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Zinc in PDB 1ozj: Crystal Structure of SMAD3-MH1 Bound to Dna at 2.4 A Resolution

Protein crystallography data

The structure of Crystal Structure of SMAD3-MH1 Bound to Dna at 2.4 A Resolution, PDB code: 1ozj was solved by J.Chai, J.-W.Wu, N.Yan, J.Massague, N.P.Pavletich, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.600, 60.400, 71.600, 90.00, 102.00, 90.00
R / Rfree (%) 21 / 27

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of SMAD3-MH1 Bound to Dna at 2.4 A Resolution (pdb code 1ozj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of SMAD3-MH1 Bound to Dna at 2.4 A Resolution, PDB code: 1ozj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1ozj

Go back to Zinc Binding Sites List in 1ozj
Zinc binding site 1 out of 2 in the Crystal Structure of SMAD3-MH1 Bound to Dna at 2.4 A Resolution


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 SMAD3-MH1 Bound to Dna at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn145

b:45.5
occ:1.00
ND1 A:HIS126 1.9 39.9 1.0
SG A:CYS109 2.3 35.9 1.0
SG A:CYS64 2.3 36.2 1.0
SG A:CYS121 2.5 33.0 1.0
CE1 A:HIS126 2.7 42.4 1.0
CG A:HIS126 3.0 39.8 1.0
CB A:CYS121 3.2 29.9 1.0
CB A:CYS109 3.3 48.7 1.0
CB A:HIS126 3.4 38.5 1.0
CB A:CYS64 3.5 38.6 1.0
CA A:CYS109 3.6 50.0 1.0
CA A:CYS64 3.7 40.9 1.0
NE2 A:HIS126 3.9 39.0 1.0
CD2 A:HIS126 4.0 38.9 1.0
C A:CYS109 4.3 50.9 1.0
N A:GLU110 4.4 54.1 1.0
CB A:ASN123 4.5 34.7 1.0
N A:CYS64 4.6 40.8 1.0
CA A:CYS121 4.6 31.8 1.0
C A:CYS64 4.8 36.8 1.0
N A:PHE111 4.8 52.2 1.0
N A:ILE65 4.8 32.6 1.0
N A:CYS109 4.8 54.0 1.0
CA A:HIS126 4.9 38.8 1.0

Zinc binding site 2 out of 2 in 1ozj

Go back to Zinc Binding Sites List in 1ozj
Zinc binding site 2 out of 2 in the Crystal Structure of SMAD3-MH1 Bound to Dna at 2.4 A Resolution


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 SMAD3-MH1 Bound to Dna at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn145

b:53.6
occ:1.00
ND1 B:HIS126 2.0 49.8 1.0
SG B:CYS64 2.3 49.2 1.0
SG B:CYS109 2.3 43.5 1.0
SG B:CYS121 2.4 48.3 1.0
CE1 B:HIS126 2.9 46.8 1.0
CG B:HIS126 3.1 49.8 1.0
CB B:CYS121 3.1 38.7 1.0
CB B:CYS109 3.3 59.3 1.0
CB B:CYS64 3.4 49.0 1.0
CA B:CYS109 3.5 62.2 1.0
CB B:HIS126 3.6 45.7 1.0
CA B:CYS64 3.7 51.3 1.0
NE2 B:HIS126 4.0 49.9 1.0
CD2 B:HIS126 4.2 46.1 1.0
N B:GLU110 4.2 64.7 1.0
C B:CYS109 4.3 64.0 1.0
N B:CYS64 4.6 55.3 1.0
CA B:CYS121 4.6 40.7 1.0
N B:PHE111 4.6 61.9 1.0
N B:CYS109 4.8 65.7 1.0
CB B:ASN123 4.8 43.7 1.0
C B:CYS64 4.9 49.4 1.0
N B:ILE65 4.9 46.3 1.0

Reference:

J.Chai, J.-W.Wu, N.Yan, J.Massague, N.P.Pavletich, Y.Shi. Features of A SMAD3 MH1-Dna Complex. Roles of Water and Zinc in Dna Binding. J.Biol.Chem. V. 278 20327 2003.
ISSN: ISSN 0021-9258
PubMed: 12686552
DOI: 10.1074/JBC.C300134200
Page generated: Mon Jan 25 16:11:14 2021

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