Calcium in PDB 9ud5: Cryo-Em Structure of Na+-Translocating Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A

Enzymatic activity of Cryo-Em Structure of Na+-Translocating Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A

All present enzymatic activity of Cryo-Em Structure of Na+-Translocating Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A:
7.2.1.1;

Other elements in 9ud5:

The structure of Cryo-Em Structure of Na+-Translocating Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A 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+-Translocating Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A (pdb code 9ud5). 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+-Translocating Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A, PDB code: 9ud5:

Calcium binding site 1 out of 1 in 9ud5

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Calcium Binding Sites List in 9ud5

Calcium binding site 1 out of 1 in the Cryo-Em Structure of Na+-Translocating Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A

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+-Translocating Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Ca301 b:152.2 occ:1.00	NE2	C:GLN93	3.3	132.1	1.0
	N	C:ALA119	3.6	137.1	1.0
	NE2	C:HIS141	3.7	119.1	1.0
	CB	C:ALA97	3.8	145.6	1.0
	CG	C:GLN93	4.0	134.3	1.0
	CH2	C:TRP238	4.1	113.2	1.0
	CD	C:GLN93	4.1	134.4	1.0
	CA	C:ARG118	4.1	136.5	1.0
	CB	C:ALA119	4.2	132.3	1.0
	CG	C:ARG118	4.4	127.4	1.0
	C	C:ARG118	4.4	140.5	1.0
	CE1	C:HIS141	4.4	117.1	1.0
	O	C:ARG117	4.5	142.9	1.0
	CA	C:ALA119	4.5	136.7	1.0
	CZ2	C:TRP238	4.6	106.0	1.0
	CD2	C:HIS141	4.8	115.9	1.0
	CB	C:ARG118	4.8	133.7	1.0
	O	C:GLN93	4.9	146.5	1.0
	CA	C:ALA97	5.0	150.1	1.0

Reference:

M.Ishikawa-Fukuda, T.Seki, J.I.Kishikawa, M.Takahiro, K.I.Okazaki, T.Kato, B.Barquera, H.Miyoshi, M.Murai. The Na + -Pumping Mechanism Driven By Redox Reactions in the Nadh-Quinone Oxidoreductase From Vibrio Cholerae Relies on Dynamic Conformational Changes. Biorxiv 2025.
ISSN: ISSN 2692-8205
PubMed: 40501732
DOI: 10.1101/2025.06.01.656757

Page generated: Thu Jul 10 10:27:23 2025

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