
occ:0.38
 O B:HOH477 3.1 43.1 1.0
O B:HOH462 3.4 20.0 0.7
O B:HOH467 3.4 38.2 1.0
CE B:MET92 3.8 22.7 1.0
CG1 B:ILE43 4.2 18.3 1.0
CA B:GLY26 4.2 28.2 1.0
O B:HOH602 4.3 37.8 0.7
CG2 B:ILE43 4.3 23.4 1.0
CD1 B:ILE43 4.4 22.7 1.0
CD1 B:LEU145 4.4 19.4 1.0
CD1 B:LEU157 4.5 18.7 1.0
CD2 B:LEU145 4.6 22.0 1.0
CD2 B:LEU157 4.8 18.8 1.0
CB B:ILE43 4.8 19.2 1.0

Iodine binding site 9 out of 9 in 4itj

Go back to Iodine Binding Sites List in 4itj
Iodine binding site 9 out of 9 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-4


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 RIP1 Kinase in Complex with Necrostatin-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I305

b:33.3
occ:0.52
 O B:HOH512 3.6 39.0 1.0
ND2 B:ASN57 3.9 33.3 1.0
CB B:ASN57 4.1 32.0 1.0
CE B:LYS11 4.2 42.1 1.0
CG2 B:ILE83 4.3 25.2 1.0
CG B:ASN57 4.5 34.3 1.0
CD1 B:ILE83 4.8 30.0 1.0
CD2 B:LEU61 4.8 42.2 1.0
NZ B:LYS11 4.8 43.4 1.0
CB B:ILE83 5.0 28.2 1.0

Reference:

T.Xie, W.Peng, Y.Liu, C.Yan, J.Maki, A.Degterev, J.Yuan, Y.Shi. Structural Basis of RIP1 Inhibition By Necrostatins. Structure V. 21 493 2013.
ISSN: ISSN 0969-2126
PubMed: 23473668
DOI: 10.1016/J.STR.2013.01.016
Page generated: Sun Aug 11 18:10:04 2024

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