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Calcium in PDB 4rqw: Crystal Structure of MYC3 N-Terminal Jaz-Binding Domain [44-238] From Arabidopsis

Protein crystallography data

The structure of Crystal Structure of MYC3 N-Terminal Jaz-Binding Domain [44-238] From Arabidopsis, PDB code: 4rqw was solved by J.Ke, F.Zhang, X.E.Zhou, J.Brunzelle, M.Zhou, H.E.Xu, K.Melcher, S.Y.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.93 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.254, 76.619, 85.857, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 26.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of MYC3 N-Terminal Jaz-Binding Domain [44-238] From Arabidopsis (pdb code 4rqw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of MYC3 N-Terminal Jaz-Binding Domain [44-238] From Arabidopsis, PDB code: 4rqw:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4rqw

Go back to Calcium Binding Sites List in 4rqw
Calcium binding site 1 out of 2 in the Crystal Structure of MYC3 N-Terminal Jaz-Binding Domain [44-238] From Arabidopsis


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 MYC3 N-Terminal Jaz-Binding Domain [44-238] From Arabidopsis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:96.7
occ:1.00
OE1 A:GLN53 2.3 76.8 1.0
OD1 A:ASP94 2.4 51.6 1.0
OE1 A:GLU124 2.5 76.7 1.0
O A:HOH421 2.7 72.8 1.0
CG A:ASP94 3.4 49.4 1.0
CD A:GLN53 3.5 74.1 1.0
OD2 A:ASP94 3.5 63.0 1.0
CD A:GLU124 3.6 72.8 1.0
OE2 A:GLU124 4.1 76.8 1.0
O A:GLY95 4.2 47.6 1.0
NE2 A:GLN53 4.4 74.8 1.0
CB A:GLN53 4.5 69.9 1.0
CG A:GLN53 4.5 71.9 1.0
CG A:GLU124 4.8 67.2 1.0
CB A:ASP94 4.8 50.1 1.0
N A:GLY95 4.9 40.2 1.0

Calcium binding site 2 out of 2 in 4rqw

Go back to Calcium Binding Sites List in 4rqw
Calcium binding site 2 out of 2 in the Crystal Structure of MYC3 N-Terminal Jaz-Binding Domain [44-238] From Arabidopsis


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 MYC3 N-Terminal Jaz-Binding Domain [44-238] From Arabidopsis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:91.8
occ:1.00
OE2 B:GLU114 2.5 98.0 1.0
OD2 A:ASP146 2.9 60.9 1.0
OD1 A:ASP146 3.2 62.9 1.0
CD B:GLU114 3.4 91.1 1.0
CG A:ASP146 3.4 59.8 1.0
OE1 B:GLU114 3.5 87.2 1.0
NH2 B:ARG118 4.2 54.4 1.0
CG B:GLU114 4.8 87.8 1.0
CB A:ASP146 4.9 56.1 1.0

Reference:

F.Zhang, J.Yao, J.Ke, L.Zhang, V.Q.Lam, X.F.Xin, X.E.Zhou, J.Chen, J.Brunzelle, P.R.Griffin, M.Zhou, H.E.Xu, K.Melcher, S.Y.He. Structural Basis of Jaz Repression of Myc Transcription Factors in Jasmonate Signalling. Nature V. 525 269 2015.
ISSN: ISSN 0028-0836
PubMed: 26258305
DOI: 10.1038/NATURE14661
Page generated: Wed Jul 9 01:57:32 2025

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