Zinc in PDB 2kmk: Gfi-1 Zinc Fingers 3-5 Complexed with Dna

The binding sites of Zinc atom in the Gfi-1 Zinc Fingers 3-5 Complexed with Dna (pdb code 2kmk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Gfi-1 Zinc Fingers 3-5 Complexed with Dna, PDB code: 2kmk:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Gfi-1 Zinc Fingers 3-5 Complexed with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Gfi-1 Zinc Fingers 3-5 Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn83 b:1.0 occ:1.00 NE2 A:HIS20 1.9 0.9 1.0 NE2 A:HIS24 2.0 1.1 1.0 SG A:CYS4 2.3 0.8 1.0 SG A:CYS7 2.3 1.5 1.0 H A:CYS7 2.5 1.3 1.0 CE1 A:HIS20 2.9 1.1 1.0 HB A:ILE6 2.9 1.1 1.0 CD2 A:HIS20 3.0 0.7 1.0 CD2 A:HIS24 3.0 0.9 1.0 CE1 A:HIS24 3.0 1.3 1.0 HE1 A:HIS20 3.1 1.3 1.0 HD2 A:HIS24 3.2 0.7 1.0 HD2 A:HIS20 3.2 0.5 1.0 HE1 A:HIS24 3.3 1.5 1.0 HB3 A:CYS7 3.3 1.7 1.0 CB A:CYS4 3.3 0.7 1.0 H A:GLY8 3.3 1.4 1.0 CB A:CYS7 3.4 1.7 1.0 HB3 A:CYS4 3.4 0.9 1.0 N A:CYS7 3.4 1.5 1.0 HB2 A:CYS4 3.4 0.7 1.0 CA A:CYS7 3.9 1.7 1.0 H A:ILE6 4.0 1.0 1.0 CB A:ILE6 4.0 1.3 1.0 ND1 A:HIS20 4.1 1.1 1.0 CG A:HIS20 4.1 0.8 1.0 ND1 A:HIS24 4.1 1.3 1.0 CG A:HIS24 4.1 1.0 1.0 H A:LYS9 4.1 1.6 1.0 N A:GLY8 4.2 1.6 1.0 HB2 A:CYS7 4.3 1.9 1.0 HB2 A:LYS9 4.4 1.7 1.0 C A:ILE6 4.5 1.6 1.0 HZ A:PHE11 4.5 1.1 1.0 HD22 A:LEU21 4.5 0.7 1.0 HG13 A:ILE6 4.5 1.4 1.0 HG22 A:ILE6 4.5 1.6 1.0 C A:CYS7 4.6 1.8 1.0 HE2 A:PHE11 4.6 1.3 1.0 N A:ILE6 4.6 1.2 1.0 CA A:ILE6 4.6 1.4 1.0 CA A:CYS4 4.7 0.6 1.0 CG2 A:ILE6 4.8 1.6 1.0 CG1 A:ILE6 4.8 1.3 1.0 HA A:CYS7 4.9 1.9 1.0 HG3 A:LYS9 4.9 2.0 1.0 HD2 A:LYS9 4.9 1.8 1.0 N A:LYS9 4.9 1.6 1.0 HG23 A:ILE6 4.9 1.9 1.0 HD1 A:HIS20 4.9 1.2 1.0 HA A:LEU21 5.0 0.3 1.0

Zinc binding site 2 out of 3 in the Gfi-1 Zinc Fingers 3-5 Complexed with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Gfi-1 Zinc Fingers 3-5 Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn84 b:0.6 occ:1.00 NE2 A:HIS48 1.9 0.4 1.0 NE2 A:HIS52 2.0 0.6 1.0 SG A:CYS32 2.3 0.7 1.0 SG A:CYS35 2.3 0.7 1.0 H A:CYS35 2.4 0.8 1.0 CE1 A:HIS48 2.9 0.4 1.0 CD2 A:HIS48 2.9 0.4 1.0 CD2 A:HIS52 3.0 0.6 1.0 CE1 A:HIS52 3.0 0.8 1.0 HB2 A:CYS32 3.1 0.6 1.0 HD2 A:HIS52 3.2 0.6 1.0 HE1 A:HIS48 3.2 0.5 1.0 N A:CYS35 3.2 0.9 1.0 HD2 A:HIS48 3.2 0.5 1.0 HB2 A:TYR34 3.2 0.8 1.0 HE1 A:HIS52 3.3 0.8 1.0 CB A:CYS32 3.3 0.6 1.0 CB A:CYS35 3.3 0.9 1.0 HB3 A:CYS35 3.4 0.9 1.0 CA A:CYS35 3.7 1.0 1.0 H A:LYS37 3.7 0.6 1.0 HB3 A:CYS32 3.8 0.7 1.0 H A:TYR34 3.8 0.9 1.0 HD1 A:TYR34 3.8 0.8 1.0 HB2 A:LYS37 4.0 0.6 1.0 ND1 A:HIS48 4.1 0.4 1.0 CG A:HIS48 4.1 0.3 1.0 C A:CYS35 4.1 1.0 1.0 CG A:HIS52 4.1 0.7 1.0 ND1 A:HIS52 4.1 0.8 1.0 CB A:TYR34 4.2 0.9 1.0 H A:GLY36 4.3 0.8 1.0 C A:TYR34 4.3 1.0 1.0 HB2 A:CYS35 4.3 1.0 1.0 N A:GLY36 4.4 0.9 1.0 N A:TYR34 4.5 1.0 1.0 CA A:TYR34 4.6 1.0 1.0 CA A:CYS32 4.6 0.8 1.0 N A:LYS37 4.6 0.7 1.0 HA A:CYS35 4.7 1.1 1.0 HA A:CYS32 4.7 0.8 1.0 O A:CYS35 4.7 1.1 1.0 CD1 A:TYR34 4.7 0.9 1.0 HE1 A:PHE39 4.8 0.5 1.0 HB3 A:TYR34 4.9 0.9 1.0 HD2 A:LYS37 4.9 0.8 1.0 HD11 A:ILE51 4.9 0.8 1.0 HD1 A:HIS48 5.0 0.4 1.0 CB A:LYS37 5.0 0.5 1.0

