Atomistry » Iodine » PDB 7fgk-7lod » 7fun
Atomistry »
  Iodine »
    PDB 7fgk-7lod »
      7fun »

Iodine in PDB 7fun: Crystal Structure of Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid

Enzymatic activity of Crystal Structure of Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid

All present enzymatic activity of Crystal Structure of Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid:
2.7.7.86;

Protein crystallography data

The structure of Crystal Structure of Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid, PDB code: 7fun was solved by L.Leibrock, J.Benz, K.Groebke-Zbinden, G.Galley, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.08 / 2.07
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 44.574, 59.125, 163.046, 90, 90, 90
R / Rfree (%) 24 / 29.4

Other elements in 7fun:

The structure of Crystal Structure of Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Zinc (Zn) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid (pdb code 7fun). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Crystal Structure of Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid, PDB code: 7fun:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 7fun

Go back to Iodine Binding Sites List in 7fun
Iodine binding site 1 out of 7 in the Crystal Structure of Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid


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 Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I603

b:85.6
occ:1.00
 CD1 A:LEU387 3.8 58.5 1.0
CE A:LYS411 3.9 68.2 1.0
CG A:LYS411 4.1 75.4 1.0
O A:LYS407 4.1 66.9 1.0
CG A:LYS407 4.1 55.9 1.0
CB A:LYS407 4.3 62.0 1.0
CD2 A:LEU410 4.3 52.6 1.0
CA A:LYS407 4.5 61.8 1.0
CG A:LEU410 4.6 54.8 1.0
CD2 A:LEU387 4.6 59.9 1.0
CD A:LYS411 4.6 76.3 1.0
CD A:LYS407 4.7 63.5 1.0
CB A:LEU410 4.7 52.9 1.0
C A:LYS407 4.7 65.9 1.0
CG A:LEU387 4.8 57.9 1.0
NZ A:LYS411 4.8 79.8 1.0
NZ A:LYS414 4.9 67.5 1.0

Iodine binding site 2 out of 7 in 7fun

Go back to Iodine Binding Sites List in 7fun
Iodine binding site 2 out of 7 in the Crystal Structure of Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid


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 Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I604

b:92.4
occ:1.00
 N A:MET229 3.6 66.7 1.0
C12 A:YU6602 3.8 72.6 1.0
C11 A:YU6602 3.9 73.4 1.0
O A:MET229 4.0 73.7 1.0
CD2 A:LEU208 4.0 90.5 1.0
ND2 A:ASN210 4.0 92.9 1.0
OD1 A:ASN210 4.0 111.2 1.0
N A:ASN210 4.1 92.4 1.0
CA A:VAL228 4.1 64.9 1.0
CG A:ASN210 4.1 112.6 1.0
O A:ASN210 4.1 99.6 1.0
N A:LEU209 4.2 83.0 1.0
CB A:VAL228 4.2 68.1 1.0
CD2 A:TYR215 4.2 121.4 1.0
C A:VAL228 4.4 68.7 1.0
CB A:LEU209 4.5 83.0 1.0
CG1 A:VAL228 4.5 68.5 1.0
CA A:MET229 4.5 68.2 1.0
CB A:LEU208 4.6 84.5 1.0
C A:MET229 4.7 74.0 1.0
CA A:LEU209 4.7 83.5 1.0
CE2 A:TYR215 4.8 122.2 1.0
O A:ASP227 4.8 68.0 1.0
CB A:MET229 4.8 70.9 1.0
C A:LEU208 4.9 87.6 1.0
CG A:LEU208 4.9 89.3 1.0
CA A:ASN210 4.9 93.3 1.0
CA A:LEU208 4.9 84.5 1.0
C A:LEU209 5.0 93.4 1.0
C A:ASN210 5.0 98.9 1.0
C13 A:YU6602 5.0 75.5 1.0
CG A:GLU216 5.0 126.4 1.0

Iodine binding site 3 out of 7 in 7fun

Go back to Iodine Binding Sites List in 7fun
Iodine binding site 3 out of 7 in the Crystal Structure of Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid


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 Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I605

b:99.3
occ:1.00
 OG A:SER378 3.2 60.7 1.0
NH2 A:ARG376 3.3 81.8 1.0
C4 A:YU6602 3.8 73.9 1.0
N2 A:YU6602 3.9 71.7 1.0
CB A:SER378 4.0 54.8 1.0
C6 A:YU6602 4.1 74.8 1.0
CG1 A:VAL360 4.2 64.6 1.0
O33 A:YU6602 4.2 49.0 1.0
N5 A:YU6602 4.2 77.2 1.0
N16 A:YU6602 4.2 49.9 1.0
C3 A:YU6602 4.3 72.9 1.0
C8 A:YU6602 4.3 77.7 1.0
O A:HOH735 4.3 73.8 1.0
OG A:SER380 4.4 59.9 1.0
CB A:SER380 4.5 49.1 1.0
C7 A:YU6602 4.5 71.5 1.0
CG2 A:VAL360 4.5 65.8 1.0
CZ A:ARG376 4.6 88.8 1.0
C1 A:YU6602 4.8 62.3 1.0
CG2 A:THR321 4.9 79.6 1.0
CB A:VAL360 4.9 66.1 1.0
C15 A:YU6602 4.9 51.4 1.0

