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Zinc in PDB 3qsv: Structural Basis For Dna Recognition By Constitutive SMAD4 MH1 Dimers

Protein crystallography data

The structure of Structural Basis For Dna Recognition By Constitutive SMAD4 MH1 Dimers, PDB code: 3qsv was solved by N.Baburajendran, R.Jauch, C.T.Y.Zhen, P.R.Kolatkar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.89 / 2.71
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 178.357, 35.354, 139.544, 90.00, 93.83, 90.00
R / Rfree (%) 21.2 / 27.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis For Dna Recognition By Constitutive SMAD4 MH1 Dimers (pdb code 3qsv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Basis For Dna Recognition By Constitutive SMAD4 MH1 Dimers, PDB code: 3qsv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3qsv

Go back to Zinc Binding Sites List in 3qsv
Zinc binding site 1 out of 4 in the Structural Basis For Dna Recognition By Constitutive SMAD4 MH1 Dimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For Dna Recognition By Constitutive SMAD4 MH1 Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:59.0
occ:1.00
SG A:CYS115 2.2 57.1 1.0
ND1 A:HIS132 2.2 63.2 1.0
SG A:CYS71 2.3 59.2 1.0
SG A:CYS127 2.4 66.6 1.0
CB A:CYS127 3.0 39.7 1.0
CB A:CYS71 3.1 55.2 1.0
CE1 A:HIS132 3.1 52.6 1.0
CG A:HIS132 3.2 45.0 1.0
CB A:CYS115 3.5 60.3 1.0
CA A:CYS71 3.5 69.2 1.0
CB A:HIS132 3.6 36.2 1.0
CA A:CYS115 3.9 64.4 1.0
NE2 A:HIS132 4.3 52.6 1.0
CD2 A:HIS132 4.3 42.7 1.0
CA A:CYS127 4.4 54.5 1.0
N A:CYS71 4.4 70.8 1.0
N A:VAL72 4.6 56.6 1.0
N A:GLN116 4.6 71.2 1.0
C A:CYS115 4.6 77.0 1.0
C A:CYS71 4.6 59.1 1.0
N A:TYR117 4.7 61.5 1.0
CB A:ASN129 4.8 54.6 1.0

Zinc binding site 2 out of 4 in 3qsv

Go back to Zinc Binding Sites List in 3qsv
Zinc binding site 2 out of 4 in the Structural Basis For Dna Recognition By Constitutive SMAD4 MH1 Dimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For Dna Recognition By Constitutive SMAD4 MH1 Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:61.1
occ:1.00
ND1 B:HIS132 2.1 59.4 1.0
SG B:CYS115 2.2 58.4 1.0
SG B:CYS71 2.3 61.2 1.0
SG B:CYS127 2.4 65.6 1.0
CB B:CYS127 3.0 38.7 1.0
CE1 B:HIS132 3.1 49.5 1.0
CG B:HIS132 3.1 42.7 1.0
CB B:CYS71 3.2 53.5 1.0
CB B:HIS132 3.5 38.6 1.0
CB B:CYS115 3.5 66.8 1.0
CA B:CYS71 3.6 72.8 1.0
CA B:CYS115 3.9 64.5 1.0
NE2 B:HIS132 4.2 57.6 1.0
CD2 B:HIS132 4.2 44.8 1.0
CA B:CYS127 4.5 52.5 1.0
N B:CYS71 4.5 70.0 1.0
N B:VAL72 4.6 54.9 1.0
C B:CYS115 4.6 70.8 1.0
C B:CYS71 4.6 61.0 1.0
N B:GLN116 4.6 66.3 1.0
CB B:ASN129 4.8 57.2 1.0
N B:TYR117 4.8 65.2 1.0
CA B:HIS132 5.0 45.5 1.0

Zinc binding site 3 out of 4 in 3qsv

Go back to Zinc Binding Sites List in 3qsv
Zinc binding site 3 out of 4 in the Structural Basis For Dna Recognition By Constitutive SMAD4 MH1 Dimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis For Dna Recognition By Constitutive SMAD4 MH1 Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3

b:95.6
occ:1.00
ND1 C:HIS132 2.4 0.5 1.0
SG C:CYS115 2.4 0.0 1.0
SG C:CYS127 2.5 0.8 1.0
SG C:CYS71 2.5 75.8 1.0
CG C:HIS132 2.6 99.4 1.0
CB C:HIS132 2.9 87.0 1.0
CE1 C:HIS132 3.1 0.1 1.0
CB C:CYS115 3.2 0.9 1.0
CB C:CYS127 3.2 85.5 1.0
CD2 C:HIS132 3.4 0.4 1.0
NE2 C:HIS132 3.6 0.1 1.0
CB C:CYS71 3.6 93.0 1.0
CA C:CYS115 3.7 0.8 1.0
CA C:CYS71 3.8 92.4 1.0
C C:CYS115 4.4 0.9 1.0
CA C:HIS132 4.4 0.2 1.0
N C:GLN116 4.5 0.9 1.0
N C:CYS71 4.6 97.7 1.0
CA C:CYS127 4.6 97.3 1.0
CB C:ASN129 4.8 95.2 1.0
N C:VAL72 4.9 89.0 1.0
O C:ASN129 4.9 81.1 1.0
C C:CYS71 4.9 87.5 1.0
N C:TYR117 4.9 0.6 1.0
N C:CYS115 5.0 0.0 1.0

Zinc binding site 4 out of 4 in 3qsv

Go back to Zinc Binding Sites List in 3qsv
Zinc binding site 4 out of 4 in the Structural Basis For Dna Recognition By Constitutive SMAD4 MH1 Dimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis For Dna Recognition By Constitutive SMAD4 MH1 Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4

b:98.2
occ:1.00
ND1 D:HIS132 2.4 0.5 1.0
SG D:CYS115 2.4 0.4 1.0
SG D:CYS127 2.4 0.9 1.0
CG D:HIS132 2.5 99.0 1.0
SG D:CYS71 2.5 87.3 1.0
CB D:HIS132 2.9 86.4 1.0
CE1 D:HIS132 3.1 1.0 1.0
CB D:CYS127 3.2 88.9 1.0
CB D:CYS115 3.2 0.8 1.0
CD2 D:HIS132 3.3 1.0 1.0
NE2 D:HIS132 3.6 0.8 1.0
CB D:CYS71 3.7 92.1 1.0
CA D:CYS115 3.8 0.7 1.0
CA D:CYS71 3.8 90.8 1.0
CA D:HIS132 4.4 99.5 1.0
C D:CYS115 4.4 0.5 1.0
N D:GLN116 4.5 0.6 1.0
N D:CYS71 4.6 0.1 1.0
CA D:CYS127 4.6 96.4 1.0
CB D:ASN129 4.7 94.3 1.0
N D:VAL72 4.8 91.2 1.0
O D:ASN129 4.8 83.5 1.0
C D:CYS71 4.9 85.1 1.0
N D:TYR117 5.0 0.6 1.0

Reference:

N.Baburajendran, R.Jauch, C.T.Y.Zhen, P.R.Kolatkar. Structural Basis For Dna Recognition By Constitutive SMAD4 MH1 Dimers To Be Published.
Page generated: Wed Dec 16 04:45:56 2020

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