Zinc in PDB 1f2i: Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna

The structure of Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna, PDB code: 1f2i was solved by B.S.Wang, 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 / 2.35
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	86.300, 86.300, 133.000, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 25.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna (pdb code 1f2i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna, PDB code: 1f2i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Cocrystal Structure of Selected Zinc Finger Dimer 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 Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1201 b:30.5 occ:1.00 NE2 G:HIS1125 2.1 17.6 1.0 NE2 G:HIS1129 2.1 24.4 1.0 SG G:CYS1112 2.2 22.7 1.0 SG G:CYS1107 2.3 19.1 1.0 CE1 G:HIS1129 2.9 20.2 1.0 CB G:CYS1112 3.0 22.3 1.0 CD2 G:HIS1125 3.0 25.1 1.0 CE1 G:HIS1125 3.1 23.9 1.0 CB G:CYS1107 3.1 18.5 1.0 CD2 G:HIS1129 3.2 25.7 1.0 ND1 G:HIS1129 4.1 20.5 1.0 ND1 G:HIS1125 4.2 20.1 1.0 CG G:HIS1125 4.2 22.4 1.0 CG G:HIS1129 4.3 17.7 1.0 CB G:ARG1114 4.3 24.2 1.0 CG G:ARG1114 4.4 24.1 1.0 CA G:CYS1112 4.4 26.5 1.0 CA G:CYS1107 4.6 20.4 1.0 CB G:VAL1109 4.7 17.0 1.0 C G:CYS1112 4.8 28.5 1.0 N G:ARG1114 4.9 22.2 1.0 O G:CYS1112 5.0 28.6 1.0

Zinc binding site 2 out of 12 in the Cocrystal Structure of Selected Zinc Finger Dimer 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 Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1202 b:63.2 occ:1.00 NE2 G:HIS1153 2.1 44.6 1.0 SG G:CYS1140 2.1 69.2 1.0 NE2 G:HIS1157 2.1 92.3 1.0 SG G:CYS1137 2.4 60.6 1.0 CD2 G:HIS1157 3.0 92.6 1.0 CE1 G:HIS1153 3.1 48.2 1.0 CD2 G:HIS1153 3.1 48.9 1.0 CB G:CYS1140 3.1 70.8 1.0 CE1 G:HIS1157 3.2 91.4 1.0 CB G:CYS1137 3.2 60.6 1.0 N G:CYS1140 3.5 69.5 1.0 CA G:CYS1140 3.8 70.0 1.0 CG G:HIS1157 4.2 91.5 1.0 ND1 G:HIS1153 4.2 46.9 1.0 CG G:HIS1153 4.2 46.9 1.0 ND1 G:HIS1157 4.2 92.0 1.0 CB G:ILE1139 4.5 65.4 1.0 C G:CYS1140 4.5 68.7 1.0 C G:ILE1139 4.7 68.1 1.0 CA G:CYS1137 4.7 61.2 1.0 CB G:ARG1142 4.7 65.8 1.0 N G:MET1141 4.7 67.9 1.0 N G:ARG1142 4.9 65.5 1.0 CG2 G:ILE1139 4.9 63.3 1.0 O G:CYS1137 4.9 64.0 1.0

Zinc binding site 3 out of 12 in the Cocrystal Structure of Selected Zinc Finger Dimer 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 Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn2201 b:45.5 occ:1.00 NE2 H:HIS2125 2.0 37.0 1.0 NE2 H:HIS2129 2.1 43.3 1.0 SG H:CYS2112 2.2 37.9 1.0 SG H:CYS2107 2.4 38.8 1.0 CD2 H:HIS2125 3.0 29.8 1.0 CB H:CYS2112 3.0 47.4 1.0 CE1 H:HIS2129 3.0 41.8 1.0 CE1 H:HIS2125 3.0 35.8 1.0 CD2 H:HIS2129 3.1 41.9 1.0 CB H:CYS2107 3.1 33.2 1.0 ND1 H:HIS2125 4.1 32.0 1.0 CG H:HIS2125 4.1 31.2 1.0 ND1 H:HIS2129 4.1 39.6 1.0 CG H:HIS2129 4.2 40.9 1.0 CB H:VAL2109 4.5 42.2 1.0 CA H:CYS2112 4.5 51.3 1.0 CA H:CYS2107 4.5 33.5 1.0 CB H:ARG2114 4.6 47.3 1.0 CG2 H:VAL2109 4.6 42.1 1.0

