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 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy