Atomistry » Iodine » PDB 4hkl-4jxj » 4itj
Atomistry »
  Iodine »
    PDB 4hkl-4jxj »
      4itj »

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

Go back to Iodine Binding Sites List in 4itj
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

Go back to Iodine Binding Sites List in 4itj
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

Go back to Iodine Binding Sites List in 4itj
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

Go back to Iodine Binding Sites List in 4itj
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

Go back to Iodine Binding Sites List in 4itj
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

Go back to Iodine Binding Sites List in 4itj
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy