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Zinc in PDB 1a1k: Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site)

Protein crystallography data

The structure of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site), PDB code: 1a1k was solved by M.Elrod-Erickson, T.E.Benson, C.O.Pabo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 42.700, 55.500, 130.400, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site) (pdb code 1a1k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site), PDB code: 1a1k:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1a1k

Go back to Zinc Binding Sites List in 1a1k
Zinc binding site 1 out of 3 in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:43.7
occ:1.00
NE2 A:HIS129 1.9 38.6 1.0
NE2 A:HIS125 2.1 45.6 1.0
SG A:CYS107 2.3 50.7 1.0
SG A:CYS112 2.3 63.6 1.0
CE1 A:HIS129 2.8 38.0 1.0
CD2 A:HIS129 2.9 38.5 1.0
CE1 A:HIS125 3.0 45.0 1.0
CB A:CYS107 3.1 54.9 1.0
CD2 A:HIS125 3.2 45.1 1.0
CB A:CYS112 3.2 64.7 1.0
ND1 A:HIS129 3.9 37.5 1.0
CG A:HIS129 4.0 37.7 1.0
ND1 A:HIS125 4.1 44.4 1.0
CG A:HIS125 4.2 44.4 1.0
CD1 A:ILE128 4.6 39.2 1.0
CA A:CYS107 4.6 56.1 1.0
CA A:CYS112 4.6 64.9 1.0
CB A:VAL109 4.7 57.8 1.0
CB A:ARG114 4.7 66.8 1.0
CG2 A:VAL109 4.8 57.3 1.0
C A:CYS112 4.9 65.2 1.0
CG1 A:ILE128 5.0 38.3 1.0

Zinc binding site 2 out of 3 in 1a1k

Go back to Zinc Binding Sites List in 1a1k
Zinc binding site 2 out of 3 in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:26.5
occ:1.00
NE2 A:HIS153 2.0 18.1 1.0
SG A:CYS137 2.1 22.4 1.0
NE2 A:HIS157 2.1 22.1 1.0
SG A:CYS140 2.2 25.8 1.0
CD2 A:HIS157 3.0 22.4 1.0
CD2 A:HIS153 3.0 18.4 1.0
CE1 A:HIS153 3.0 17.4 1.0
CB A:CYS137 3.1 23.8 1.0
CE1 A:HIS157 3.2 22.2 1.0
CB A:CYS140 3.3 28.2 1.0
N A:CYS140 3.5 28.8 1.0
CA A:CYS140 3.9 29.1 1.0
O A:HOH363 4.0 36.0 1.0
ND1 A:HIS153 4.1 18.0 1.0
CG A:HIS153 4.1 19.0 1.0
CG A:HIS157 4.2 22.8 1.0
ND1 A:HIS157 4.2 21.5 1.0
CB A:ILE139 4.3 27.2 1.0
CA A:CYS137 4.5 25.2 1.0
C A:ILE139 4.5 28.7 1.0
C A:CYS140 4.6 30.0 1.0
N A:MET141 4.8 31.0 1.0
CA A:ILE139 4.8 27.9 1.0
N A:ILE139 4.8 28.3 1.0
C A:CYS137 4.8 26.8 1.0
O A:CYS137 4.9 26.8 1.0
CB A:ARG142 4.9 27.0 1.0
N A:ARG142 4.9 29.7 1.0
CG1 A:ILE139 4.9 26.7 1.0

Zinc binding site 3 out of 3 in 1a1k

Go back to Zinc Binding Sites List in 1a1k
Zinc binding site 3 out of 3 in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:21.8
occ:1.00
NE2 A:HIS185 1.9 19.7 1.0
SG A:CYS165 2.2 18.5 1.0
NE2 A:HIS181 2.2 18.0 1.0
SG A:CYS168 2.3 21.1 1.0
CE1 A:HIS185 2.9 20.2 1.0
CD2 A:HIS181 2.9 18.0 1.0
CD2 A:HIS185 3.0 20.1 1.0
CB A:CYS165 3.1 18.3 1.0
CE1 A:HIS181 3.3 17.4 1.0
CB A:CYS168 3.3 20.5 1.0
N A:CYS168 3.5 20.3 1.0
CA A:CYS168 3.9 20.6 1.0
ND1 A:HIS185 4.0 19.7 1.0
CG A:HIS185 4.1 21.2 1.0
CG A:HIS181 4.2 17.4 1.0
ND1 A:HIS181 4.3 16.6 1.0
CB A:ILE167 4.4 18.1 1.0
C A:ILE167 4.5 19.9 1.0
O A:HOH392 4.5 41.0 1.0
CA A:CYS165 4.5 19.1 1.0
C A:CYS168 4.6 20.5 1.0
N A:GLY169 4.7 20.2 1.0
CB A:ARG170 4.7 20.3 1.0
CA A:ILE167 4.7 18.7 1.0
N A:ILE167 4.7 18.6 1.0
C A:CYS165 4.9 19.7 1.0
N A:ARG170 4.9 20.1 1.0
CA A:THR182 4.9 21.4 1.0

Reference:

M.Elrod-Erickson, T.E.Benson, C.O.Pabo. High-Resolution Structures of Variant ZIF268-Dna Complexes: Implications For Understanding Zinc Finger-Dna Recognition. Structure V. 6 451 1998.
ISSN: ISSN 0969-2126
PubMed: 9562555
DOI: 10.1016/S0969-2126(98)00047-1
Page generated: Wed Dec 16 02:44:20 2020

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