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Zinc in PDB 1aay: ZIF268 Zinc Finger-Dna Complex

Protein crystallography data

The structure of ZIF268 Zinc Finger-Dna Complex, PDB code: 1aay was solved by M.Elrod-Erickson, M.A.Rould, C.O.Pabo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 45.400, 56.200, 130.800, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 24.2

Zinc Binding Sites:

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

Zinc binding site 1 out of 3 in 1aay

Go back to Zinc Binding Sites List in 1aay
Zinc binding site 1 out of 3 in the ZIF268 Zinc Finger-Dna Complex


Mono view


Stereo pair view

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

b:31.6
occ:1.00
NE2 A:HIS129 1.9 29.2 1.0
NE2 A:HIS125 2.1 23.1 1.0
SG A:CYS107 2.2 30.2 1.0
SG A:CYS112 2.4 41.7 1.0
CD2 A:HIS129 2.8 29.2 1.0
CE1 A:HIS125 3.0 22.6 1.0
CE1 A:HIS129 3.0 29.9 1.0
CB A:CYS107 3.1 31.5 1.0
CD2 A:HIS125 3.1 23.2 1.0
CB A:CYS112 3.2 45.6 1.0
CG A:HIS129 4.0 30.3 1.0
ND1 A:HIS129 4.1 31.4 1.0
ND1 A:HIS125 4.1 22.8 1.0
CG A:HIS125 4.2 22.4 1.0
CG A:ARG114 4.5 49.1 1.0
CA A:CYS107 4.5 31.8 1.0
CA A:CYS112 4.6 47.3 1.0
CB A:VAL109 4.7 40.4 1.0
CB A:ARG114 4.7 46.9 1.0
CD1 A:ILE128 4.8 42.8 1.0
CG2 A:VAL109 4.8 41.2 1.0
C A:CYS112 4.9 48.6 1.0

Zinc binding site 2 out of 3 in 1aay

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Zinc binding site 2 out of 3 in the ZIF268 Zinc Finger-Dna Complex


Mono view


Stereo pair view

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

b:23.9
occ:1.00
NE2 A:HIS153 2.1 19.4 1.0
NE2 A:HIS157 2.1 22.8 1.0
SG A:CYS140 2.2 26.2 1.0
SG A:CYS137 2.3 21.5 1.0
CD2 A:HIS157 2.9 21.9 1.0
CD2 A:HIS153 3.0 18.3 1.0
CE1 A:HIS153 3.1 18.1 1.0
CB A:CYS137 3.1 23.8 1.0
CE1 A:HIS157 3.2 22.0 1.0
CB A:CYS140 3.3 26.9 1.0
N A:CYS140 3.5 27.1 1.0
CA A:CYS140 3.9 26.7 1.0
CG A:HIS157 4.1 23.6 1.0
ND1 A:HIS153 4.2 17.1 1.0
ND1 A:HIS157 4.2 22.2 1.0
CG A:HIS153 4.2 18.1 1.0
CA A:CYS137 4.6 25.6 1.0
CB A:ILE139 4.6 28.2 1.0
C A:ILE139 4.6 27.6 1.0
C A:CYS140 4.7 28.2 1.0
N A:MET141 4.8 28.6 1.0
CA A:ILE139 4.9 28.6 1.0
N A:ILE139 5.0 29.8 1.0

Zinc binding site 3 out of 3 in 1aay

Go back to Zinc Binding Sites List in 1aay
Zinc binding site 3 out of 3 in the ZIF268 Zinc Finger-Dna Complex


Mono view


Stereo pair view

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

b:19.7
occ:1.00
NE2 A:HIS181 2.0 18.4 1.0
NE2 A:HIS185 2.1 22.7 1.0
SG A:CYS168 2.2 21.0 1.0
SG A:CYS165 2.3 17.5 1.0
CE1 A:HIS181 3.0 18.8 1.0
CE1 A:HIS185 3.0 22.7 1.0
CD2 A:HIS181 3.1 16.9 1.0
CB A:CYS165 3.1 17.3 1.0
CD2 A:HIS185 3.1 19.9 1.0
CB A:CYS168 3.3 20.7 1.0
N A:CYS168 3.6 20.3 1.0
CA A:CYS168 4.0 20.9 1.0
ND1 A:HIS181 4.1 18.4 1.0
ND1 A:HIS185 4.1 19.9 1.0
CG A:HIS181 4.2 17.5 1.0
CG A:HIS185 4.2 21.2 1.0
CA A:CYS165 4.6 18.6 1.0
CB A:ILE167 4.6 21.6 1.0
C A:ILE167 4.6 22.2 1.0
C A:CYS168 4.7 21.7 1.0
N A:GLY169 4.8 21.1 1.0
CB A:ARG170 4.8 26.6 1.0
CA A:ILE167 4.9 20.1 1.0
N A:ILE167 4.9 19.9 1.0
N A:ARG170 5.0 23.0 1.0
CG2 A:ILE167 5.0 23.0 1.0

Reference:

M.Elrod-Erickson, M.A.Rould, L.Nekludova, C.O.Pabo. ZIF268 Protein-Dna Complex Refined at 1.6 A: A Model System For Understanding Zinc Finger-Dna Interactions. Structure V. 4 1171 1996.
ISSN: ISSN 0969-2126
PubMed: 8939742
DOI: 10.1016/S0969-2126(96)00125-6
Page generated: Wed Dec 16 02:44:31 2020

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