Magnesium in PDB 6k8k: Crystal Structure of Arabidopsis Thaliana BIC2-CRY2 Complex

The structure of Crystal Structure of Arabidopsis Thaliana BIC2-CRY2 Complex, PDB code: 6k8k was solved by X.Wang, L.Ma, Z.Guan, P.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.43 / 2.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.552, 142.552, 526.434, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 22.3

The binding sites of Magnesium atom in the Crystal Structure of Arabidopsis Thaliana BIC2-CRY2 Complex (pdb code 6k8k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Arabidopsis Thaliana BIC2-CRY2 Complex, PDB code: 6k8k:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Arabidopsis Thaliana BIC2-CRY2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Arabidopsis Thaliana BIC2-CRY2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:64.2 occ:1.00 C5' A:FAD701 2.7 40.9 1.0 OG1 A:THR244 3.0 44.6 1.0 N A:ASN356 3.0 40.9 1.0 CG2 A:THR244 3.5 37.0 1.0 CB A:ASN356 3.7 32.5 1.0 CA A:HIS355 3.7 31.4 1.0 O5' A:FAD701 3.7 40.7 1.0 CG A:HIS355 3.8 39.5 1.0 CB A:THR244 3.8 40.2 1.0 CD2 A:HIS355 3.8 39.0 1.0 C4' A:FAD701 3.8 48.2 1.0 CZ2 A:TRP353 3.8 39.0 1.0 O3P A:FAD701 3.8 40.9 1.0 C A:HIS355 3.9 46.0 1.0 CA A:ASN356 4.0 38.7 1.0 ND1 A:HIS355 4.0 43.8 1.0 NE2 A:HIS355 4.0 37.9 1.0 O1P A:FAD701 4.0 32.0 1.0 CE1 A:HIS355 4.1 36.9 1.0 CH2 A:TRP353 4.1 30.9 1.0 P A:FAD701 4.1 36.6 1.0 CB A:HIS355 4.3 38.0 1.0 C3' A:FAD701 4.3 57.3 1.0 O2A A:FAD701 4.6 38.8 1.0 O A:MET354 4.6 42.7 1.0 O3' A:FAD701 4.7 51.0 1.0 PA A:FAD701 4.8 38.5 1.0 O4' A:FAD701 4.9 57.4 1.0 N A:HIS355 4.9 37.3 1.0 CE2 A:TRP353 4.9 33.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Arabidopsis Thaliana BIC2-CRY2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Arabidopsis Thaliana BIC2-CRY2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg703 b:62.2 occ:1.00 OG1 D:THR351 2.7 41.7 1.0 OE1 D:GLU347 2.8 63.1 1.0 NE F:ARG48 3.2 64.1 1.0 NH2 F:ARG48 3.2 56.6 1.0 CB D:THR351 3.2 33.7 1.0 CG D:GLU347 3.4 51.3 1.0 CG2 D:THR351 3.4 35.1 1.0 CD D:GLU347 3.5 58.5 1.0 CZ F:ARG48 3.6 59.5 1.0 O D:TRP353 3.7 37.3 1.0 CE3 D:TRP353 3.8 41.0 1.0 CD F:ARG48 4.3 63.7 1.0 CB D:TRP353 4.4 35.3 1.0 C D:TRP353 4.4 37.1 1.0 CG F:ARG48 4.5 61.7 1.0 CD2 F:LEU44 4.5 50.8 1.0 CZ3 D:TRP353 4.6 32.7 1.0 CD1 F:LEU44 4.7 54.6 1.0 O D:GLU347 4.7 44.6 1.0 OE2 D:GLU347 4.7 63.4 1.0 CA D:THR351 4.7 38.7 1.0 CD2 D:TRP353 4.7 29.8 1.0 CA D:TRP353 4.8 39.6 1.0 CG F:LEU44 4.8 50.0 1.0 NH1 F:ARG48 4.9 70.5 1.0 CB D:GLU347 4.9 40.7 1.0 N D:TRP353 5.0 29.8 1.0 CZ2 D:TRP433 5.0 35.6 1.0 CG D:TRP353 5.0 32.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Arabidopsis Thaliana BIC2-CRY2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Arabidopsis Thaliana BIC2-CRY2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg704 b:71.0 occ:1.00 O3P D:AMP702 2.3 0.8 1.0 OH D:TYR399 2.7 74.4 1.0 CE1 D:HIS408 3.3 67.9 1.0 P D:AMP702 3.4 0.3 1.0 O5' D:AMP702 3.5 1.0 1.0 NH1 D:ARG357 3.8 88.3 1.0 NH2 D:ARG357 3.9 93.0 1.0 CZ D:TYR399 4.0 61.6 1.0 O3' D:AMP702 4.0 90.3 1.0 ND1 D:HIS408 4.1 68.3 1.0 NH2 D:ARG412 4.3 79.3 1.0 O1P D:AMP702 4.3 0.5 1.0 NE2 D:HIS408 4.3 67.9 1.0 CZ D:ARG357 4.3 89.7 1.0 C3' D:AMP702 4.4 88.4 1.0 CE2 D:TYR399 4.4 58.7 1.0 O2P D:AMP702 4.4 0.3 1.0 C5' D:AMP702 4.8 94.8 1.0 CZ D:ARG412 5.0 86.3 1.0 NH1 D:ARG412 5.0 88.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Arabidopsis Thaliana BIC2-CRY2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Arabidopsis Thaliana BIC2-CRY2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg703 b:65.0 occ:1.00 N G:ASN356 2.9 40.3 1.0 OG1 G:THR244 2.9 46.4 1.0 O3' G:FAD701 3.1 51.3 1.0 O5' G:FAD701 3.5 44.7 1.0 CA G:HIS355 3.6 37.0 1.0 CG2 G:THR244 3.7 33.2 1.0 C G:HIS355 3.7 41.2 1.0 CZ2 G:TRP353 3.7 48.7 1.0 CB G:THR244 3.8 42.2 1.0 CD2 G:HIS355 3.8 35.9 1.0 CB G:ASN356 3.8 34.6 1.0 CG G:HIS355 3.8 34.3 1.0 O2P G:FAD701 3.8 47.7 1.0 CA G:ASN356 3.9 41.7 1.0 O3P G:FAD701 3.9 35.8 1.0 C3' G:FAD701 4.0 51.4 1.0 P G:FAD701 4.0 33.5 1.0 NE2 G:HIS355 4.1 37.0 1.0 CH2 G:TRP353 4.1 54.0 1.0 ND1 G:HIS355 4.1 42.1 1.0 CB G:HIS355 4.2 41.1 1.0 CE1 G:HIS355 4.3 37.2 1.0 O2A G:FAD701 4.4 35.6 1.0 O G:MET354 4.4 49.5 1.0 C5' G:FAD701 4.5 60.8 1.0 N G:HIS355 4.7 39.5 1.0 PA G:FAD701 4.8 40.9 1.0 CE2 G:TRP353 4.8 45.6 1.0 C4' G:FAD701 4.9 52.3 1.0 O G:HIS355 4.9 41.8 1.0

L.Ma, X.Wang, Z.Guan, L.Wang, Y.Wang, L.Zheng, Z.Gong, C.Shen, J.Wang, D.Zhang, Z.Liu, P.Yin. Structural Insights Into Bic Mediated Inactivation of Arabidopsis Cryptochrome 2 Nat.Struct.Mol.Biol. 2020.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-020-0410-Z