Calcium in PDB 5mey: Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site.

Protein crystallography data

The structure of Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site., PDB code: 5mey was solved by Z.Kaczmarska, R.Freier, J.A.Marquez, M.J.Macias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.70 / 2.05
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 64.170, 79.000, 90.100, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 23.8

Other elements in 5mey:

The structure of Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site. also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site. (pdb code 5mey). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site., PDB code: 5mey:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5mey

Go back to Calcium Binding Sites List in 5mey
Calcium binding site 1 out of 5 in the Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca102

b:0.7
occ:1.00
N3 D:DG6 2.5 37.2 1.0
C2 D:DG6 3.3 35.7 1.0
C1' D:DG6 3.3 47.5 1.0
N2 D:DG6 3.3 35.1 1.0
O4' D:DG7 3.4 43.6 1.0
C4 D:DG6 3.5 39.5 1.0
O4' D:DG6 3.7 50.4 1.0
N9 D:DG6 3.8 43.0 1.0
N2 D:DG5 4.0 45.0 1.0
O D:HOH218 4.0 63.2 1.0
N9 D:DG7 4.2 35.6 1.0
O3' D:DG6 4.2 52.4 1.0
C5' D:DG7 4.2 46.7 1.0
C8 D:DG7 4.2 33.8 1.0
C4' D:DG7 4.3 44.8 1.0
C4' D:DG6 4.3 52.2 1.0
C1' D:DG7 4.4 40.2 1.0
C2' D:DG6 4.5 49.1 1.0
C4 D:DG7 4.6 33.2 1.0
N1 D:DG6 4.6 36.3 1.0
C3' D:DG6 4.7 51.3 1.0
N7 D:DG7 4.7 33.6 1.0
C2 D:DG5 4.7 45.0 1.0
C5 D:DG6 4.8 39.1 1.0
N3 D:DG5 4.8 46.7 1.0
C5 D:DG7 4.8 32.9 1.0
O5' D:DG7 5.0 49.5 1.0

Calcium binding site 2 out of 5 in 5mey

Go back to Calcium Binding Sites List in 5mey
Calcium binding site 2 out of 5 in the Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca103

b:98.0
occ:1.00
O2 D:DC14 2.3 52.0 1.0
O4' D:DG15 3.2 59.0 1.0
C1' D:DC14 3.4 57.1 1.0
C2 D:DC14 3.4 52.3 1.0
O4' D:DC14 3.6 58.7 1.0
N1 D:DC14 3.9 54.0 1.0
N9 D:DG15 3.9 51.3 1.0
C1' D:DG15 4.0 56.5 1.0
C4 D:DG15 4.0 48.0 1.0
C4' D:DG15 4.2 60.1 1.0
N3 D:DG15 4.3 46.0 1.0
C4' D:DC14 4.3 59.4 1.0
O3' D:DC14 4.4 61.8 1.0
C8 D:DG15 4.4 49.9 1.0
C5 D:DG15 4.6 47.4 1.0
CA D:CA104 4.6 0.5 1.0
C2' D:DC14 4.6 58.4 1.0
N3 D:DC14 4.6 51.6 1.0
C5' D:DG15 4.7 60.8 1.0
C3' D:DC14 4.7 59.9 1.0
N7 D:DG15 4.8 48.6 1.0
O2 D:DC13 4.9 47.1 1.0
C2 D:DG15 4.9 44.9 1.0

Calcium binding site 3 out of 5 in 5mey

Go back to Calcium Binding Sites List in 5mey
Calcium binding site 3 out of 5 in the Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca104

