Zinc in PDB 5ue8: The Crystal Structure of MUNC13-1 C1C2BMUN Domain

The structure of The Crystal Structure of MUNC13-1 C1C2BMUN Domain, PDB code: 5ue8 was solved by D.R.Tomchick, J.Rizo, J.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.60 / 3.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	176.145, 86.351, 202.142, 90.00, 115.54, 90.00
R / Rfree (%)	25.2 / 29

The structure of The Crystal Structure of MUNC13-1 C1C2BMUN Domain also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the The Crystal Structure of MUNC13-1 C1C2BMUN Domain (pdb code 5ue8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of MUNC13-1 C1C2BMUN Domain, PDB code: 5ue8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Crystal Structure of MUNC13-1 C1C2BMUN Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of MUNC13-1 C1C2BMUN Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:15.4 occ:1.00 ND1 A:HIS605 2.0 24.1 1.0 SG A:CYS583 2.3 24.2 1.0 SG A:CYS608 2.3 27.2 1.0 SG A:CYS580 2.4 22.6 1.0 CE1 A:HIS605 2.9 24.0 1.0 H A:HIS605 2.9 24.6 1.0 HB2 A:HIS605 3.0 26.4 1.0 HB2 A:CYS608 3.0 33.5 1.0 HE1 A:HIS605 3.1 25.5 1.0 CG A:HIS605 3.1 24.4 1.0 HB2 A:CYS580 3.1 21.7 1.0 CB A:CYS580 3.2 22.4 1.0 CB A:CYS608 3.3 27.0 1.0 H A:CYS583 3.3 22.7 1.0 HB3 A:CYS580 3.3 21.7 1.0 CB A:HIS605 3.5 24.8 1.0 HB3 A:CYS608 3.6 33.5 1.0 N A:HIS605 3.7 23.6 1.0 CB A:CYS583 3.8 24.6 1.0 HB3 A:CYS583 3.8 24.2 1.0 HB3 A:GLU582 4.0 48.7 1.0 HE3 A:LYS607 4.0 54.3 1.0 NE2 A:HIS605 4.1 24.2 1.0 N A:CYS583 4.1 23.3 1.0 HB2 A:CYS604 4.2 28.7 1.0 CD2 A:HIS605 4.2 24.5 1.0 CA A:HIS605 4.2 24.3 1.0 HA A:CYS604 4.2 26.1 1.0 H A:GLY585 4.3 27.7 1.0 HB3 A:HIS605 4.3 26.4 1.0 HG3 A:LYS607 4.3 54.3 1.0 HB2 A:CYS583 4.5 24.2 1.0 HE2 A:LYS607 4.5 54.3 1.0 H A:GLU582 4.5 40.8 1.0 CA A:CYS583 4.5 23.9 1.0 CA A:CYS608 4.6 29.1 1.0 CA A:CYS580 4.7 21.8 1.0 HG2 A:LYS607 4.7 54.3 1.0 CE A:LYS607 4.7 44.4 1.0 C A:CYS604 4.7 23.8 1.0 CA A:CYS604 4.8 22.4 1.0 H A:CYS608 4.8 34.3 1.0 HA3 A:GLY585 4.8 29.3 1.0 HE2 A:HIS605 4.8 25.3 1.0 HA A:HIS605 4.9 26.4 1.0 N A:CYS608 4.9 27.7 1.0 HA A:CYS580 4.9 21.0 1.0 CB A:CYS604 4.9 23.0 1.0 H A:GLU584 4.9 46.5 1.0 CB A:GLU582 4.9 39.7 1.0 CG A:LYS607 5.0 44.4 1.0 HA A:CYS608 5.0 36.0 1.0