Zinc binding site 4 out of 12 in the Cocrystal Structure of Selected Zinc Finger Dimer 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 Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn2202 b:34.4 occ:1.00 NE2 H:HIS2157 1.9 32.3 1.0 NE2 H:HIS2153 2.1 34.6 1.0 SG H:CYS2140 2.1 33.9 1.0 SG H:CYS2137 2.4 34.7 1.0 CE1 H:HIS2157 2.7 37.5 1.0 CE1 H:HIS2153 2.8 35.3 1.0 CD2 H:HIS2157 3.1 40.8 1.0 CD2 H:HIS2153 3.2 36.1 1.0 CB H:CYS2140 3.2 26.7 1.0 CB H:CYS2137 3.3 28.2 1.0 N H:CYS2140 3.7 29.9 1.0 ND1 H:HIS2157 3.9 41.2 1.0 ND1 H:HIS2153 4.0 34.7 1.0 CA H:CYS2140 4.0 28.9 1.0 CG H:HIS2157 4.1 41.1 1.0 CG H:HIS2153 4.2 34.4 1.0 CB H:ILE2139 4.5 32.7 1.0 C H:ILE2139 4.6 32.2 1.0 CG2 H:ILE2139 4.7 29.9 1.0 CA H:CYS2137 4.8 31.4 1.0 C H:CYS2140 4.9 30.0 1.0 CB H:ARG2142 4.9 30.7 1.0 CD1 H:ILE2154 4.9 43.9 1.0 CA H:ILE2139 5.0 33.2 1.0

Zinc binding site 5 out of 12 in the Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn3201 b:36.9 occ:1.00 NE2 I:HIS3125 2.0 22.9 1.0 NE2 I:HIS3129 2.0 41.2 1.0 SG I:CYS3112 2.3 37.5 1.0 SG I:CYS3107 2.3 42.5 1.0 CD2 I:HIS3125 2.9 24.7 1.0 CE1 I:HIS3129 3.0 44.0 1.0 CD2 I:HIS3129 3.0 44.4 1.0 CE1 I:HIS3125 3.0 23.4 1.0 CB I:CYS3112 3.0 38.9 1.0 CB I:CYS3107 3.1 26.8 1.0 ND1 I:HIS3125 4.1 23.4 1.0 CG I:HIS3125 4.1 23.1 1.0 ND1 I:HIS3129 4.1 42.8 1.0 CG I:HIS3129 4.1 41.4 1.0 CB I:ARG3114 4.2 53.4 1.0 CA I:CYS3112 4.5 43.9 1.0 CB I:VAL3109 4.6 37.2 1.0 CA I:CYS3107 4.6 32.1 1.0 CG2 I:VAL3109 4.6 32.2 1.0 CG I:ARG3114 4.7 56.4 1.0

Zinc binding site 6 out of 12 in the Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn3202 b:37.9 occ:1.00 NE2 I:HIS3157 2.1 38.9 1.0 NE2 I:HIS3153 2.1 33.0 1.0 SG I:CYS3140 2.3 35.0 1.0 SG I:CYS3137 2.4 32.2 1.0 CE1 I:HIS3153 2.9 30.6 1.0 CE1 I:HIS3157 2.9 41.8 1.0 CD2 I:HIS3157 3.2 44.3 1.0 CB I:CYS3137 3.2 30.6 1.0 CD2 I:HIS3153 3.2 38.2 1.0 CB I:CYS3140 3.3 28.1 1.0 N I:CYS3140 3.6 28.4 1.0 CA I:CYS3140 4.0 24.5 1.0 ND1 I:HIS3153 4.1 32.8 1.0 ND1 I:HIS3157 4.1 45.0 1.0 CG I:HIS3153 4.2 34.6 1.0 CG I:HIS3157 4.2 47.2 1.0 CB I:ILE3139 4.4 26.9 1.0 CA I:CYS3137 4.6 30.6 1.0 C I:CYS3140 4.6 26.7 1.0 C I:ILE3139 4.7 26.7 1.0 CB I:ARG3142 4.7 32.4 1.0 N I:MET3141 4.8 21.4 1.0 CD I:ARG3142 4.9 50.3 1.0 N I:ARG3142 4.9 22.8 1.0 CG2 I:ILE3139 4.9 24.6 1.0 CA I:ILE3139 4.9 26.9 1.0

Zinc binding site 7 out of 12 in the Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn4201 b:32.7 occ:1.00 NE2 J:HIS4125 2.1 17.2 1.0 NE2 J:HIS4129 2.1 30.0 1.0 SG J:CYS4112 2.2 27.3 1.0 SG J:CYS4107 2.3 33.5 1.0 CE1 J:HIS4129 2.7 32.2 1.0 CD2 J:HIS4125 3.0 30.1 1.0 CB J:CYS4112 3.1 29.1 1.0 CE1 J:HIS4125 3.1 27.2 1.0 CB J:CYS4107 3.2 23.8 1.0 CD2 J:HIS4129 3.3 30.3 1.0 ND1 J:HIS4129 3.9 23.6 1.0 CG J:HIS4129 4.2 28.4 1.0 CG J:HIS4125 4.2 23.9 1.0 ND1 J:HIS4125 4.2 24.7 1.0 CG2 J:VAL4109 4.3 27.1 1.0 CB J:VAL4109 4.4 33.4 1.0 CA J:CYS4112 4.5 40.2 1.0 CB J:ARG4114 4.5 23.1 1.0 CA J:CYS4107 4.6 27.4 1.0 O J:CYS4112 4.7 46.7 1.0 C J:CYS4112 4.8 43.8 1.0