b:0.5
occ:1.00
N3 D:DG15 2.5 46.0 1.0
O4' D:DC16 3.1 59.7 1.0
C2 D:DG15 3.3 44.9 1.0
N2 D:DG15 3.3 45.0 1.0
C1' D:DG15 3.4 56.5 1.0
C4 D:DG15 3.5 48.0 1.0
C4' D:DC16 3.7 61.0 1.0
C1' D:DC16 3.8 57.5 1.0
N9 D:DG15 3.8 51.3 1.0
O4' D:DG15 4.1 59.0 1.0
C5' D:DC16 4.2 62.4 1.0
N1 D:DC16 4.3 53.3 1.0
C2' D:DG15 4.4 58.7 1.0
CA D:CA103 4.6 98.0 1.0
N1 D:DG15 4.6 45.1 1.0
C2 D:DC16 4.7 51.8 1.0
O3' D:DG15 4.8 63.0 1.0
O2 D:DC16 4.8 51.9 1.0
C5 D:DG15 4.8 47.4 1.0
C6 D:DC16 4.8 51.6 1.0
CA D:CA105 4.9 0.6 1.0
C4' D:DG15 4.9 60.1 1.0
O5' D:DC16 5.0 63.6 1.0
C3' D:DG15 5.0 60.6 1.0

Calcium binding site 4 out of 5 in 5mey

Go back to Calcium Binding Sites List in 5mey
Calcium binding site 4 out of 5 in the Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca105

b:0.6
occ:1.00
O2 D:DC16 2.6 51.9 1.0
O4' D:DA17 3.1 56.2 1.0
C1' D:DC16 3.6 57.5 1.0
C2 D:DC16 3.7 51.8 1.0
N2 D:DG15 3.9 45.0 1.0
C4' D:DA17 4.0 57.4 1.0
C2' D:DC16 4.1 59.5 1.0
N1 D:DC16 4.1 53.3 1.0
C1' D:DA17 4.1 54.1 1.0
N9 D:DA17 4.2 49.5 1.0
C5' D:DA17 4.2 58.8 1.0
C4 D:DA17 4.5 47.1 1.0
C8 D:DA17 4.5 47.8 1.0
O4' D:DC16 4.5 59.7 1.0
C2 D:DG15 4.7 44.9 1.0
N3 D:DC16 4.8 50.7 1.0
CA D:CA104 4.9 0.5 1.0
N3 D:DA17 4.9 47.1 1.0
C4' D:DC16 4.9 61.0 1.0
O5' D:DA17 4.9 60.4 1.0
C3' D:DC16 5.0 61.2 1.0
C5 D:DA17 5.0 45.5 1.0

Calcium binding site 5 out of 5 in 5mey

Go back to Calcium Binding Sites List in 5mey
Calcium binding site 5 out of 5 in the Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of SMAD4-MH1 Bound to the Ggcgc Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca106

b:0.9
occ:1.00
N7 D:DA17 2.5 46.4 1.0
N6 D:DA17 2.8 44.5 1.0
C5 D:DA17 3.2 45.5 1.0
C5 D:DC16 3.3 50.5 1.0
C6 D:DA17 3.4 44.2 1.0
C6 D:DC16 3.5 51.6 1.0
C4 D:DC16 3.5 50.2 1.0
C8 D:DA17 3.6 47.8 1.0
O4 D:DT18 3.8 44.0 1.0
N1 D:DC16 3.8 53.3 1.0
N3 D:DC16 3.9 50.7 1.0
C2 D:DC16 4.0 51.8 1.0
N4 D:DC16 4.1 49.7 1.0
C2' D:DC16 4.4 59.5 1.0
C4 D:DT18 4.5 43.9 1.0
C4 D:DA17 4.5 47.1 1.0
N9 D:DA17 4.7 49.5 1.0
C1' D:DC16 4.7 57.5 1.0
N1 D:DA17 4.7 44.5 1.0
O2 D:DC16 4.8 51.9 1.0
C7 D:DT18 4.9 45.5 1.0
O D:HOH226 4.9 57.4 1.0

Reference:

P.Martin-Malpartida, M.Batet, Z.Kaczmarska, R.Freier, T.Gomes, E.Aragon, Y.Zou, Q.Wang, Q.Xi, L.Ruiz, A.Vea, J.A.Marquez, J.Massague, M.J.Macias. Structural Basis For Genome Wide Recognition of 5-Bp Gc Motifs By Smad Transcription Factors. Nat Commun V. 8 2070 2017.
ISSN: ESSN 2041-1723
PubMed: 29234012
DOI: 10.1038/S41467-017-02054-6
Page generated: Sat Dec 12 05:37:18 2020

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