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Zinc in PDB 4r2d: EGR1/ZIF268 Zinc Fingers in Complex with Formylated Dna

Protein crystallography data

The structure of EGR1/ZIF268 Zinc Fingers in Complex with Formylated Dna, PDB code: 4r2d was solved by H.Hashimoto, Y.O.Olanrewaju, Y.Zheng, G.G.Wilson, X.Zhang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.55 / 2.09
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 43.948, 55.912, 127.921, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.9

Zinc Binding Sites:

The binding sites of Zinc atom in the EGR1/ZIF268 Zinc Fingers in Complex with Formylated Dna (pdb code 4r2d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the EGR1/ZIF268 Zinc Fingers in Complex with Formylated Dna, PDB code: 4r2d:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4r2d

Go back to Zinc Binding Sites List in 4r2d
Zinc binding site 1 out of 3 in the EGR1/ZIF268 Zinc Fingers in Complex with Formylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of EGR1/ZIF268 Zinc Fingers in Complex with Formylated Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:38.5
occ:1.00
NE2 A:HIS362 2.0 36.5 1.0
NE2 A:HIS358 2.0 42.7 1.0
SG A:CYS340 2.3 37.1 1.0
SG A:CYS345 2.3 46.1 1.0
CB A:CYS345 2.9 48.1 1.0
CD2 A:HIS362 2.9 38.7 1.0
CD2 A:HIS358 3.0 36.6 1.0
CE1 A:HIS358 3.0 48.9 1.0
CE1 A:HIS362 3.1 47.6 1.0
CB A:CYS340 3.2 44.2 1.0
CG A:HIS358 4.1 42.5 1.0
ND1 A:HIS358 4.1 41.2 1.0
CG A:HIS362 4.1 34.4 1.0
ND1 A:HIS362 4.1 40.7 1.0
CA A:CYS345 4.4 56.6 1.0
CB A:VAL342 4.5 46.1 1.0
CA A:CYS340 4.7 46.3 1.0
CG2 A:VAL342 4.7 50.7 1.0
C A:CYS345 5.0 51.8 1.0

Zinc binding site 2 out of 3 in 4r2d

Go back to Zinc Binding Sites List in 4r2d
Zinc binding site 2 out of 3 in the EGR1/ZIF268 Zinc Fingers in Complex with Formylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of EGR1/ZIF268 Zinc Fingers in Complex with Formylated Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:25.3
occ:1.00
NE2 A:HIS386 2.0 28.0 1.0
NE2 A:HIS390 2.0 23.7 1.0
SG A:CYS373 2.3 28.4 1.0
SG A:CYS370 2.3 23.4 1.0
CD2 A:HIS390 2.9 22.9 1.0
CE1 A:HIS386 3.0 32.8 1.0
CD2 A:HIS386 3.0 25.3 1.0
CE1 A:HIS390 3.1 34.4 1.0
CB A:CYS370 3.2 24.3 1.0
CB A:CYS373 3.3 23.4 1.0
N A:CYS373 3.7 25.7 1.0
O A:HOH637 3.9 43.9 1.0
CA A:CYS373 4.0 30.1 1.0
CG A:HIS390 4.0 22.8 1.0
ND1 A:HIS386 4.1 21.3 1.0
CG A:HIS386 4.1 22.5 1.0
ND1 A:HIS390 4.1 25.3 1.0
CB A:ILE372 4.5 23.5 1.0
CA A:CYS370 4.6 30.2 1.0
C A:CYS373 4.7 37.2 1.0
C A:ILE372 4.7 30.4 1.0
N A:MET374 4.9 32.4 1.0
CB A:ARG375 5.0 27.4 1.0
CA A:ILE372 5.0 34.3 1.0

Zinc binding site 3 out of 3 in 4r2d

Go back to Zinc Binding Sites List in 4r2d
Zinc binding site 3 out of 3 in the EGR1/ZIF268 Zinc Fingers in Complex with Formylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of EGR1/ZIF268 Zinc Fingers in Complex with Formylated Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:19.6
occ:1.00
NE2 A:HIS418 2.0 21.5 1.0
NE2 A:HIS414 2.0 17.9 1.0
SG A:CYS401 2.3 20.5 1.0
SG A:CYS398 2.3 19.6 1.0
CE1 A:HIS418 3.0 26.7 1.0
CD2 A:HIS414 3.0 23.2 1.0
CE1 A:HIS414 3.0 22.6 1.0
CD2 A:HIS418 3.1 20.2 1.0
CB A:CYS398 3.2 26.3 1.0
CB A:CYS401 3.3 20.3 1.0
N A:CYS401 3.6 26.2 1.0
CA A:CYS401 4.0 18.8 1.0
ND1 A:HIS418 4.1 26.6 1.0
CG A:HIS414 4.1 19.5 1.0
ND1 A:HIS414 4.1 16.8 1.0
CG A:HIS418 4.2 23.8 1.0
CB A:ILE400 4.3 18.9 1.0
C A:ILE400 4.6 25.7 1.0
CA A:CYS398 4.6 23.9 1.0
N A:GLY402 4.7 19.1 1.0
C A:CYS401 4.7 24.0 1.0
CB A:ARG403 4.8 24.1 1.0
CA A:ILE400 4.8 23.1 1.0
N A:ILE400 4.9 23.3 1.0
N A:ARG403 5.0 21.0 1.0

Reference:

H.Hashimoto, Y.O.Olanrewaju, Y.Zheng, G.G.Wilson, X.Zhang, X.Cheng. Wilms Tumor Protein Recognizes 5-Carboxylcytosine Within A Specific Dna Sequence. Genes Dev. 2014.
ISSN: ISSN 0890-9369
PubMed: 25258363
DOI: 10.1101/GAD.250746.114
Page generated: Wed Dec 16 05:44:33 2020

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