Zinc in PDB 6y2c: Crystal Structure of the Third Kh Domain of FUBP1

Protein crystallography data

The structure of Crystal Structure of the Third Kh Domain of FUBP1, PDB code: 6y2c was solved by X.Ni, A.C.Joerger, A.Chaikuad, C.H.Arrowsmith, A.M.Edwards, C.Bountra, S.Knapp, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.09 / 2.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 47.409, 47.409, 147.893, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 24

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Third Kh Domain of FUBP1 (pdb code 6y2c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Third Kh Domain of FUBP1, PDB code: 6y2c:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6y2c

Go back to Zinc Binding Sites List in 6y2c
Zinc binding site 1 out of 3 in the Crystal Structure of the Third Kh Domain of FUBP1


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 the Third Kh Domain of FUBP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:36.0
occ:1.00
OE1 A:GLU337 1.8 35.4 1.0
OD2 A:ASP341 2.1 32.4 1.0
O A:HOH608 2.4 39.6 1.0
CG A:ASP341 2.8 29.5 1.0
OD1 A:ASP341 2.8 29.9 1.0
CD A:GLU337 2.8 37.0 1.0
CG A:GLU337 3.2 33.1 1.0
OE2 A:GLU337 4.0 39.6 1.0
CB A:ASP341 4.2 28.1 1.0
NH2 A:ARG344 4.2 62.0 1.0
O A:GLU337 4.4 31.2 1.0
O A:HOH601 4.6 46.9 1.0
CB A:GLU337 4.7 32.8 1.0

Zinc binding site 2 out of 3 in 6y2c

Go back to Zinc Binding Sites List in 6y2c
Zinc binding site 2 out of 3 in the Crystal Structure of the Third Kh Domain of FUBP1


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 the Third Kh Domain of FUBP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn407

b:27.5
occ:1.00
OD2 B:ASP304 1.8 25.8 1.0
NE2 B:HIS334 1.9 24.4 1.0
N B:SER259 2.3 29.4 1.0
O B:SER259 2.3 27.0 1.0
O B:HOH508 2.3 27.2 1.0
CG B:ASP304 2.8 27.3 1.0
CD2 B:HIS334 2.9 25.8 1.0
CE1 B:HIS334 2.9 25.9 1.0
C B:SER259 3.0 28.7 1.0
OD1 B:ASP304 3.1 28.9 1.0
CA B:SER259 3.1 30.0 1.0
CB B:SER259 3.7 31.8 1.0
CD1 B:ILE338 3.9 29.2 1.0
O B:HOH515 3.9 46.5 1.0
ND1 B:HIS334 4.0 25.2 1.0
CG B:HIS334 4.0 25.9 1.0
O B:ASP304 4.1 28.0 1.0
CB B:ASP304 4.2 26.9 1.0
N B:MET260 4.3 28.5 1.0
C B:ASP304 4.4 28.0 1.0
OG B:SER259 4.5 34.4 1.0
CG2 B:VAL264 4.8 30.2 1.0
CA B:ASP304 4.9 28.0 1.0
N B:ALA305 4.9 26.1 1.0
CG1 B:ILE338 4.9 27.4 1.0

Zinc binding site 3 out of 3 in 6y2c

Go back to Zinc Binding Sites List in 6y2c
Zinc binding site 3 out of 3 in the Crystal Structure of the Third Kh Domain of FUBP1


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 the Third Kh Domain of FUBP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn408

b:27.5
occ:1.00
OD2 B:ASP341 2.0 33.1 1.0
O B:HOH519 2.3 9.2 1.0
CG B:ASP341 2.8 28.1 1.0
OD1 B:ASP341 3.3 30.2 1.0
CB B:ASP341 3.8 26.6 1.0
O2 B:EDO404 4.1 33.1 1.0
N B:PHE261 4.4 27.3 1.0
CB B:PHE261 4.4 28.9 1.0
CB B:MET260 4.6 30.9 1.0
C2 B:EDO404 4.9 41.9 1.0

Reference:

X.Ni, A.C.Joerger, A.Chaikuad, C.H.Arrowsmith, A.M.Edwards, C.Bountra, S.Knapp, Structural Genomics Consortium (Sgc). Crystal Structure of the Fourth Kh Domain of FUBP1 To Be Published.
Page generated: Wed Dec 16 13:13:50 2020

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