Zinc in PDB 6wbe: Crystal Structure of Coiled Coil Region of Human Septin 1

The structure of Crystal Structure of Coiled Coil Region of Human Septin 1, PDB code: 6wbe was solved by D.A.L.Cabrejos, I.Cavini, F.A.Sala, N.F.Valadares, H.M.Pereira, J.Brandao-Neto, A.F.Z.Nascimento, I.Uson, A.P.U.Araujo, R.C.Garratt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.82 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	26.23, 60.45, 81.639, 90, 90, 90
R / Rfree (%)	20.8 / 25.7

The binding sites of Zinc atom in the Crystal Structure of Coiled Coil Region of Human Septin 1 (pdb code 6wbe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Coiled Coil Region of Human Septin 1, PDB code: 6wbe:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of Coiled Coil Region of Human Septin 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Coiled Coil Region of Human Septin 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:56.5 occ:1.00 OD1 A:ASP328 2.3 58.4 1.0 OE1 A:GLU330 2.4 54.8 1.0 CG A:ASP328 3.0 57.9 1.0 OD2 A:ASP328 3.2 51.1 1.0 CD A:GLU330 3.3 51.7 1.0 OE2 A:GLU330 3.6 52.9 1.0 N A:THR329 4.1 48.7 1.0 CB A:ASP328 4.3 61.1 1.0 N A:GLU330 4.3 47.7 1.0 CA A:ASP328 4.5 64.5 1.0 CG A:GLU330 4.6 48.9 1.0 C A:ASP328 4.7 53.4 1.0 CB A:GLU330 4.8 47.8 1.0 CA A:THR329 5.0 45.1 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of Coiled Coil Region of Human Septin 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Coiled Coil Region of Human Septin 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:32.7 occ:1.00 OD1 A:ASP337 2.0 32.5 1.0 OD1 C:ASP337 2.1 33.9 1.0 O A:ACT406 2.1 30.1 1.0 NH2 A:ARG341 2.3 40.2 1.0 CZ A:ARG341 2.9 52.0 1.0 CG A:ASP337 2.9 31.6 1.0 C A:ACT406 2.9 32.3 1.0 NH1 A:ARG341 3.0 46.2 1.0 CG C:ASP337 3.0 34.9 1.0 OD2 A:ASP337 3.1 33.1 1.0 OXT A:ACT406 3.2 34.8 1.0 OD2 C:ASP337 3.4 31.4 1.0 NE A:ARG341 4.0 55.4 1.0 NE D:ARG341 4.0 27.1 1.0 CH3 A:ACT406 4.2 21.1 1.0 CB A:ASP337 4.2 31.0 1.0 O D:HOH502 4.3 24.3 1.0 NH2 D:ARG341 4.3 22.4 1.0 CB C:ASP337 4.3 27.1 1.0 CZ D:ARG341 4.6 30.2 1.0 CA C:ASP337 4.7 33.1 1.0 CG C:ARG341 4.8 28.6 1.0 CA A:ASP337 4.8 34.7 1.0 O C:ASP337 4.8 33.9 1.0 O A:ASP337 4.9 41.6 1.0 NE C:ARG341 4.9 27.9 1.0 CD D:ARG341 5.0 23.6 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of Coiled Coil Region of Human Septin 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Coiled Coil Region of Human Septin 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:53.8 occ:1.00 OE2 A:GLU345 2.1 58.2 1.0 OE1 A:GLU348 2.3 58.4 1.0 OE2 D:GLU338 2.5 52.5 1.0 OE1 A:GLU345 2.6 53.2 1.0 CD A:GLU345 2.7 47.6 1.0 OE1 D:GLU338 2.7 55.1 1.0 CD A:GLU348 2.9 58.0 1.0 CD D:GLU338 2.9 43.3 1.0 OE2 A:GLU348 2.9 56.5 1.0 O A:HOH501 3.0 24.8 1.0 O D:HOH501 3.6 47.7 1.0 CG A:GLU345 4.2 41.9 1.0 CG A:GLU348 4.3 53.5 1.0 CG D:GLU338 4.4 35.3 1.0 CB A:GLU348 4.8 43.7 1.0 CB A:GLU345 4.9 40.9 1.0 CA A:GLU345 4.9 29.0 