Zinc binding site 3 out of 3 in the Gfi-1 Zinc Fingers 3-5 Complexed with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Gfi-1 Zinc Fingers 3-5 Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn85 b:0.7 occ:1.00 NE2 A:HIS76 2.0 0.7 1.0 NE2 A:HIS80 2.0 0.8 1.0 SG A:CYS63 2.3 0.9 1.0 SG A:CYS60 2.3 0.6 1.0 H A:CYS63 2.6 0.8 1.0 HB A:VAL62 2.8 0.7 1.0 CE1 A:HIS76 2.9 0.8 1.0 CD2 A:HIS76 3.0 0.6 1.0 CD2 A:HIS80 3.0 0.7 1.0 CE1 A:HIS80 3.0 0.9 1.0 HE1 A:HIS76 3.2 0.9 1.0 HD2 A:HIS80 3.2 0.6 1.0 HE1 A:HIS80 3.2 1.0 1.0 HD2 A:HIS76 3.2 0.5 1.0 HB3 A:CYS63 3.3 1.1 1.0 CB A:CYS63 3.3 1.1 1.0 N A:CYS63 3.4 0.9 1.0 CB A:CYS60 3.4 0.5 1.0 HB3 A:CYS60 3.5 0.6 1.0 HB2 A:CYS60 3.5 0.5 1.0 HB3 A:LYS65 3.8 0.9 1.0 CA A:CYS63 3.9 1.0 1.0 H A:LYS65 3.9 0.9 1.0 CB A:VAL62 3.9 0.7 1.0 ND1 A:HIS76 4.1 0.8 1.0 CG A:HIS76 4.1 0.7 1.0 ND1 A:HIS80 4.1 0.9 1.0 HB2 A:LYS65 4.1 0.9 1.0 CG A:HIS80 4.1 0.7 1.0 H A:VAL62 4.2 0.6 1.0 HG11 A:VAL62 4.2 0.9 1.0 HE2 A:PHE67 4.3 0.7 1.0 HB2 A:CYS63 4.3 1.2 1.0 C A:VAL62 4.3 0.9 1.0 C A:CYS63 4.4 1.0 1.0 CB A:LYS65 4.4 0.9 1.0 CA A:VAL62 4.6 0.7 1.0 CG1 A:VAL62 4.6 0.8 1.0 HG21 A:VAL62 4.7 0.6 1.0 N A:LYS65 4.7 0.9 1.0 HG23 A:VAL62 4.7 0.7 1.0 CG2 A:VAL62 4.7 0.6 1.0 N A:VAL62 4.8 0.7 1.0 H A:GLY64 4.8 0.9 1.0 CA A:CYS60 4.8 0.4 1.0 HZ A:PHE67 4.8 1.0 1.0 HD2 A:LYS65 4.8 1.8 1.0 N A:GLY64 4.9 0.9 1.0 HA A:CYS63 4.9 1.1 1.0 O A:CYS63 5.0 1.1 1.0 HG12 A:VAL62 5.0 0.9 1.0 HD1 A:HIS76 5.0 0.9 1.0 O A:CYS60 5.0 0.7 1.0

S.Lee, K.Doddapaneni, A.Hogue, L.Mcghee, S.Meyers, Z.Wu. Solution Structure of Gfi-1 Zinc Domain Bound to Consensus Dna. J.Mol.Biol. V. 397 1055 2010.
ISSN: ISSN 0022-2836
PubMed: 20153336
DOI: 10.1016/J.JMB.2010.02.006