Atomistry » Zinc » PDB 12ca-1add » 1a1k
Atomistry »
  Zinc »
    PDB 12ca-1add »
      1a1k »

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: Sat Oct 12 21:44:08 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy