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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

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