Calcium in PDB 9udg: Cryo-Em Structure of Na+-Translocating Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae Reduced By Nadh, with Bound Aurachin D-42

Enzymatic activity of Cryo-Em Structure of Na+-Translocating Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae Reduced By Nadh, with Bound Aurachin D-42

All present enzymatic activity of Cryo-Em Structure of Na+-Translocating Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae Reduced By Nadh, with Bound Aurachin D-42:
7.2.1.1;

Other elements in 9udg:

The structure of Cryo-Em Structure of Na+-Translocating Nadh-Ubiquinone Oxidoreductase From Vibrio Cholerae Reduced By Nadh, with Bound Aurachin D-42 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 Aurachin D-42 (pdb code 9udg). 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 Aurachin D-42, PDB code: 9udg:

Calcium binding site 1 out of 1 in 9udg

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Calcium Binding Sites List in 9udg

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 Aurachin D-42

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 Aurachin D-42 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Ca302 b:159.4 occ:1.00	NE2	C:GLN93	3.1	124.7	1.0
	N	C:ALA119	3.5	130.6	1.0
	NE2	C:HIS141	3.8	105.1	1.0
	CA	C:ARG118	3.9	127.2	1.0
	CG	C:GLN93	4.0	123.8	1.0
	CD	C:GLN93	4.0	123.1	1.0
	CG	C:ARG118	4.1	128.2	1.0
	CH2	C:TRP238	4.1	102.5	1.0
	CB	C:ALA97	4.2	137.6	1.0
	CB	C:ALA119	4.2	128.9	1.0
	C	C:ARG118	4.2	129.6	1.0
	CA	C:ALA119	4.4	130.6	1.0
	CB	C:ARG118	4.6	126.1	1.0
	CZ2	C:TRP238	4.6	99.7	1.0
	CE1	C:HIS141	4.6	104.4	1.0
	O	C:ARG117	4.8	141.4	1.0
	CD2	C:HIS141	4.9	100.5	1.0
	O	C:GLN93	4.9	135.6	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 10:27:41 2025

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