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Zinc in PDB 1llm: Crystal Structure of A ZIF23-GCN4 Chimera Bound to Dna

Protein crystallography data

The structure of Crystal Structure of A ZIF23-GCN4 Chimera Bound to Dna, PDB code: 1llm was solved by S.A.Wolfe, R.A.Grant, C.O.Pabo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.50
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 87.398, 87.398, 118.693, 90.00, 90.00, 120.00
R / Rfree (%) 21.6 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A ZIF23-GCN4 Chimera Bound to Dna (pdb code 1llm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A ZIF23-GCN4 Chimera Bound to Dna, PDB code: 1llm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1llm

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Zinc binding site 1 out of 4 in the Crystal Structure of A ZIF23-GCN4 Chimera Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A ZIF23-GCN4 Chimera Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:20.1
occ:1.00
 NE2 C:HIS126 2.0 17.7 1.0
NE2 C:HIS122 2.1 14.9 1.0
SG C:CYS109 2.3 16.2 1.0
SG C:CYS106 2.3 15.1 1.0
CD2 C:HIS126 3.0 16.3 1.0
CD2 C:HIS122 3.0 14.4 1.0
CE1 C:HIS126 3.0 17.8 1.0
CE1 C:HIS122 3.1 13.9 1.0
CB C:CYS106 3.1 13.8 1.0
CB C:CYS109 3.4 16.4 1.0
N C:CYS109 3.6 17.3 1.0
CA C:CYS109 4.1 17.1 1.0
ND1 C:HIS126 4.1 18.7 1.0
CG C:HIS126 4.2 18.3 1.0
O C:HOH1143 4.2 31.1 1.0
ND1 C:HIS122 4.2 14.7 1.0
CG C:HIS122 4.2 14.9 1.0
CB C:ILE108 4.3 18.4 1.0
CA C:CYS106 4.6 15.2 1.0
C C:ILE108 4.7 17.5 1.0
C C:CYS109 4.8 16.9 1.0
N C:MET110 4.8 16.7 1.0
N C:ILE108 4.9 17.5 1.0
CA C:ILE108 4.9 17.8 1.0
C C:CYS106 4.9 15.5 1.0
CB C:ARG111 5.0 14.7 1.0
CG2 C:ILE108 5.0 17.1 1.0
O C:HOH1201 5.0 30.6 1.0

Zinc binding site 2 out of 4 in 1llm

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Zinc binding site 2 out of 4 in the Crystal Structure of A ZIF23-GCN4 Chimera Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A ZIF23-GCN4 Chimera Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:21.3
occ:1.00
 NE2 C:HIS155 2.1 15.7 1.0
NE2 C:HIS150 2.2 16.0 1.0
SG C:CYS137 2.2 19.6 1.0
SG C:CYS134 2.4 17.5 1.0
CD2 C:HIS155 3.0 15.1 1.0
CD2 C:HIS150 3.0 14.9 1.0
CE1 C:HIS155 3.1 15.7 1.0
CB C:CYS134 3.2 18.7 1.0
CE1 C:HIS150 3.2 14.6 1.0
CB C:CYS137 3.2 19.9 1.0
N C:CYS137 3.7 20.4 1.0
CA C:CYS137 4.0 19.6 1.0
CG C:HIS155 4.2 14.0 1.0
CG C:HIS150 4.2 14.6 1.0
ND1 C:HIS155 4.2 15.3 1.0
O C:HOH1265 4.3 33.7 1.0
ND1 C:HIS150 4.3 14.7 1.0
CA C:CYS134 4.6 19.0 1.0
C C:CYS137 4.6 20.2 1.0
C C:ILE136 4.7 20.9 1.0
N C:GLY138 4.7 20.6 1.0
CB C:ARG139 4.7 18.5 1.0
O C:HOH1285 4.7 37.2 1.0
CB C:ILE136 4.8 20.2 1.0
N C:ARG139 4.8 20.0 1.0

Zinc binding site 3 out of 4 in 1llm

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Zinc binding site 3 out of 4 in the Crystal Structure of A ZIF23-GCN4 Chimera Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A ZIF23-GCN4 Chimera Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn303

b:18.3
occ:1.00
 NE2 D:HIS226 2.0 16.3 1.0
NE2 D:HIS222 2.1 17.6 1.0
SG D:CYS209 2.3 16.4 1.0
SG D:CYS206 2.3 14.5 1.0
CD2 D:HIS226 2.9 15.4 1.0
CE1 D:HIS226 3.1 15.8 1.0
CD2 D:HIS222 3.1 15.9 1.0
CE1 D:HIS222 3.1 16.1 1.0
CB D:CYS206 3.2 14.7 1.0
CB D:CYS209 3.4 16.5 1.0
N D:CYS209 3.6 16.1 1.0
CA D:CYS209 4.0 17.1 1.0
CG D:HIS226 4.1 16.8 1.0
ND1 D:HIS226 4.1 16.6 1.0
ND1 D:HIS222 4.2 15.1 1.0
CG D:HIS222 4.2 15.1 1.0
CB D:ILE208 4.4 16.4 1.0
CA D:CYS206 4.6 16.5 1.0
C D:ILE208 4.6 17.4 1.0
C D:CYS209 4.7 17.0 1.0
CG2 D:ILE208 4.8 14.3 1.0
CB D:ARG211 4.9 14.7 1.0
CA D:ILE208 4.9 17.4 1.0
N D:MET210 4.9 16.4 1.0
N D:ILE208 4.9 18.5 1.0
C D:CYS206 5.0 18.2 1.0

Zinc binding site 4 out of 4 in 1llm

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Zinc binding site 4 out of 4 in the Crystal Structure of A ZIF23-GCN4 Chimera Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A ZIF23-GCN4 Chimera Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn304

b:24.0
occ:1.00
 NE2 D:HIS255 2.1 19.3 1.0
NE2 D:HIS250 2.1 16.3 1.0
SG D:CYS234 2.3 18.9 1.0
SG D:CYS237 2.3 22.2 1.0
CD2 D:HIS255 3.0 18.4 1.0
CD2 D:HIS250 3.0 15.1 1.0
CE1 D:HIS255 3.1 18.0 1.0
CB D:CYS234 3.1 19.8 1.0
CE1 D:HIS250 3.2 15.9 1.0
CB D:CYS237 3.3 23.0 1.0
N D:CYS237 3.6 24.4 1.0
CA D:CYS237 4.0 23.0 1.0
CG D:HIS255 4.2 18.0 1.0
ND1 D:HIS255 4.2 19.0 1.0
CG D:HIS250 4.2 16.1 1.0
ND1 D:HIS250 4.3 15.5 1.0
O D:HOH1224 4.3 48.8 1.0
CB D:ILE236 4.6 23.6 1.0
CA D:CYS234 4.6 20.4 1.0
C D:ILE236 4.6 25.4 1.0
C D:CYS237 4.7 23.2 1.0
N D:GLY238 4.7 22.5 1.0
CB D:ARG239 4.9 21.5 1.0
CA D:ILE236 4.9 24.5 1.0
N D:ILE236 4.9 23.7 1.0
N D:ARG239 5.0 21.2 1.0
CG2 D:ILE236 5.0 23.9 1.0
C D:CYS234 5.0 21.1 1.0

Reference:

S.A.Wolfe, R.A.Grant, C.O.Pabo. Structure of A Designed Dimeric Zinc Finger Protein Bound to Dna. Biochemistry V. 42 13401 2003.
ISSN: ISSN 0006-2960
PubMed: 14621985
DOI: 10.1021/BI034830B
Page generated: Sun Oct 13 05:06:36 2024

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