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Zinc in PDB 6dhy: Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines

Protein crystallography data

The structure of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines, PDB code: 6dhy was solved by F.A.Tezcan, L.A.Churchfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.84 / 2.22
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 52.510, 52.510, 255.670, 90.00, 90.00, 120.00
R / Rfree (%) 22.9 / 25.8

Other elements in 6dhy:

The structure of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines (pdb code 6dhy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines, PDB code: 6dhy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 6dhy

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Zinc binding site 1 out of 10 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:27.6
occ:1.00
 OD2 C:ASP74 2.0 25.1 1.0
NE2 A:HIS77 2.2 28.1 1.0
NE2 D:HIS63 2.2 33.3 1.0
NE2 A:HIS73 2.3 28.7 1.0
CG C:ASP74 2.9 25.6 1.0
CE1 A:HIS77 3.0 28.3 1.0
CD2 D:HIS63 3.1 33.5 1.0
OD1 C:ASP74 3.1 24.7 1.0
CD2 A:HIS73 3.2 28.8 1.0
CE1 A:HIS73 3.2 28.4 1.0
CE1 D:HIS63 3.2 33.9 1.0
CD2 A:HIS77 3.3 29.3 1.0
CB C:ASP74 4.2 25.8 1.0
ND1 A:HIS77 4.2 29.5 1.0
CD1 D:ILE67 4.3 26.0 1.0
CG D:HIS63 4.3 34.1 1.0
ND1 A:HIS73 4.3 27.7 1.0
ND1 D:HIS63 4.3 33.9 1.0
CG A:HIS73 4.3 28.8 1.0
CG A:HIS77 4.4 30.6 1.0
CA C:ASP74 4.7 26.8 1.0

Zinc binding site 2 out of 10 in 6dhy

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Zinc binding site 2 out of 10 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:43.2
occ:1.00
 O A:ALA1 2.0 35.4 1.0
OD2 A:ASP39 2.3 35.5 1.0
C A:ALA1 2.8 34.2 1.0
CG A:ASP39 3.0 34.7 1.0
CA A:ALA1 3.1 32.9 1.0
OD1 A:ASP39 3.1 33.9 1.0
N A:ASP2 4.1 34.5 1.0
CB A:ALA1 4.2 32.1 1.0
CB A:ASP39 4.3 35.1 1.0
O A:ASP39 4.4 33.8 1.0
ND2 A:ASN6 4.4 28.3 1.0
O A:HOH303 4.5 32.7 1.0
CA A:ASP2 4.7 34.6 1.0
C A:ASP39 4.9 34.6 1.0

Zinc binding site 3 out of 10 in 6dhy

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Zinc binding site 3 out of 10 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:25.6
occ:1.00
 NE2 B:HIS73 1.9 24.9 1.0
NE2 B:HIS77 2.1 30.4 1.0
OD1 D:ASP74 2.1 20.4 1.0
NE2 C:HIS63 2.2 21.5 1.0
OD2 D:ASP74 2.2 22.0 1.0
CG D:ASP74 2.5 21.3 1.0
CE1 B:HIS73 2.6 25.8 1.0
CE1 B:HIS77 3.0 29.9 1.0
CD2 C:HIS63 3.0 21.6 1.0
CD2 B:HIS77 3.0 30.6 1.0
CD2 B:HIS73 3.2 25.8 1.0
CE1 C:HIS63 3.3 21.9 1.0
ND1 B:HIS73 3.8 26.2 1.0
CB D:ASP74 4.0 21.1 1.0
ND1 B:HIS77 4.0 29.9 1.0
CD1 C:ILE67 4.1 26.4 1.0
CG B:HIS73 4.1 25.9 1.0
CG B:HIS77 4.1 30.4 1.0
O B:HOH307 4.2 17.9 1.0
CG C:HIS63 4.2 23.1 1.0
ND1 C:HIS63 4.3 22.3 1.0
O D:HOH302 4.4 28.6 1.0
CA D:ASP74 4.6 21.1 1.0
O B:HOH310 4.7 22.4 1.0
O D:ASP74 4.8 20.5 1.0
CE3 C:TRP66 4.9 34.1 1.0
O B:HIS73 5.0 29.0 1.0

Zinc binding site 4 out of 10 in 6dhy

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Zinc binding site 4 out of 10 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn204

b:42.5
occ:1.00
 NE2 B:HIS63 1.9 34.5 1.0
NE2 C:HIS73 2.0 35.2 1.0
OD1 A:ASP74 2.1 35.1 1.0
NE2 C:HIS77 2.1 32.0 1.0
CD2 B:HIS63 2.5 34.6 1.0
CE1 C:HIS73 2.6 35.1 1.0
CG A:ASP74 2.7 35.2 1.0
OD2 A:ASP74 2.7 35.3 1.0
CE1 C:HIS77 3.0 31.5 1.0
CE1 B:HIS63 3.1 34.7 1.0
CD2 C:HIS73 3.2 34.5 1.0
CD2 C:HIS77 3.2 32.4 1.0
CG B:HIS63 3.7 34.7 1.0
ND1 C:HIS73 3.8 34.3 1.0
CD1 B:ILE67 3.9 26.9 1.0
ND1 B:HIS63 4.0 34.9 1.0
CG C:HIS73 4.1 34.2 1.0
CB A:ASP74 4.1 34.7 1.0
ND1 C:HIS77 4.2 31.4 1.0
CG C:HIS77 4.3 32.5 1.0
CE3 B:TRP66 4.3 44.9 1.0
CZ3 B:TRP66 4.8 45.6 1.0
O B:HIS63 4.9 36.1 1.0
CA A:ASP74 5.0 34.5 1.0
CG1 B:ILE67 5.0 26.5 1.0
O A:ASP74 5.0 37.6 1.0

