Zinc in PDB 5mt9: Human Insulin in Complex with Serotonin and Arginine

The structure of Human Insulin in Complex with Serotonin and Arginine, PDB code: 5mt9 was solved by A.M.Brzozowski, J.P.Turkenburg, J.Jiracek, L.Zakova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.99 / 1.88
Space group	H 3 1
Cell size a, b, c (Å), α, β, γ (°)	159.310, 159.310, 76.500, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 26.9

The structure of Human Insulin in Complex with Serotonin and Arginine also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Zinc atom in the Human Insulin in Complex with Serotonin and Arginine (pdb code 5mt9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Human Insulin in Complex with Serotonin and Arginine, PDB code: 5mt9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Human Insulin in Complex with Serotonin and Arginine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Insulin in Complex with Serotonin and Arginine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:39.3 occ:0.33 NE2 B:HIS10 2.1 39.6 1.0 CL B:CL102 2.7 58.3 0.3 CE1 B:HIS10 3.0 37.9 1.0 CD2 B:HIS10 3.1 35.9 1.0 ND1 B:HIS10 4.1 36.2 1.0 CG B:HIS10 4.2 39.2 1.0 CA B:ARG103 4.9 86.8 1.0

Zinc binding site 2 out of 8 in the Human Insulin in Complex with Serotonin and Arginine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Insulin in Complex with Serotonin and Arginine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:25.8 occ:0.33 NE2 D:HIS10 2.0 27.4 1.0 CL D:CL102 2.4 30.1 0.3 CE1 D:HIS10 3.0 31.0 1.0 CD2 D:HIS10 3.0 30.9 1.0 ND1 D:HIS10 4.1 27.9 1.0 CG D:HIS10 4.2 26.4 1.0 O D:LEU6 4.8 36.5 1.0 CB D:LEU6 5.0 43.0 1.0 O D:HOH209 5.0 48.7 1.0

Zinc binding site 3 out of 8 in the Human Insulin in Complex with Serotonin and Arginine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Insulin in Complex with Serotonin and Arginine within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:32.9 occ:1.00 NE2 F:HIS10 2.0 30.5 1.0 NE2 L:HIS10 2.1 33.1 1.0 NE2 N:HIS10 2.1 30.0 1.0 CL F:CL102 2.4 66.6 1.0 CE1 F:HIS10 2.9 31.1 1.0 CE1 L:HIS10 3.0 30.6 1.0 CE1 N:HIS10 3.1 33.1 1.0 CD2 L:HIS10 3.1 28.3 1.0 CD2 N:HIS10 3.1 28.6 1.0 CD2 F:HIS10 3.1 31.2 1.0 O F:ARG103 3.7 97.3 1.0 OXT L:ARG101 3.9 61.0 1.0 ND1 F:HIS10 4.1 34.3 1.0 ND1 L:HIS10 4.1 32.0 1.0 ND1 N:HIS10 4.2 31.9 1.0 CG L:HIS10 4.2 31.7 1.0 CG F:HIS10 4.2 30.4 1.0 CG N:HIS10 4.2 28.5 1.0 C L:ARG101 4.6 45.9 0.5 C F:ARG103 4.7 0.7 1.0 OXT N:ARG101 4.7 49.6 0.5 O L:ARG101 4.8 46.1 0.5 CA N:ARG101 5.0 47.3 0.5

Zinc binding site 4 out of 8 in the Human Insulin in Complex with Serotonin and Arginine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Insulin in Complex with Serotonin and Arginine within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn101 b:17.7 occ:1.00 NE2 P:HIS10 1.9 16.7 1.0 NE2 H:HIS10 2.0 17.2 1.0 NE2 J:HIS10 2.1 18.5 1.0 CL P:CL101 2.2 21.9 1.0 CE1 P:HIS10 2.8 22.7 1.0 CE1 H:HIS10 3.0 24.0 1.0 CE1 J:HIS10 3.0 22.5 1.0 CD2 P:HIS10 3.0 21.8 1.0 CD2 H:HIS10 3.0 17.6 1.0 CD2 J:HIS10 3.1 20.8 1.0 ND1 P:HIS10 4.0 20.6 1.0 CG P:HIS10 4.1 19.7 1.0 ND1 H:HIS10 4.1 21.1 1.0 ND1 J:HIS10 4.2 18.5 1.0 CG H:HIS10 4.2 19.3 1.0 CG J:HIS10 4.2 19.1 1.0 O P:LEU6 4.7 23.6 1.0 CB J:LEU6 4.8 22.7 1.0 O H:HOH219 4.8 38.4 1.0 CB P:LEU6 4.9 25.3 1.0 CB H:LEU6 4.9 23.6 1.0 O H:LEU6 4.9 19.5 1.0 O J:LEU6 4.9 24.0 1.0 O J:HOH102 5.0 47.3 1.0

