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Magnesium in PDB 4nc4: Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K

Protein crystallography data

The structure of Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K, PDB code: 4nc4 was solved by X.Yang, X.Zeng, K.-H.Zhao, Z.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.49 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.798, 79.119, 189.340, 90.00, 95.18, 90.00
R / Rfree (%) 14.9 / 18.4

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K (pdb code 4nc4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 18 binding sites of Magnesium where determined in the Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K, PDB code: 4nc4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 18 in 4nc4

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Magnesium binding site 1 out of 18 in the Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K


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 Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:43.2
occ:1.00
 O A:HOH766 2.0 41.2 1.0
O A:HOH904 2.0 35.7 1.0
O B:HOH757 2.0 50.9 1.0
O B:HOH758 2.1 46.6 1.0
O B:HOH759 2.2 32.8 1.0
O A:HOH767 3.9 54.1 1.0
O B:HOH871 4.1 35.8 1.0
O B:HOH691 4.2 22.3 1.0
O B:HOH760 4.3 39.1 1.0
O A:THR356 4.4 21.6 1.0
O B:HOH634 4.5 21.5 1.0
O B:HOH633 4.7 25.4 1.0

Magnesium binding site 2 out of 18 in 4nc4

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Magnesium binding site 2 out of 18 in the Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K


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 Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:56.8
occ:1.00
 O C:HOH878 2.0 38.4 1.0
O C:HOH917 2.2 41.2 1.0
O A:HOH910 2.3 42.1 1.0
O A:HOH878 2.4 42.2 1.0
O C:HOH688 2.4 35.4 1.0
O A:HOH911 2.6 50.3 1.0
O D:HOH803 4.0 46.4 1.0
O D:HOH515 4.1 31.1 1.0
O A:HOH918 4.2 45.9 1.0
O C:ARG200 4.3 22.9 1.0
O D:HOH521 4.3 12.5 1.0
O A:HOH908 4.4 46.9 1.0
OE1 A:GLU262 4.4 32.9 0.5
O A:HOH848 4.4 49.0 1.0
O C:HOH539 4.6 33.7 1.0
CD C:ARG209 4.7 22.6 0.5
OE2 A:GLU262 4.7 25.2 0.5
CD C:ARG209 4.8 24.7 0.5
O D:HOH861 5.0 39.4 1.0
CD A:GLU262 5.0 30.2 0.5

Magnesium binding site 3 out of 18 in 4nc4

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Magnesium binding site 3 out of 18 in the Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K


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 Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:39.9
occ:1.00
 O A:HOH712 2.2 24.0 1.0
O A:HIS49 2.2 21.0 1.0
O A:HOH710 2.3 26.6 1.0
C A:HIS49 3.4 18.9 1.0
O A:HOH760 4.0 34.0 1.0
OD1 A:ASP51 4.2 31.7 1.0
CA A:GLY50 4.2 18.7 1.0
N A:GLY50 4.3 17.6 1.0
CA A:HIS49 4.3 18.1 1.0
CB A:HIS49 4.4 18.4 1.0
O A:HOH598 4.5 20.7 1.0
N A:ASP51 4.6 25.0 1.0
C A:GLY50 4.7 24.9 1.0

Magnesium binding site 4 out of 18 in 4nc4

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Magnesium binding site 4 out of 18 in the Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K


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 Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:55.8
occ:1.00
 O A:HOH866 2.3 45.8 1.0
OD2 A:ASP156 2.3 37.1 1.0
O A:HOH629 2.4 39.9 1.0
O A:HOH681 2.5 38.7 1.0
CG A:ASP156 3.4 34.1 1.0
OD1 A:ASP156 3.7 32.8 1.0
O A:HOH779 4.0 40.8 1.0
OE1 A:GLN164 4.1 38.5 1.0
NE2 A:GLN164 4.6 35.9 1.0
CB A:LEU154 4.6 20.8 1.0
O A:LEU154 4.7 25.3 1.0
CB A:ASP156 4.7 29.4 1.0
CD A:GLN164 4.8 37.6 1.0
CD1 A:LEU154 4.9 24.1 1.0
OE2 A:GLU158 5.0 68.7 1.0

