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Iodine in PDB 4ith: Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog

Enzymatic activity of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog

All present enzymatic activity of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog, PDB code: 4ith 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) 37.89 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.128, 93.605, 129.070, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 24.7

Other elements in 4ith:

The structure of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog (pdb code 4ith). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog, PDB code: 4ith:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 4ith

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Iodine binding site 1 out of 10 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog


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-1 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:42.2
occ:0.92
 CD1 A:ILE232 3.5 60.7 1.0
N A:ILE232 3.7 57.7 1.0
N A:LEU237 3.9 32.4 1.0
CA A:LEU237 3.9 30.1 1.0
C A:GLN236 4.1 48.9 1.0
CA A:ALA231 4.1 45.2 1.0
O A:GLN236 4.2 47.9 1.0
CB A:GLN236 4.3 52.7 1.0
CB A:ALA231 4.3 43.8 1.0
CD1 A:LEU237 4.3 28.0 1.0
CB A:LEU237 4.4 29.5 1.0
C A:ALA231 4.5 47.2 1.0
CB A:ILE232 4.5 61.3 1.0
CG1 A:ILE232 4.5 62.2 1.0
O A:ALA233 4.7 41.9 1.0
CA A:ILE232 4.7 60.4 1.0
CB A:ALA240 4.9 37.8 1.0
CA A:GLN236 4.9 49.9 1.0
N A:ALA233 4.9 44.9 1.0
I A:IOD302 4.9 53.5 0.5

Iodine binding site 2 out of 10 in 4ith

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Iodine binding site 2 out of 10 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog


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-1 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:53.5
occ:0.49
 N A:ALA231 4.0 45.9 1.0
CA A:TYR228 4.1 31.0 1.0
CA A:ALA231 4.2 45.2 1.0
C A:ASN230 4.2 64.9 1.0
CD1 A:TYR228 4.2 27.6 1.0
CB A:ASN230 4.3 66.5 1.0
CB A:ALA231 4.4 43.8 1.0
CB A:TYR228 4.4 29.4 1.0
C A:TYR228 4.5 33.5 1.0
O A:ASN230 4.6 66.2 1.0
CA A:ASN230 4.6 65.2 1.0
CD1 A:LEU237 4.6 28.0 1.0
N A:ASN230 4.6 62.3 1.0
O A:TYR228 4.6 34.3 1.0
CG A:TYR228 4.8 27.3 1.0
I A:IOD301 4.9 42.2 0.9

Iodine binding site 3 out of 10 in 4ith

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Iodine binding site 3 out of 10 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog


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-1 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:48.6
occ:0.86
 CA A:PHE285 4.1 33.0 1.0
CG A:LYS284 4.1 52.3 1.0
CD2 A:PHE285 4.1 29.6 1.0
O A:GLU259 4.2 44.0 1.0
CB A:LYS284 4.3 49.9 1.0
N A:PHE285 4.4 34.1 1.0
C A:LYS284 4.4 48.8 1.0
O A:LYS284 4.4 49.8 1.0
CB A:PHE288 4.5 46.0 1.0
CB A:PHE285 4.5 31.5 1.0
CG A:PHE288 4.6 45.5 1.0
CD2 A:LEU263 4.6 26.6 1.0
CD1 A:PHE288 4.7 44.2 1.0
CB A:LEU263 4.8 27.8 1.0
CG A:PHE285 4.8 30.0 1.0
CB A:GLU259 4.8 48.2 1.0
C A:GLU259 4.9 44.6 1.0

Iodine binding site 4 out of 10 in 4ith

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Iodine binding site 4 out of 10 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog


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-1 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:61.8
occ:0.64
 O A:HOH424 3.0 34.6 1.0
NE A:ARG286 3.5 40.8 1.0
CD A:ARG286 3.6 41.8 1.0
OE1 A:GLU282 3.8 39.0 1.0
CG A:GLU282 3.8 38.1 1.0
CD A:GLU282 4.0 39.0 1.0
CB A:ARG286 4.2 39.2 1.0
CG A:ARG286 4.5 39.9 1.0
O A:GLU282 4.5 39.1 1.0
CZ A:ARG286 4.7 39.2 1.0
C A:GLU282 4.7 39.5 1.0
N A:GLU283 4.8 61.6 1.0
CA A:GLU283 4.8 63.5 1.0
CB A:GLU282 4.9 37.5 1.0
OE2 A:GLU282 4.9 39.3 1.0

Iodine binding site 5 out of 10 in 4ith

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Iodine binding site 5 out of 10 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog


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-1 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:88.6
occ:0.55
 NH1 A:ARG258 3.2 67.7 1.0
OG A:SER262 3.9 41.7 1.0
CD B:LYS265 4.0 44.2 1.0
NZ B:LYS265 4.0 47.4 1.0
CB A:GLU259 4.4 48.2 1.0
CZ A:ARG258 4.4 68.8 1.0
CB A:SER262 4.5 38.4 1.0
CA A:GLU259 4.5 47.2 1.0
CE B:LYS265 4.6 45.4 1.0