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of Coiled Coil Region of Human Septin 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Coiled Coil Region of Human Septin 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:91.8 occ:1.00 O A:ACT407 2.4 70.1 1.0 OE2 A:GLU338 3.2 82.5 1.0 C A:ACT407 3.2 65.3 1.0 OXT A:ACT407 3.3 62.3 1.0 CD A:GLU338 4.3 78.7 1.0 O A:HOH504 4.6 54.9 1.0 CH3 A:ACT407 4.7 63.6 1.0 OE1 A:GLU338 4.8 84.0 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of Coiled Coil Region of Human Septin 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Coiled Coil Region of Human Septin 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:33.2 occ:1.00 OE2 D:GLU348 2.0 28.6 1.0 NH2 B:ARG341 2.0 47.9 1.0 OD2 B:ASP337 2.0 37.1 1.0 OE2 C:GLU348 2.1 43.9 1.0 CG B:ASP337 2.7 29.1 1.0 OE1 C:GLU348 2.7 40.4 1.0 OD1 B:ASP337 2.7 37.5 1.0 CD C:GLU348 2.8 34.6 1.0 CD D:GLU348 3.0 30.4 1.0 CZ B:ARG341 3.0 47.0 1.0 CG D:GLU348 3.3 30.8 1.0 NH1 B:ARG341 3.4 31.2 1.0 CG C:GLN344 4.1 40.2 1.0 OE1 D:GLU348 4.1 34.8 1.0 CB B:ASP337 4.1 26.4 1.0 NE B:ARG341 4.2 48.1 1.0 NE2 C:GLN344 4.2 53.2 1.0 CG C:GLU348 4.3 29.6 1.0 OE1 D:GLN344 4.5 37.5 1.0 CD B:ARG341 4.7 44.2 1.0 CG D:GLN344 4.7 32.2 1.0 CD C:GLN344 4.7 51.5 1.0 CB D:GLU348 4.8 26.5 1.0 CD D:GLN344 5.0 35.2 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of Coiled Coil Region of Human Septin 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Coiled Coil Region of Human Septin 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:29.8 occ:1.00 OD2 D:ASP337 1.9 33.8 1.0 OE1 B:GLU348 2.0 28.4 1.0 O A:HOH505 2.3 43.3 1.0 CG D:ASP337 2.6 31.1 1.0 OD1 D:ASP337 2.6 28.4 1.0 CD B:GLU348 3.0 33.4 1.0 CG B:GLU348 3.3 30.5 1.0 NH1 C:ARG341 3.9 29.5 1.0 CB D:ASP337 4.1 28.2 1.0 NE2 B:GLN344 4.1 24.4 1.0 OE2 B:GLU348 4.1 33.3 1.0 O C:HOH501 4.3 33.5 1.0 CB B:GLN344 4.4 26.2 1.0 O A:HOH503 4.5 47.2 1.0 CG B:GLN344 4.6 32.5 1.0 NE2 A:GLN344 4.6 53.5 1.0 O B:GLN344 4.8 33.0 1.0 CB B:GLU348 4.8 28.6 1.0 O D:ASP337 4.8 27.4 1.0 CD B:GLN344 4.9 29.2 1.0 C D:ASP337 4.9 28.8 1.0 CA D:ASP337 5.0 27.3 1.0 OE1 A:GLN344 5.0 60.9 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of Coiled Coil Region of Human Septin 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Coiled Coil Region of Human Septin 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:70.0 occ:1.00 OE2 B:GLU335 2.2 81.0 1.0 CD B:GLU335 2.9 55.5 1.0 OE1 B:GLU335 3.1 50.4 1.0 O B:HOH510 3.3 53.0 1.0 CG B:GLU335 4.3 46.7 1.0

D.A.Leonardo, I.A.Cavini, F.A.Sala, D.C.Mendonca, H.V D Rosa, P.S.Kumagai, E.Crusca Jr., N.F.Valadares, I.A.Marques, J.Brandao-Neto, C.E.Munte, H.R.Kalbitzer, N.Soler, I.Uson, I.Andre, A.P U Araujo, H.D'muniz Pereira, R.C.Garratt. Orientational Ambiguity in Septin Coiled Coils and Its Structural Basis. J.Mol.Biol. 66889 2021.
ISSN: ESSN 1089-8638
PubMed: 33639214
DOI: 10.1016/J.JMB.2021.166889