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Zinc in PDB 5mcv: New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-LWC1)

Protein crystallography data

The structure of New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-LWC1), PDB code: 5mcv was solved by D.Golovenko, H.Rozenberg, Z.Shakked, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.48 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 138.078, 49.533, 68.047, 90.00, 92.91, 90.00
R / Rfree (%) 15.4 / 18.8

Zinc Binding Sites:

The binding sites of Zinc atom in the New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-LWC1) (pdb code 5mcv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-LWC1), PDB code: 5mcv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5mcv

Go back to Zinc Binding Sites List in 5mcv
Zinc binding site 1 out of 2 in the New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-LWC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-LWC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:12.6
occ:1.00
ND1 A:HIS179 2.1 13.8 1.0
SG A:CYS176 2.3 12.6 1.0
SG A:CYS238 2.3 13.0 1.0
SG A:CYS242 2.4 12.5 1.0
HB2 A:HIS179 2.9 16.6 1.0
CE1 A:HIS179 3.0 11.8 1.0
CG A:HIS179 3.1 13.1 1.0
CB A:CYS242 3.1 11.6 1.0
HE1 A:HIS179 3.2 14.2 1.0
CB A:CYS238 3.3 7.5 1.0
CB A:CYS176 3.4 13.1 1.0
CB A:HIS179 3.5 13.9 1.0
H A:HIS179 3.7 16.5 1.0
CA A:CYS238 3.9 9.7 1.0
H A:ASN239 4.0 14.0 1.0
N A:CYS176 4.0 10.9 1.0
HB3 A:HIS179 4.1 16.6 1.0
NE2 A:HIS179 4.1 17.7 1.0
CD2 A:HIS179 4.2 15.0 1.0
CA A:CYS176 4.3 13.3 1.0
N A:HIS179 4.4 13.8 1.0
N A:ASN239 4.5 11.7 1.0
CA A:HIS179 4.6 13.3 1.0
CA A:CYS242 4.6 11.4 1.0
O A:MET237 4.6 10.8 1.0
HD2 A:HIS178 4.6 24.3 1.0
HB3 A:HIS178 4.7 17.0 1.0
O A:HOH499 4.7 12.3 1.0
C A:CYS238 4.8 10.6 1.0
HE A:ARG175 4.8 21.2 1.0
O A:CYS176 4.9 15.1 1.0
HA A:ARG175 4.9 14.5 1.0
HB3 A:ARG175 4.9 21.4 1.0
C A:CYS176 4.9 11.2 1.0
HE2 A:HIS179 4.9 21.3 1.0
N A:CYS238 5.0 9.2 1.0

Zinc binding site 2 out of 2 in 5mcv

Go back to Zinc Binding Sites List in 5mcv
Zinc binding site 2 out of 2 in the New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-LWC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins (Complex P53DBD-LWC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:12.6
occ:1.00
ND1 B:HIS179 2.0 15.7 1.0
SG B:CYS176 2.3 13.3 1.0
SG B:CYS238 2.3 14.0 1.0
SG B:CYS242 2.4 13.7 1.0
HB2 B:HIS179 2.9 18.3 1.0
CE1 B:HIS179 2.9 15.8 1.0
HE1 B:HIS179 3.1 19.0 1.0
CG B:HIS179 3.1 16.0 1.0
CB B:CYS242 3.2 14.2 1.0
CB B:CYS238 3.2 10.6 1.0
CB B:CYS176 3.4 14.7 1.0
CB B:HIS179 3.5 15.2 1.0
H B:HIS179 3.7 18.8 1.0
CA B:CYS238 3.8 12.2 1.0
H B:ASN239 4.0 14.4 1.0
N B:CYS176 4.0 11.6 1.0
HB3 B:HIS179 4.1 18.3 1.0
NE2 B:HIS179 4.1 19.7 1.0
CD2 B:HIS179 4.2 18.6 1.0
CA B:CYS176 4.3 13.9 1.0
N B:HIS179 4.4 15.7 1.0
N B:ASN239 4.5 12.0 1.0
HD2 B:HIS178 4.6 25.9 1.0
CA B:CYS242 4.6 12.0 1.0
CA B:HIS179 4.6 15.4 1.0
O B:MET237 4.6 12.6 1.0
O B:HOH501 4.6 11.2 1.0
HB3 B:HIS178 4.7 23.8 1.0
C B:CYS238 4.7 11.6 1.0
HE2 B:HIS179 4.9 23.7 1.0
HE B:ARG175 4.9 21.1 1.0
HA B:ARG175 4.9 14.8 1.0
HB3 B:ARG175 4.9 22.3 1.0
O B:CYS176 4.9 13.3 1.0
C B:CYS176 4.9 12.2 1.0
N B:CYS238 5.0 10.3 1.0

Reference:

D.Golovenko, B.Brauning, P.Vyas, T.E.Haran, H.Rozenberg, Z.Shakked. New Insights Into the Role of Dna Shape on Its Recognition By P53 Proteins. Structure V. 26 1237 2018.
ISSN: ISSN 1878-4186
PubMed: 30057026
DOI: 10.1016/J.STR.2018.06.006
Page generated: Wed Dec 16 06:32:46 2020

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