Zinc binding site 2 out of 4 in the The Crystal Structure of MUNC13-1 C1C2BMUN Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of MUNC13-1 C1C2BMUN Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:23.3 occ:1.00 HG A:CYS616 1.4 64.7 1.0 ND1 A:HIS567 2.1 35.2 1.0 SG A:CYS600 2.3 22.6 1.0 SG A:CYS597 2.3 22.9 1.0 SG A:CYS616 2.4 53.0 1.0 HA A:HIS567 2.4 48.0 1.0 CG A:HIS567 2.9 35.0 1.0 CE1 A:HIS567 3.0 34.0 1.0 HB3 A:HIS567 3.1 45.7 1.0 CA A:HIS567 3.2 39.2 1.0 CB A:HIS567 3.2 37.2 1.0 HE1 A:HIS567 3.3 41.8 1.0 H A:CYS600 3.4 45.2 1.0 HB2 A:CYS600 3.4 33.8 1.0 HB2 A:CYS616 3.4 64.7 1.0 CB A:CYS600 3.5 27.3 1.0 CB A:CYS616 3.5 53.0 1.0 H A:ASN568 3.5 48.3 1.0 HA A:CYS616 3.7 63.6 1.0 CB A:CYS597 3.7 22.7 1.0 HB2 A:CYS597 3.7 22.0 1.0 N A:CYS600 3.9 36.8 1.0 HB3 A:CYS597 4.0 22.0 1.0 CD2 A:HIS567 4.0 34.7 1.0 NE2 A:HIS567 4.0 34.0 1.0 HB2 A:GLU599 4.0 52.8 1.0 N A:HIS567 4.1 41.2 1.0 N A:ASN568 4.1 39.4 1.0 CA A:CYS616 4.2 52.1 1.0 HB3 A:CYS600 4.2 33.8 1.0 HB2 A:HIS567 4.2 45.7 1.0 C A:HIS567 4.2 39.3 1.0 HB3 A:CYS616 4.3 64.7 1.0 CA A:CYS600 4.3 34.2 1.0 H A:HIS567 4.4 50.5 1.0 H A:GLU599 4.5 49.0 1.0 HB3 A:GLU599 4.6 52.8 1.0 HG12 A:VAL602 4.7 36.1 1.0 HA A:CYS600 4.7 42.1 1.0 CB A:GLU599 4.7 43.1 1.0 O A:PRO566 4.8 40.3 1.0 C A:PRO566 4.8 40.1 1.0 HE2 A:HIS567 4.8 41.9 1.0 HD2 A:HIS567 4.8 42.7 1.0 C A:GLU599 4.9 37.7 1.0

Zinc binding site 3 out of 4 in the The Crystal Structure of MUNC13-1 C1C2BMUN Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of MUNC13-1 C1C2BMUN Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1602 b:80.9 occ:1.00 ND1 B:HIS605 2.0 80.0 1.0 SG B:CYS583 2.4 69.0 1.0 SG B:CYS580 2.4 83.1 1.0 SG B:CYS608 2.4 90.9 1.0 HB2 B:HIS605 2.9 94.5 1.0 HB2 B:CYS608 3.0 0.8 1.0 CE1 B:HIS605 3.0 81.6 1.0 H B:HIS605 3.0 78.0 1.0 CG B:HIS605 3.1 82.8 1.0 HE1 B:HIS605 3.2 99.0 1.0 CB B:CYS608 3.2 91.5 1.0 H B:CYS583 3.3 91.8 1.0 HB2 B:CYS580 3.4 99.2 1.0 CB B:CYS580 3.4 81.8 1.0 CB B:HIS605 3.4 77.8 1.0 HB3 B:CYS608 3.4 0.8 1.0 HB3 B:CYS580 3.5 99.2 1.0 HB3 B:CYS583 3.7 78.6 1.0 CB B:CYS583 3.7 69.9 1.0 N B:HIS605 3.8 69.3 1.0 HB3 B:GLU582 3.8 0.4 1.0 NE2 B:HIS605 4.1 80.9 1.0 N B:CYS583 4.1 75.6 1.0 CD2 B:HIS605 4.2 81.4 1.0 HB2 B:CYS604 4.2 82.3 1.0 HB3 B:HIS605 4.2 94.5 1.0 CA B:HIS605 4.2 73.5 1.0 HA B:CYS604 4.4 82.2 1.0 H B:GLY585 4.4 92.6 1.0 HB2 B:CYS583 4.4 78.6 1.0 H B:GLU582 4.5 0.1 1.0 CA B:CYS583 4.5 70.0 1.0 CA B:CYS608 4.6 91.9 1.0 HE3 B:LYS607 4.7 85.8 1.0 HG3 B:LYS607 4.7 97.4 1.0 C B:CYS604 4.8 74.0 1.0 CB B:GLU582 4.8 0.6 1.0 H B:CYS608 4.8 0.4 1.0 HA3 B:GLY585 4.8 88.9 1.0 CA B:CYS580 4.9 80.2 1.0 HA B:HIS605 4.9 89.2 1.0 HE2 B:HIS605 4.9 98.1 1.0 CA B:CYS604 4.9 69.1 1.0 N B:CYS608 5.0 92.8 1.0 CB B:CYS604 5.0 70.0 1.0

