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Zinc in PDB 5kb2: Crystal Structure of A Tris-Thiolate Zn(II)S3O Complex in A De Novo Three-Stranded Coiled Coil Peptide

Protein crystallography data

The structure of Crystal Structure of A Tris-Thiolate Zn(II)S3O Complex in A De Novo Three-Stranded Coiled Coil Peptide, PDB code: 5kb2 was solved by L.Ruckthong, M.L.Zastrow, J.A.Stuckey, V.L.Pecoraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.01 / 1.89
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 37.853, 37.853, 141.072, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 22.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Tris-Thiolate Zn(II)S3O Complex in A De Novo Three-Stranded Coiled Coil Peptide (pdb code 5kb2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Tris-Thiolate Zn(II)S3O Complex in A De Novo Three-Stranded Coiled Coil Peptide, PDB code: 5kb2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5kb2

Go back to Zinc Binding Sites List in 5kb2
Zinc binding site 1 out of 2 in the Crystal Structure of A Tris-Thiolate Zn(II)S3O Complex in A De Novo Three-Stranded Coiled Coil Peptide


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 A Tris-Thiolate Zn(II)S3O Complex in A De Novo Three-Stranded Coiled Coil Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:32.7
occ:1.00
NE2 A:HIS35 2.0 31.4 1.0
OE1 A:GLU31 2.0 32.6 1.0
OE2 A:GLU34 2.0 23.1 0.4
OE2 A:GLU34 2.1 29.1 0.6
CD A:GLU34 2.9 38.5 0.4
HG2 A:GLU34 2.9 51.8 0.4
CD A:GLU31 2.9 34.1 1.0
CD2 A:HIS35 2.9 28.7 1.0
CE1 A:HIS35 3.0 36.9 1.0
HD2 A:HIS35 3.1 34.5 1.0
OE2 A:GLU31 3.2 32.6 1.0
CD A:GLU34 3.2 39.8 0.6
HE1 A:HIS35 3.2 44.3 1.0
CG A:GLU34 3.4 43.1 0.4
HG2 A:GLU34 3.4 55.1 0.6
HB3 A:GLU34 3.5 36.0 0.6
HB3 A:GLU34 3.6 36.1 0.4
CG A:GLU34 3.7 45.9 0.6
OE1 A:GLU34 3.8 33.4 0.4
HA A:GLU31 4.0 29.6 1.0
ND1 A:HIS35 4.1 33.0 1.0
CB A:GLU34 4.1 30.1 0.4
CG A:HIS35 4.1 27.2 1.0
CB A:GLU34 4.1 30.0 0.6
HG3 A:GLU34 4.2 51.8 0.4
OE1 A:GLU34 4.2 28.7 0.6
CG A:GLU31 4.3 31.0 1.0
HB3 A:GLU31 4.3 28.7 1.0
HB2 A:GLU34 4.5 36.1 0.4
HB2 A:GLU34 4.5 36.0 0.6
HG3 A:GLU34 4.6 55.1 0.6
CB A:GLU31 4.7 23.9 1.0
HG3 A:GLU31 4.8 37.2 1.0
CA A:GLU31 4.8 24.6 1.0
HD1 A:HIS35 4.8 39.5 1.0
HG2 A:GLU31 4.9 37.2 1.0

Zinc binding site 2 out of 2 in 5kb2

Go back to Zinc Binding Sites List in 5kb2
Zinc binding site 2 out of 2 in the Crystal Structure of A Tris-Thiolate Zn(II)S3O Complex in A De Novo Three-Stranded Coiled Coil Peptide


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 A Tris-Thiolate Zn(II)S3O Complex in A De Novo Three-Stranded Coiled Coil Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:39.5
occ:0.17
O A:HOH230 2.2 42.8 0.3
SG A:CYS16 2.3 56.4 0.9
HB2 A:CYS16 2.6 54.0 0.1
HB2 A:CYS16 3.1 54.2 0.9
CB A:CYS16 3.2 45.1 0.9
CB A:CYS16 3.3 45.0 0.1
HA A:CYS16 3.4 50.0 0.1
SG A:CYS16 3.4 55.4 0.1
HA A:CYS16 3.4 50.2 0.9
HG A:CYS16 3.6 66.5 0.1
CA A:CYS16 3.9 41.8 0.9
CA A:CYS16 3.9 41.6 0.1
HD12 A:LEU19 4.0 65.0 1.0
HB3 A:CYS16 4.1 54.2 0.9
HB3 A:CYS16 4.1 54.0 0.1
N A:CYS16 4.7 36.5 1.0
H A:CYS16 4.8 43.8 0.9
H A:CYS16 4.8 43.8 0.1
CD1 A:LEU19 4.9 54.2 1.0
HB2 A:LEU19 5.0 39.8 1.0
HD13 A:LEU19 5.0 65.0 1.0

Reference:

L.Ruckthong, M.L.Zastrow, J.A.Stuckey, V.L.Pecoraro. A Crystallographic Examination of Predisposition Versus Preorganization in De Novo Designed Metalloproteins. J.Am.Chem.Soc. V. 138 11979 2016.
ISSN: ESSN 1520-5126
PubMed: 27532255
DOI: 10.1021/JACS.6B07165
Page generated: Wed Dec 16 06:26:42 2020

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