Zinc binding site 5 out of 8 in the Human Insulin in Complex with Serotonin and Arginine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Insulin in Complex with Serotonin and Arginine within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn101 b:35.2 occ:1.00 NE2 V:HIS10 1.8 32.3 1.0 NE2 Z:HIS10 2.0 33.5 1.0 NE2 R:HIS10 2.1 33.0 1.0 CL Z:CL101 2.3 89.8 1.0 CE1 V:HIS10 2.7 36.6 1.0 CE1 Z:HIS10 2.9 36.2 1.0 CD2 V:HIS10 3.0 30.5 1.0 CE1 R:HIS10 3.0 33.8 1.0 CD2 Z:HIS10 3.0 31.1 1.0 CD2 R:HIS10 3.1 31.5 1.0 ND1 V:HIS10 3.9 33.1 1.0 ND1 Z:HIS10 4.0 33.2 1.0 CG V:HIS10 4.0 29.4 1.0 CG Z:HIS10 4.1 30.8 1.0 ND1 R:HIS10 4.1 35.7 1.0 CG R:HIS10 4.2 33.2 1.0 O R:HOH201 4.9 46.9 1.0 O Z:HOH207 5.0 63.6 1.0

Zinc binding site 6 out of 8 in the Human Insulin in Complex with Serotonin and Arginine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Insulin in Complex with Serotonin and Arginine within 5.0Å range: probe atom residue distance (Å) B Occ T:Zn101 b:20.2 occ:1.00 NE2 T:HIS10 2.0 22.3 1.0 NE2 b:HIS10 2.0 20.1 1.0 NE2 X:HIS10 2.0 20.0 1.0 CL T:CL102 2.2 22.2 1.0 CE1 b:HIS10 2.8 26.4 1.0 CE1 T:HIS10 2.9 21.9 1.0 CE1 X:HIS10 3.0 26.3 1.0 CD2 T:HIS10 3.0 22.6 1.0 CD2 X:HIS10 3.1 23.3 1.0 CD2 b:HIS10 3.1 20.5 1.0 ND1 b:HIS10 4.0 23.9 1.0 ND1 T:HIS10 4.0 22.3 1.0 ND1 X:HIS10 4.1 26.1 1.0 CG T:HIS10 4.1 21.1 1.0 CG b:HIS10 4.2 20.3 1.0 CG X:HIS10 4.2 22.8 1.0 O X:LEU6 4.7 29.3 1.0 O T:LEU6 4.8 25.7 1.0 O b:LEU6 4.8 19.6 1.0 CB X:LEU6 4.8 28.2 1.0 O b:HOH119 4.9 46.3 1.0 CB T:LEU6 4.9 25.2 1.0 CB b:LEU6 5.0 25.6 1.0

Zinc binding site 7 out of 8 in the Human Insulin in Complex with Serotonin and Arginine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Insulin in Complex with Serotonin and Arginine within 5.0Å range: probe atom residue distance (Å) B Occ d:Zn101 b:28.3 occ:0.33 CL d:CL102 1.7 61.0 0.3 NE2 d:HIS10 2.0 27.7 1.0 CE1 d:HIS10 2.9 29.3 1.0 CD2 d:HIS10 3.1 27.3 1.0 ND1 d:HIS10 4.1 30.1 1.0 CG d:HIS10 4.2 27.0 1.0 O d:HOH209 4.8 42.8 1.0

Zinc binding site 8 out of 8 in the Human Insulin in Complex with Serotonin and Arginine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human Insulin in Complex with Serotonin and Arginine within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn101 b:19.6 occ:0.33 NE2 f:HIS10 2.0 23.6 1.0 CL f:CL102 2.2 21.5 0.3 CE1 f:HIS10 2.9 26.9 1.0 CD2 f:HIS10 3.1 23.1 1.0 ND1 f:HIS10 4.0 25.8 1.0 CG f:HIS10 4.1 19.6 1.0 O f:LEU6 4.9 23.3 1.0 CB f:LEU6 5.0 29.2 1.0

V.Palivec, C.M.Viola, M.Kozak, T.R.Ganderton, K.Krizkova, J.P.Turkenburg, P.Haluskova, L.Zakova, J.Jiracek, P.Jungwirth, A.M.Brzozowski. Computational and Structural Evidence For Neurotransmitter-Mediated Modulation of the Oligomeric States of Human Insulin in Storage Granules. J. Biol. Chem. V. 292 8342 2017.
ISSN: ESSN 1083-351X
PubMed: 28348075
DOI: 10.1074/JBC.M117.775924