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Zinc in PDB 1jk2: ZIF268 D20A Mutant Bound to the Gct Dna Site

Protein crystallography data

The structure of ZIF268 D20A Mutant Bound to the Gct Dna Site, PDB code: 1jk2 was solved by J.C.Miller, C.O.Pabo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.65
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 43.600, 56.050, 131.560, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 27.3

Zinc Binding Sites:

The binding sites of Zinc atom in the ZIF268 D20A Mutant Bound to the Gct Dna Site (pdb code 1jk2). 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 D20A Mutant Bound to the Gct Dna Site, PDB code: 1jk2:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1jk2

Go back to Zinc Binding Sites List in 1jk2
Zinc binding site 1 out of 3 in the ZIF268 D20A Mutant Bound to the Gct Dna Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of ZIF268 D20A Mutant Bound to the Gct Dna Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:40.8
occ:1.00
NE2 A:HIS129 1.9 26.1 1.0
SG A:CYS107 2.3 59.4 1.0
NE2 A:HIS125 2.5 32.9 1.0
SG A:CYS112 2.5 63.5 1.0
CD2 A:HIS129 2.8 26.6 1.0
CE1 A:HIS129 2.9 26.0 1.0
CB A:CYS112 3.0 65.0 1.0
CE1 A:HIS125 3.3 32.1 1.0
CD2 A:HIS125 3.4 32.1 1.0
CB A:CYS107 3.5 63.9 1.0
CG A:HIS129 4.0 27.0 1.0
ND1 A:HIS129 4.0 26.8 1.0
ND1 A:HIS125 4.4 31.8 1.0
CA A:CYS112 4.4 65.9 1.0
CG A:HIS125 4.5 31.8 1.0
CB A:ARG114 4.6 66.5 1.0
CB A:VAL109 4.6 62.4 1.0
CG2 A:VAL109 4.8 61.9 1.0
CA A:CYS107 4.8 65.7 1.0
C A:CYS112 4.9 65.7 1.0
CG A:ARG114 4.9 66.6 1.0

Zinc binding site 2 out of 3 in 1jk2

Go back to Zinc Binding Sites List in 1jk2
Zinc binding site 2 out of 3 in the ZIF268 D20A Mutant Bound to the Gct Dna Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of ZIF268 D20A Mutant Bound to the Gct Dna Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:22.9
occ:1.00
NE2 A:HIS153 2.1 15.8 1.0
NE2 A:HIS157 2.1 17.3 1.0
SG A:CYS140 2.2 22.6 1.0
SG A:CYS137 2.3 19.2 1.0
CE1 A:HIS153 3.1 15.6 1.0
CD2 A:HIS153 3.1 16.1 1.0
CE1 A:HIS157 3.1 17.5 1.0
CD2 A:HIS157 3.1 16.0 1.0
CB A:CYS140 3.2 23.7 1.0
CB A:CYS137 3.2 20.4 1.0
N A:CYS140 3.6 24.5 1.0
CA A:CYS140 3.9 24.2 1.0
ND1 A:HIS153 4.2 15.5 1.0
ND1 A:HIS157 4.2 17.0 1.0
CG A:HIS153 4.2 16.1 1.0
CG A:HIS157 4.2 16.4 1.0
O A:HOH413 4.6 27.4 1.0
CB A:ILE139 4.6 23.8 1.0
C A:ILE139 4.6 24.1 1.0
C A:CYS140 4.7 25.4 1.0
CA A:CYS137 4.7 21.7 1.0
N A:MET141 4.8 26.5 1.0
CB A:ARG142 4.9 22.2 1.0
CA A:ILE139 4.9 23.7 1.0

Zinc binding site 3 out of 3 in 1jk2

Go back to Zinc Binding Sites List in 1jk2
Zinc binding site 3 out of 3 in the ZIF268 D20A Mutant Bound to the Gct Dna Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of ZIF268 D20A Mutant Bound to the Gct Dna Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:18.5
occ:1.00
NE2 A:HIS185 2.0 18.1 1.0
NE2 A:HIS181 2.1 15.3 1.0
SG A:CYS168 2.3 17.2 1.0
SG A:CYS165 2.4 16.6 1.0
CE1 A:HIS185 3.0 18.9 1.0
CD2 A:HIS185 3.0 17.4 1.0
CD2 A:HIS181 3.0 14.9 1.0
CE1 A:HIS181 3.1 14.7 1.0
CB A:CYS165 3.1 14.9 1.0
CB A:CYS168 3.3 15.9 1.0
N A:CYS168 3.6 17.1 1.0
CA A:CYS168 4.0 17.2 1.0
ND1 A:HIS185 4.1 17.9 1.0
CG A:HIS185 4.1 19.4 1.0
ND1 A:HIS181 4.2 14.7 1.0
CG A:HIS181 4.2 15.2 1.0
C A:ILE167 4.6 17.6 1.0
CA A:CYS165 4.6 15.1 1.0
C A:CYS168 4.7 16.7 1.0
CB A:ILE167 4.7 18.7 1.0
CB A:ARG170 4.7 18.8 1.0
N A:GLY169 4.7 17.3 1.0
N A:ARG170 4.9 18.2 1.0
CA A:ILE167 4.9 18.0 1.0
N A:ILE167 5.0 17.5 1.0

Reference:

J.C.Miller, C.O.Pabo. Rearrangement of Side-Chains in A ZIF268 Mutant Highlights the Complexities of Zinc Finger-Dna Recognition. J.Mol.Biol. V. 313 309 2001.
ISSN: ISSN 0022-2836
PubMed: 11800559
DOI: 10.1006/JMBI.2001.4975
Page generated: Wed Dec 16 02:53:54 2020

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