Magnesium binding site 5 out of 18 in 4nc4

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Magnesium binding site 5 out of 18 in the Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:50.8
occ:1.00
 O A:HOH548 2.2 29.9 1.0
O A:CYS231 2.3 18.7 1.0
O A:GLY283 2.6 22.3 1.0
O A:HOH549 2.7 25.9 1.0
O A:HOH723 2.8 43.6 1.0
O A:HOH670 3.2 41.5 1.0
C A:CYS231 3.5 23.8 1.0
MG A:MG406 3.5 61.0 1.0
C A:GLY283 3.7 20.4 1.0
O A:HOH618 3.9 33.0 1.0
O A:HOH550 3.9 21.9 1.0
CA A:GLY232 4.1 18.8 1.0
N A:GLY232 4.2 20.3 1.0
CA A:GLY283 4.3 17.9 1.0
N A:GLY283 4.3 16.4 1.0
O A:HOH617 4.4 40.5 1.0
O A:ALA179 4.4 17.8 1.0
O A:HOH551 4.5 26.3 1.0
O A:HOH673 4.5 32.6 1.0
CA A:CYS231 4.6 17.5 1.0
O A:HOH672 4.7 29.9 1.0
N A:CYS231 4.7 15.7 1.0
N A:GLY284 4.7 19.2 1.0
C A:GLY232 4.8 17.7 1.0
O A:HOH688 4.8 37.0 1.0
O A:HOH556 4.8 39.8 1.0
CA A:GLY284 5.0 18.3 1.0

Magnesium binding site 6 out of 18 in 4nc4

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Magnesium binding site 6 out of 18 in the Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:61.0
occ:1.00
 O A:HOH688 2.1 37.0 1.0
O A:HOH723 2.5 43.6 1.0
O A:HOH556 2.8 39.8 1.0
O A:CYS335 2.8 19.5 1.0
OG A:SER282 3.2 20.3 1.0
O A:HOH549 3.4 25.9 1.0
MG A:MG405 3.5 50.8 1.0
O A:GLY283 3.6 22.3 1.0
N A:CYS335 3.6 18.2 1.0
OG A:SER334 3.8 20.2 1.0
C A:CYS335 3.8 19.1 1.0
O A:HOH616 3.8 40.1 1.0
CA A:CYS335 4.1 16.2 1.0
O A:HOH673 4.1 32.6 1.0
O A:HOH687 4.2 31.2 1.0
CB A:CYS335 4.2 16.9 1.0
O A:HOH672 4.2 29.9 1.0
O A:ALA22 4.3 20.0 1.0
C A:SER334 4.5 17.6 1.0
CB A:SER282 4.5 19.7 1.0
C A:GLY283 4.5 20.4 1.0
N A:GLY283 4.6 16.4 1.0
CA A:SER334 4.7 19.0 1.0
O A:HOH670 4.7 41.5 1.0
O A:HOH557 4.8 35.2 1.0
CB A:SER334 4.8 17.5 1.0

Magnesium binding site 7 out of 18 in 4nc4

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Magnesium binding site 7 out of 18 in the Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:49.0
occ:1.00
 O B:HOH869 2.1 46.1 1.0
O B:HOH870 2.1 51.0 1.0
O B:HOH872 2.2 46.2 1.0
O B:HOH871 2.4 35.8 1.0
O A:HOH591 4.3 24.3 1.0
O B:HOH873 4.3 58.2 1.0
O A:HOH589 4.3 26.4 1.0
O B:THR356 4.5 22.3 1.0
O A:HOH590 4.6 28.8 1.0
O A:HOH904 4.6 35.7 1.0