Zinc binding site 8 out of 12 in the Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn4202 b:47.9 occ:1.00 NE2 J:HIS4157 2.0 40.5 1.0 NE2 J:HIS4153 2.1 39.9 1.0 SG J:CYS4140 2.2 47.7 1.0 SG J:CYS4137 2.4 51.0 1.0 CE1 J:HIS4157 2.9 42.1 1.0 CD2 J:HIS4153 3.0 39.2 1.0 CE1 J:HIS4153 3.1 40.5 1.0 CD2 J:HIS4157 3.2 43.5 1.0 CB J:CYS4137 3.4 47.7 1.0 CB J:CYS4140 3.4 46.3 1.0 N J:CYS4140 3.7 44.3 1.0 ND1 J:HIS4157 4.1 44.0 1.0 CA J:CYS4140 4.1 44.3 1.0 CG J:HIS4153 4.1 39.3 1.0 ND1 J:HIS4153 4.2 40.8 1.0 CG J:HIS4157 4.2 45.8 1.0 CB J:ILE4139 4.4 37.4 1.0 C J:ILE4139 4.7 45.2 1.0 CG2 J:ILE4139 4.8 37.7 1.0 CA J:CYS4137 4.8 49.1 1.0 CB J:ARG4142 4.8 51.1 1.0 CD J:ARG4142 4.9 63.7 1.0 C J:CYS4140 4.9 45.9 1.0 NH1 J:ARG4142 4.9 74.9 1.0 CA J:ILE4139 4.9 44.4 1.0 N J:MET4141 5.0 47.2 1.0

Zinc binding site 9 out of 12 in the Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn5201 b:35.0 occ:1.00 NE2 K:HIS5129 2.0 22.2 1.0 NE2 K:HIS5125 2.0 28.7 1.0 SG K:CYS5112 2.3 29.5 1.0 SG K:CYS5107 2.3 32.9 1.0 CE1 K:HIS5129 2.6 27.3 1.0 CE1 K:HIS5125 2.9 29.3 1.0 CB K:CYS5112 3.0 19.3 1.0 CD2 K:HIS5125 3.1 33.9 1.0 CB K:CYS5107 3.2 25.0 1.0 CD2 K:HIS5129 3.2 30.5 1.0 ND1 K:HIS5129 3.8 27.4 1.0 ND1 K:HIS5125 4.0 29.8 1.0 CG K:HIS5129 4.1 25.9 1.0 CG K:HIS5125 4.1 30.9 1.0 CB K:VAL5109 4.5 22.6 1.0 CA K:CYS5112 4.5 26.3 1.0 CB K:ARG5114 4.5 30.4 1.0 CG2 K:VAL5109 4.6 24.9 1.0 CA K:CYS5107 4.6 23.5 1.0 C K:CYS5112 4.9 27.2 1.0

Zinc binding site 10 out of 12 in the Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cocrystal Structure of Selected Zinc Finger Dimer Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn5202 b:0.0 occ:1.00 NE2 K:HIS5153 2.4 0.0 1.0 CE1 K:HIS5153 2.6 0.0 1.0 SG K:CYS5140 2.6 99.3 1.0 NE2 K:HIS5157 2.7 0.0 1.0 CB K:CYS5140 3.0 0.0 1.0 SG K:CYS5137 3.3 87.2 1.0 N K:CYS5140 3.5 0.0 1.0 CE1 K:HIS5157 3.6 99.2 1.0 CD2 K:HIS5153 3.6 98.9 1.0 CD2 K:HIS5157 3.8 0.0 1.0 ND1 K:HIS5153 3.8 0.0 1.0 CA K:CYS5140 3.8 0.0 1.0 CB K:CYS5137 3.9 97.3 1.0 CG K:HIS5153 4.3 98.5 1.0 CB K:ILE5139 4.5 98.0 1.0 C K:CYS5140 4.5 0.0 1.0 C K:ILE5139 4.7 0.0 1.0 ND1 K:HIS5157 4.7 99.6 1.0 CB K:ARG5142 4.8 99.4 1.0 CG K:HIS5157 4.9 0.0 1.0 N K:MET5141 4.9 0.0 1.0

B.S.Wang, R.A.Grant, C.O.Pabo. Selected Peptide Extension Contacts Hydrophobic Patch on Neighboring Zinc Finger and Mediates Dimerization on Dna. Nat.Struct.Biol. V. 8 589 2001.
ISSN: ISSN 1072-8368
PubMed: 11427887
DOI: 10.1038/89617