Calcium in PDB 7xk4: Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 2

Enzymatic activity of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 2

All present enzymatic activity of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 2:
7.2.1.1;

Other elements in 7xk4:

The structure of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 2 also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 2 (pdb code 7xk4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 2, PDB code: 7xk4:

Calcium binding site 1 out of 1 in 7xk4

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Calcium Binding Sites List in 7xk4

Calcium binding site 1 out of 1 in the Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 2

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Na+-Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae, State 2 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
E:Ca201 b:79.0 occ:1.00	CE1	E:TYR142	2.4	41.8	1.0
	CD1	E:TYR142	2.5	41.8	1.0
	NH1	E:ARG132	2.6	48.5	1.0
	OG	E:SER11	2.9	35.4	1.0
	CZ	E:TYR142	3.6	41.8	1.0
	OH	E:TYR134	3.7	53.7	1.0
	OE2	E:GLU15	3.7	38.7	1.0
	CG	E:TYR142	3.8	41.8	1.0
	CZ	E:ARG132	3.9	48.5	1.0
	CB	E:SER11	4.1	35.4	1.0
	OH	E:TYR142	4.3	41.8	1.0
	CD1	E:LEU7	4.4	44.8	1.0
	CA	E:SER11	4.5	35.4	1.0
	CB	E:TYR142	4.6	41.8	1.0
	NH2	E:ARG132	4.6	48.5	1.0
	CE2	E:TYR142	4.6	41.8	1.0
	CZ	E:TYR134	4.6	53.7	1.0
	CE2	E:TYR134	4.6	53.7	1.0
	CD2	E:TYR142	4.6	41.8	1.0
	OG	E:SER146	4.7	30.1	1.0
	NE	E:ARG132	4.8	48.5	1.0
	CD	E:ARG132	4.8	48.5	1.0
	CD	E:GLU15	4.9	38.7	1.0
	CD	E:LYS10	5.0	38.8	1.0
	N	E:SER11	5.0	35.4	1.0

Reference:

J.I.Kishikawa, M.Ishikawa, T.Masuya, M.Murai, Y.Kitazumi, N.L.Butler, T.Kato, B.Barquera, H.Miyoshi. Cryo-Em Structures of Na + -Pumping Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae. Nat Commun V. 13 4082 2022.
ISSN: ESSN 2041-1723
PubMed: 35882843
DOI: 10.1038/S41467-022-31718-1

Page generated: Thu Jul 10 02:27:26 2025

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