Iodine binding site 4 out of 7 in 7fun

Go back to Iodine Binding Sites List in 7fun
Iodine binding site 4 out of 7 in the Crystal Structure of Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid


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 Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I606

b:121.1
occ:1.00
 CG A:GLU418 3.7 90.8 1.0
CE A:LYS421 3.8 77.5 1.0
CD A:LYS421 3.8 73.2 1.0
N A:SER435 3.8 59.2 1.0
CB A:SER435 4.3 63.5 1.0
CA A:GLU418 4.3 78.0 1.0
CG A:LYS219 4.4 131.0 1.0
C A:SER434 4.4 64.8 1.0
CA A:SER434 4.4 64.5 1.0
CD2 A:LEU417 4.5 71.8 1.0
CA A:SER435 4.5 58.7 1.0
N A:GLU418 4.5 77.2 1.0
CE A:LYS219 4.6 153.4 1.0
CB A:GLU418 4.6 78.9 1.0
CG A:LEU417 4.7 75.6 1.0
OE2 A:GLU418 4.7 124.9 1.0
CD A:GLU418 4.7 126.7 1.0
OG A:SER435 4.7 78.1 1.0
C A:LEU417 5.0 79.2 1.0
CD A:LYS219 5.0 143.8 1.0

Iodine binding site 5 out of 7 in 7fun

Go back to Iodine Binding Sites List in 7fun
Iodine binding site 5 out of 7 in the Crystal Structure of Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid


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 Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I607

b:122.5
occ:0.50
 O A:HOH739 3.4 73.1 1.0
CG A:LYS392 3.6 61.4 1.0
CD A:LYS392 3.8 71.7 1.0
N A:SER393 4.5 55.5 1.0
CB A:LYS392 4.5 58.1 1.0
CA A:SER393 4.7 55.6 1.0
C A:LYS392 4.7 59.4 1.0
CB A:SER393 4.7 58.4 1.0
OE1 A:GLN451 4.7 102.3 1.0
O A:LYS392 5.0 58.0 1.0
OD2 A:ASP452 5.0 83.9 1.0

Iodine binding site 6 out of 7 in 7fun

Go back to Iodine Binding Sites List in 7fun
Iodine binding site 6 out of 7 in the Crystal Structure of Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid


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 Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:137.1
occ:1.00
 NH1 A:ARG349 3.4 58.4 1.0
O A:HOH756 3.7 59.5 1.0
O A:ALA346 3.8 66.4 1.0
N A:LYS350 3.8 56.6 1.0
CD A:ARG349 4.0 65.0 1.0
CB A:LYS350 4.1 60.0 1.0
CA A:LYS350 4.1 56.6 1.0
CB A:ARG349 4.1 52.7 1.0
CG A:ARG349 4.1 59.4 1.0
C A:ARG349 4.4 58.0 1.0
CZ A:ARG349 4.5 78.9 1.0
CG A:LYS350 4.5 69.3 1.0
C A:ALA346 4.7 64.6 1.0
NE A:ARG349 4.8 63.8 1.0
CA A:ALA346 4.8 58.5 1.0
CA A:ARG349 4.9 53.7 1.0
CB A:ALA346 4.9 59.4 1.0
CD A:ARG353 5.0 67.6 1.0
O A:ARG349 5.0 57.5 1.0

Iodine binding site 7 out of 7 in 7fun

Go back to Iodine Binding Sites List in 7fun
Iodine binding site 7 out of 7 in the Crystal Structure of Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid


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 Human Cyclic Gmp-Amp Synthase in Complex with 2- [(4-Benzylpiperazin-1-Yl)Methyl]-6-(2-Chloro-4-Methylphenyl)-1H- Benzimidazole-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:131.2
occ:1.00
 O A:HOH707 3.9 61.0 1.0
CD2 A:LEU490 4.0 65.7 1.0
CE2 A:TYR436 4.1 55.9 1.0
CE2 A:PHE488 4.1 73.9 1.0
OH A:TYR248 4.4 76.5 1.0
O A:HOH740 4.4 70.2 1.0
CZ A:PHE488 4.5 70.6 1.0
CD A:ARG376 4.6 64.8 1.0
O A:HOH758 4.6 70.9 1.0
CD2 A:TYR436 4.6 54.9 1.0
CE A:LYS362 4.7 107.7 1.0
NZ A:LYS362 4.9 122.6 1.0

Reference:

K.Groebke-Zbinden, A.Vandemeulebroucke, M.Hilbert, M.G.Rudolph. Crystal Structure of A Human Cyclic Gmp-Amp Synthase Complex To Be Published.
Page generated: Mon Aug 12 01:10:16 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