Zinc binding site 4 out of 4 in the The Crystal Structure of MUNC13-1 C1C2BMUN Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of MUNC13-1 C1C2BMUN Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1603 b:58.0 occ:1.00 ND1 B:HIS567 2.0 0.5 1.0 SG B:CYS600 2.3 72.5 1.0 SG B:CYS597 2.3 91.3 1.0 SG B:CYS616 2.4 78.0 1.0 HA B:HIS567 2.5 0.2 1.0 HB3 B:HIS567 2.9 0.0 1.0 CG B:HIS567 2.9 0.6 1.0 CE1 B:HIS567 3.1 0.4 1.0 CB B:HIS567 3.1 0.2 1.0 HB2 B:CYS600 3.1 83.5 1.0 CA B:HIS567 3.2 0.5 1.0 H B:ASN568 3.4 0.7 1.0 CB B:CYS600 3.4 71.4 1.0 HE1 B:HIS567 3.4 0.7 1.0 H B:CYS600 3.4 80.5 1.0 HB2 B:CYS616 3.4 96.9 1.0 CB B:CYS616 3.5 79.9 1.0 HB2 B:CYS597 3.6 0.4 1.0 CB B:CYS597 3.6 91.2 1.0 HA B:CYS616 3.9 0.8 1.0 HB3 B:CYS597 3.9 0.4 1.0 N B:CYS600 4.0 71.4 1.0 N B:ASN568 4.0 0.2 1.0 CD2 B:HIS567 4.0 0.3 1.0 HB3 B:CYS600 4.1 83.5 1.0 HB2 B:HIS567 4.1 0.0 1.0 NE2 B:HIS567 4.1 0.8 1.0 HB2 B:GLU599 4.2 0.3 1.0 C B:HIS567 4.2 0.9 1.0 N B:HIS567 4.3 1.0 1.0 CA B:CYS616 4.3 83.1 1.0 HB3 B:CYS616 4.3 96.9 1.0 CA B:CYS600 4.3 71.0 1.0 HG12 B:VAL602 4.4 79.7 1.0 H B:GLU599 4.5 0.6 1.0 H B:HIS567 4.5 0.0 1.0 HA B:CYS600 4.8 80.0 1.0 HB3 B:GLU599 4.8 0.3 1.0 HD2 B:HIS567 4.9 0.8 1.0 HG11 B:VAL602 4.9 79.7 1.0 CB B:GLU599 4.9 0.7 1.0 HE2 B:HIS567 4.9 0.2 1.0 CA B:CYS597 4.9 92.0 1.0 HA B:CYS597 5.0 0.5 1.0 C B:GLU599 5.0 0.1 1.0

J.Xu, M.Camacho, Y.Xu, V.Esser, X.Liu, T.Trimbuch, Y.Z.Pan, C.Ma, D.R.Tomchick, C.Rosenmund, J.Rizo. Mechanistic Insights Into Neurotransmitter Release and Presynaptic Plasticity From the Crystal Structure of MUNC13-1 C1C2BMUN. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28177287
DOI: 10.7554/ELIFE.22567