Iodine binding site 6 out of 10 in 4ith

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Iodine binding site 6 out of 10 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog


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-1 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I301

b:63.8
occ:0.67
 CD2 B:HIS56 3.6 80.2 1.0
CG B:HIS56 4.0 77.3 1.0
CB B:HIS56 4.2 73.7 1.0
NE2 B:HIS56 4.4 82.7 1.0
CA B:LEU168 4.4 70.0 1.0
CD2 B:LEU168 4.5 72.4 1.0
N B:LEU168 4.6 69.6 1.0
CG B:LEU168 4.6 70.0 1.0
CG2 B:ILE54 4.7 99.5 1.0
CB B:LEU168 4.8 68.1 1.0
ND1 B:HIS56 4.8 78.6 1.0
C B:LYS167 4.9 73.6 1.0
CD1 B:ILE54 5.0 0.6 1.0
CE1 B:HIS56 5.0 81.7 1.0

Iodine binding site 7 out of 10 in 4ith

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Iodine binding site 7 out of 10 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog


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-1 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I302

b:45.2
occ:0.75
 NE B:ARG286 3.8 33.2 1.0
CA B:GLU283 4.0 51.4 1.0
CD B:ARG286 4.0 34.2 1.0
O B:GLU282 4.1 46.6 1.0
CG B:GLU282 4.2 44.1 1.0
CG B:GLU283 4.2 53.6 1.0
CD B:GLU282 4.2 45.0 1.0
N B:GLU283 4.3 50.0 1.0
OE1 B:GLU282 4.3 45.5 1.0
C B:GLU282 4.3 45.7 1.0
CB B:ARG286 4.5 32.8 1.0
CB B:GLU283 4.7 52.5 1.0
OE2 B:GLU282 4.8 45.5 1.0
CB B:GLU282 4.8 43.3 1.0
CG B:ARG286 4.9 33.3 1.0
CZ B:ARG286 4.9 32.3 1.0
C B:GLU283 5.0 51.7 1.0

Iodine binding site 8 out of 10 in 4ith

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Iodine binding site 8 out of 10 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog


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-1 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I303

b:58.1
occ:0.60
 NH1 B:ARG286 3.4 32.9 1.0
CD2 B:LEU290 4.0 41.3 1.0
CD2 B:LEU120 4.7 26.3 1.0
CZ B:ARG286 4.7 32.3 1.0
CG B:LEU290 4.8 42.0 1.0
CD1 B:LEU290 4.8 42.8 1.0
CD B:ARG286 5.0 34.2 1.0

Iodine binding site 9 out of 10 in 4ith

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Iodine binding site 9 out of 10 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog


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-1 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I304

b:52.6
occ:0.69
 O B:LYS284 4.0 57.3 1.0
CA B:PHE285 4.1 32.6 1.0
C B:LYS284 4.2 56.0 1.0
CD2 B:PHE285 4.2 32.1 1.0
N B:PHE285 4.3 33.5 1.0
CB B:LYS284 4.4 57.1 1.0
O B:GLU259 4.4 38.3 1.0
CB B:PHE288 4.5 38.6 1.0
CD2 B:LEU263 4.5 33.9 1.0
CB B:PHE285 4.6 31.7 1.0
CB B:GLU259 4.6 42.2 1.0
CG B:PHE288 4.6 39.1 1.0
CB B:LEU263 4.7 35.7 1.0
CD1 B:PHE288 4.8 38.5 1.0
CG B:PHE285 4.9 31.7 1.0
C B:GLU259 4.9 39.0 1.0
O B:HOH455 4.9 67.4 1.0
O B:HOH460 4.9 45.2 1.0
CA B:LYS284 5.0 55.9 1.0
CG B:LEU263 5.0 34.6 1.0

Iodine binding site 10 out of 10 in 4ith

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Iodine binding site 10 out of 10 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-1 Analog


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 RIP1 Kinase in Complex with Necrostatin-1 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I305

b:48.4
occ:0.62
 NE1 B:TRP268 3.4 27.2 1.0
CG B:LYS265 4.2 41.2 1.0
CD1 B:TRP268 4.2 27.0 1.0
CG B:ARG246 4.3 27.8 1.0
CE2 B:TRP268 4.4 26.3 1.0
O B:HOH433 4.4 51.8 1.0
CD B:LYS265 4.4 44.2 1.0
CE B:LYS265 4.5 45.4 1.0
CB B:LYS265 4.6 39.9 1.0
CZ2 B:TRP268 4.7 26.5 1.0
CB B:ARG246 4.8 26.5 1.0
CD A:ARG258 4.8 63.9 1.0
CA B:LYS265 5.0 39.0 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 18:10:01 2024

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