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

Protein crystallography data

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

Zinc Binding Sites:

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 6wbe

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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 6wbe

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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 6wbe

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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 6wbe

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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 6wbe

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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 6wbe

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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 6wbe

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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

Reference:

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
Page generated: Sat Apr 3 18:27:02 2021

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