Calcium in PDB 9uda: Cryo-Em Structure of Na+-Translocating Nadh-Ubiquinone Oxidoreductase Nqrb-G141A Mutant From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A, Stable State

Enzymatic activity of Cryo-Em Structure of Na+-Translocating Nadh-Ubiquinone Oxidoreductase Nqrb-G141A Mutant From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A, Stable State

All present enzymatic activity of Cryo-Em Structure of Na+-Translocating Nadh-Ubiquinone Oxidoreductase Nqrb-G141A Mutant From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A, Stable State:
7.2.1.1;

Other elements in 9uda:

The structure of Cryo-Em Structure of Na+-Translocating Nadh-Ubiquinone Oxidoreductase Nqrb-G141A Mutant From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A, Stable State 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 Nqrb-G141A Mutant From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A, Stable State (pdb code 9uda). 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 Nqrb-G141A Mutant From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A, Stable State, PDB code: 9uda:

Calcium binding site 1 out of 1 in 9uda

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Calcium Binding Sites List in 9uda

Calcium binding site 1 out of 1 in the Cryo-Em Structure of Na+-Translocating Nadh-Ubiquinone Oxidoreductase Nqrb-G141A Mutant From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A, Stable State

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 Nqrb-G141A Mutant From Vibrio Cholerae Reduced By Nadh, with Bound Korormicin A, Stable State within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Ca302 b:156.0 occ:1.00	CA	C:ARG94	3.5	134.5	1.0
	NE2	C:HIS141	3.8	110.2	1.0
	N	C:ARG94	3.9	134.2	1.0
	O	C:GLN93	4.0	139.8	1.0
	CE1	C:HIS141	4.0	110.0	1.0
	C	C:GLN93	4.1	134.6	1.0
	CG	C:ARG94	4.2	127.2	1.0
	CB	C:ARG94	4.2	131.8	1.0
	CG	C:GLN93	4.4	135.0	1.0
	CB	C:ALA97	4.4	141.5	1.0
	CD2	C:HIS141	4.5	106.9	1.0
	NE2	C:GLN93	4.5	133.2	1.0
	C	C:ARG94	4.6	137.1	1.0
	O	C:ARG94	4.6	138.9	1.0
	CB	C:GLN93	4.6	132.6	1.0
	ND1	C:HIS141	4.7	106.0	1.0
	CD	C:GLN93	4.7	135.6	1.0
	CE2	C:TYR150	4.8	106.3	1.0
	CG	C:HIS141	4.9	105.3	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 10:27:38 2025

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