Calcium in PDB 7oui: Structure of C2S2M2-Type Photosystem Supercomplex From Arabidopsis Thaliana (Digitonin-Extracted)

Enzymatic activity of Structure of C2S2M2-Type Photosystem Supercomplex From Arabidopsis Thaliana (Digitonin-Extracted)

All present enzymatic activity of Structure of C2S2M2-Type Photosystem Supercomplex From Arabidopsis Thaliana (Digitonin-Extracted):
1.10.3.9;

Other elements in 7oui:

The structure of Structure of C2S2M2-Type Photosystem Supercomplex From Arabidopsis Thaliana (Digitonin-Extracted) also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Magnesium	(Mg)	222 atoms
Chlorine	(Cl)	2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of C2S2M2-Type Photosystem Supercomplex From Arabidopsis Thaliana (Digitonin-Extracted) (pdb code 7oui). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of C2S2M2-Type Photosystem Supercomplex From Arabidopsis Thaliana (Digitonin-Extracted), PDB code: 7oui:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7oui

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Calcium Binding Sites List in 7oui

Calcium binding site 1 out of 4 in the Structure of C2S2M2-Type Photosystem Supercomplex From Arabidopsis Thaliana (Digitonin-Extracted)

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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of C2S2M2-Type Photosystem Supercomplex From Arabidopsis Thaliana (Digitonin-Extracted) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca416 b:49.2 occ:1.00	NE2	A:GLN165	2.3	20.8	1.0
	OD1	A:ASP170	2.4	29.2	1.0
	CG	A:ASP170	2.8	29.2	1.0
	OD2	A:ASP170	2.9	29.2	1.0
	CD	A:GLN165	3.3	20.8	1.0
	CG	A:GLN165	3.5	20.8	1.0
	CB	A:GLN165	3.7	20.8	1.0
	O	A:HOH501	3.7	35.7	1.0
	CB	A:ASP170	3.9	29.2	1.0
	OH	A:TYR161	3.9	22.6	1.0
	OE2	A:GLU189	4.0	35.8	1.0
	NH1	C:ARG357	4.0	27.2	1.0
	OE1	A:GLU189	4.2	35.8	1.0
	O	A:HOH518	4.2	50.5	1.0
	OE1	A:GLN165	4.4	20.8	1.0
	CD	A:GLU189	4.5	35.8	1.0
	CZ	A:TYR161	4.5	22.6	1.0
	O	A:HOH515	4.6	45.6	1.0
	CE2	A:TYR161	4.6	22.6	1.0
	O	C:HOH613	4.7	48.2	1.0
	CA	A:GLN165	4.9	20.8	1.0
	CA	A:ASP170	4.9	29.2	1.0
	NH2	C:ARG357	5.0	27.2	1.0

Calcium binding site 2 out of 4 in 7oui

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Calcium Binding Sites List in 7oui

Calcium binding site 2 out of 4 in the Structure of C2S2M2-Type Photosystem Supercomplex From Arabidopsis Thaliana (Digitonin-Extracted)

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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of C2S2M2-Type Photosystem Supercomplex From Arabidopsis Thaliana (Digitonin-Extracted) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Ca627 b:68.2 occ:1.00	O	B:GLU266	3.9	34.5	1.0
	O	B:ILE80	4.1	40.2	1.0
	O	B:PRO50	4.2	38.8	1.0
	CB	B:PRO50	4.4	38.8	1.0
	CE	B:MET55	4.6	34.4	1.0
	OE1	B:GLU266	4.6	34.5	1.0
	CG1	B:ILE80	4.7	40.2	1.0
	C	B:GLU266	4.7	34.5	1.0
	CG	B:MET55	4.7	34.4	1.0
	CB	B:PRO54	4.8	32.4	1.0
	O	B:HOH709	4.8	39.6	1.0
	CB	B:GLU266	4.8	34.5	1.0
	CA	B:PRO50	4.8	38.8	1.0
	N	B:MET55	4.9	34.4	1.0
	CH2	B:TRP167	5.0	28.3	1.0
	C	B:PRO50	5.0	38.8	1.0

Calcium binding site 3 out of 4 in 7oui

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Calcium Binding Sites List in 7oui

Calcium binding site 3 out of 4 in the Structure of C2S2M2-Type Photosystem Supercomplex From Arabidopsis Thaliana (Digitonin-Extracted)

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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of C2S2M2-Type Photosystem Supercomplex From Arabidopsis Thaliana (Digitonin-Extracted) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
a:Ca416 b:49.5 occ:1.00	NE2	a:GLN165	2.3	21.1	1.0
	OD1	a:ASP170	2.4	29.4	1.0
	CG	a:ASP170	2.8	29.4	1.0
	OD2	a:ASP170	2.9	29.4	1.0
	CD	a:GLN165	3.3	21.1	1.0
	CG	a:GLN165	3.5	21.1	1.0
	CB	a:GLN165	3.7	21.1	1.0
	O	a:HOH501	3.7	36.0	1.0
	CB	a:ASP170	3.9	29.4	1.0
	OH	a:TYR161	3.9	22.4	1.0
	OE2	a:GLU189	4.0	36.2	1.0
	NH1	c:ARG357	4.0	26.7	1.0
	OE1	a:GLU189	4.2	36.2	1.0
	O	a:HOH518	4.2	50.5	1.0
	OE1	a:GLN165	4.4	21.1	1.0
	CD	a:GLU189	4.5	36.2	1.0
	CZ	a:TYR161	4.5	22.4	1.0
	O	a:HOH515	4.6	46.3	1.0
	CE2	a:TYR161	4.6	22.4	1.0
	O	c:HOH613	4.7	47.6	1.0
	CA	a:GLN165	4.9	21.1	1.0
	CA	a:ASP170	4.9	29.4	1.0
	NH2	c:ARG357	5.0	26.7	1.0

Calcium binding site 4 out of 4 in 7oui

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Calcium Binding Sites List in 7oui

Calcium binding site 4 out of 4 in the Structure of C2S2M2-Type Photosystem Supercomplex From Arabidopsis Thaliana (Digitonin-Extracted)

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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of C2S2M2-Type Photosystem Supercomplex From Arabidopsis Thaliana (Digitonin-Extracted) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
b:Ca627 b:68.0 occ:1.00	O	b:GLU266	3.9	34.4	1.0
	O	b:ILE80	4.1	40.7	1.0
	O	b:PRO50	4.2	38.2	1.0
	CB	b:PRO50	4.4	38.2	1.0
	CE	b:MET55	4.6	33.9	1.0
	OE1	b:GLU266	4.6	34.4	1.0
	CG1	b:ILE80	4.7	40.7	1.0
	C	b:GLU266	4.7	34.4	1.0
	CG	b:MET55	4.7	33.9	1.0
	CB	b:PRO54	4.8	32.2	1.0
	O	b:HOH709	4.8	39.5	1.0
	CB	b:GLU266	4.8	34.4	1.0
	CA	b:PRO50	4.8	38.2	1.0
	N	b:MET55	4.9	33.9	1.0
	CH2	b:TRP167	5.0	28.5	1.0
	C	b:PRO50	5.0	38.2	1.0

Reference:

A.T.Graca, M.Hall, K.Persson, W.P.Schroder. High-Resolution Model of Arabidopsis Photosystem II Reveals the Structural Consequences of Digitonin-Extraction. Sci Rep V. 11 15534 2021.
ISSN: ESSN 2045-2322
PubMed: 34330992
DOI: 10.1038/S41598-021-94914-X

Page generated: Fri Jul 19 02:40:10 2024

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