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

Protein crystallography data

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

Magnesium Binding Sites:

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 6k8k

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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 6k8k

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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 6k8k

Go back to Magnesium Binding Sites List in 6k8k
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 6k8k

Go back to Magnesium Binding Sites List in 6k8k
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

Reference:

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
Page generated: Tue Oct 1 06:48:24 2024

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