Magnesium binding site 8 out of 18 in 4nc4

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Magnesium binding site 8 out of 18 in the Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:45.7
occ:1.00
 O A:HOH777 1.9 43.4 1.0
O B:HOH636 2.2 39.2 1.0
O A:HOH792 2.3 45.9 1.0
O B:HOH804 2.3 39.4 1.0
O A:HOH678 2.4 39.9 1.0
O B:HOH766 2.6 50.9 1.0
O A:HOH843 3.6 36.5 1.0
O B:HOH803 3.6 30.0 1.0
O B:HOH637 3.9 40.0 1.0
OD2 B:ASP77 4.0 30.0 1.0
O B:HOH509 4.0 41.5 1.0
O B:HOH503 4.2 37.9 1.0
O B:HOH513 4.3 28.5 1.0
CZ3 B:TRP337 4.5 23.0 1.0
O B:HOH639 4.6 37.2 1.0
CH2 B:TRP337 4.6 18.2 1.0
O B:HOH722 4.6 34.3 1.0
O A:HOH679 4.7 40.1 1.0
O B:HOH504 4.9 39.7 1.0
CG B:ASP77 5.0 28.9 1.0

Magnesium binding site 9 out of 18 in 4nc4

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Magnesium binding site 9 out of 18 in the Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:35.2
occ:1.00
 O A:HOH588 2.0 24.9 1.0
O A:HOH714 3.2 29.4 1.0
NE B:ARG41 3.3 24.1 1.0
ND2 B:ASN357 3.4 22.0 1.0
O B:HOH512 3.4 29.1 1.0
OD1 A:ASN357 3.5 24.8 1.0
ND2 A:ASN357 3.6 22.8 1.0
CD B:ARG41 3.6 26.6 1.0
CG A:ASN357 3.9 27.7 1.0
O B:HOH633 4.1 25.4 1.0
OD1 B:ASN357 4.2 23.2 1.0
CG B:ASN357 4.2 23.8 1.0
O B:HOH504 4.2 39.7 1.0
OE2 B:GLU43 4.3 27.5 1.0
CG B:ARG41 4.3 19.3 1.0
CZ B:ARG41 4.4 28.7 1.0
CD A:ARG41 4.5 25.0 1.0
O B:HOH509 4.5 41.5 1.0
O A:HOH896 4.5 27.8 1.0
NE A:ARG41 4.5 25.0 1.0
O B:HOH611 4.6 26.0 1.0
NH2 B:ARG41 4.7 22.6 1.0
O B:HOH650 4.7 32.2 1.0
CD B:GLU43 4.9 24.2 1.0
O A:HOH590 5.0 28.8 1.0

Magnesium binding site 10 out of 18 in 4nc4

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Magnesium binding site 10 out of 18 in the Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Photoreceptor ATUVR8 Mutant W285F and Light- Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:72.5
occ:1.00
 O B:HOH668 2.0 38.0 1.0
O B:HOH805 2.1 42.4 1.0
O B:HOH863 2.2 52.6 1.0
O B:HOH862 2.3 54.2 1.0
O B:HOH808 2.4 42.5 1.0
O B:HOH861 2.6 52.9 1.0
O B:HOH885 3.8 49.4 1.0
O B:HOH586 3.9 30.0 1.0
OG1 B:THR73 3.9 28.7 1.0
O B:VAL72 4.0 24.7 1.0
O B:HOH667 4.3 32.3 1.0
OG B:SER71 4.3 36.6 1.0
O B:HOH836 4.4 47.8 1.0
O B:HOH669 4.6 28.3 1.0
O B:ILE125 4.8 29.5 1.0
CG2 B:ILE19 4.9 31.4 1.0
O B:HOH714 4.9 49.3 1.0
CB B:THR73 4.9 24.4 1.0
CG2 B:THR73 5.0 20.5 1.0

Reference:

X.Zeng, Z.Ren, Q.Wu, J.Fan, P.P.Peng, K.Tang, R.Zhang, K.H.Zhao, X.Yang. Dynamic Crystallography Reveals Early Signalling Events in Ultraviolet Photoreceptor UVR8. Nat Plants V. 1 2015.
ISSN: ISSN 2055-0278
PubMed: 26097745
DOI: 10.1038/NPLANTS.2014.6
Page generated: Mon Aug 19 23:32:27 2024

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