Zinc binding site 5 out of 10 in 6dhy

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Zinc binding site 5 out of 10 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn205

b:27.8
occ:1.00
 OD2 C:ASP12 1.8 25.9 1.0
OE1 C:GLU8 1.8 30.4 1.0
CG C:ASP12 2.5 27.4 1.0
OD1 C:ASP12 2.6 27.3 1.0
CD C:GLU8 3.0 30.8 1.0
OE2 C:GLU8 3.8 31.2 1.0
CB C:ASP12 3.9 28.1 1.0
CG C:GLU8 4.0 30.7 1.0
CB C:GLU8 4.3 31.0 1.0
O C:GLU8 4.5 31.8 1.0
C C:GLU8 4.9 30.8 1.0
CA C:ASP12 5.0 29.2 1.0

Zinc binding site 6 out of 10 in 6dhy

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Zinc binding site 6 out of 10 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn206

b:42.9
occ:1.00
 ZN C:ZN208 2.3 44.3 1.0
OD2 C:ASP5 2.5 37.9 1.0
ZN C:ZN207 2.8 40.7 1.0
CG C:ASP5 2.9 37.1 1.0
OD1 C:ASP5 2.9 38.2 1.0
CA C:CA203 3.7 34.3 1.0
CB C:ASP5 4.1 35.4 1.0
OD2 C:ASP2 4.2 44.4 1.0
N C:ASP2 4.8 39.3 1.0
CG C:ASP2 4.9 43.7 1.0
CA C:ALA1 4.9 38.9 1.0

Zinc binding site 7 out of 10 in 6dhy

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Zinc binding site 7 out of 10 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn207

b:40.7
occ:1.00
 ZN C:ZN208 2.7 44.3 1.0
ZN C:ZN206 2.8 42.9 1.0
OD2 C:ASP5 4.3 37.9 1.0
OD1 C:ASP5 4.5 38.2 1.0
CG C:ASP5 4.8 37.1 1.0
CA C:CA203 4.9 34.3 1.0

Zinc binding site 8 out of 10 in 6dhy

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Zinc binding site 8 out of 10 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn208

b:44.3
occ:1.00
 ZN C:ZN206 2.3 42.9 1.0
OD1 C:ASP5 2.4 38.2 1.0
ZN C:ZN207 2.7 40.7 1.0
OD2 C:ASP2 3.2 44.4 1.0
CG C:ASP5 3.2 37.1 1.0
OD2 C:ASP5 3.5 37.9 1.0
CG C:ASP2 4.1 43.7 1.0
OD1 C:ASP2 4.3 45.4 1.0
CB C:ASP5 4.6 35.4 1.0

Zinc binding site 9 out of 10 in 6dhy

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Zinc binding site 9 out of 10 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:29.7
occ:1.00
 OD2 B:ASP74 2.0 29.9 1.0
NE2 A:HIS63 2.0 32.0 1.0
NE2 D:HIS77 2.1 24.6 1.0
NE2 D:HIS73 2.2 24.8 1.0
CG B:ASP74 2.7 30.1 1.0
CD2 A:HIS63 2.8 31.0 1.0
OD1 B:ASP74 2.9 30.6 1.0
CE1 D:HIS73 3.0 24.9 1.0
CE1 D:HIS77 3.0 25.1 1.0
CE1 A:HIS63 3.1 31.6 1.0
CD2 D:HIS77 3.2 25.0 1.0
CD2 D:HIS73 3.4 24.6 1.0
CG A:HIS63 4.0 30.5 1.0
CD1 A:ILE67 4.1 24.6 1.0
O B:HOH310 4.1 22.4 1.0
ND1 A:HIS63 4.1 31.3 1.0
CB B:ASP74 4.1 29.5 1.0
ND1 D:HIS77 4.1 25.2 1.0
ND1 D:HIS73 4.2 24.6 1.0
CG D:HIS77 4.3 25.6 1.0
CG D:HIS73 4.4 24.1 1.0
CA B:ASP74 4.8 28.9 1.0
CG1 A:ILE67 4.9 24.3 1.0

Zinc binding site 10 out of 10 in 6dhy

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Zinc binding site 10 out of 10 in the Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystallogrpahic Tetramer of Zn-Bound RIDC1 Variant Bearing Two Disulfide Bonded Cysteines within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn203

b:44.2
occ:1.00
 OD1 D:ASP5 2.6 58.7 1.0
OD2 D:ASP5 2.7 57.0 1.0
CG D:ASP5 2.9 57.1 1.0
OD1 D:ASP2 3.6 63.2 1.0
OD2 D:ASP2 3.7 61.7 1.0
CG D:ASP2 4.0 63.5 1.0
CB D:ASP5 4.3 57.2 1.0
N D:ASP5 4.5 58.2 1.0
CA D:ASP5 4.7 56.2 1.0

Reference:

L.A.Churchfield, R.G.Alberstein, L.M.Williamson, F.A.Tezcan. Determining the Structural and Energetic Basis of Allostery in A De Novo Designed Metalloprotein Assembly. J. Am. Chem. Soc. V. 140 10043 2018.
ISSN: ESSN 1520-5126
PubMed: 29996654
DOI: 10.1021/JACS.8B05812
Page generated: Mon Oct 28 19:31:55 2024

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