9YBI | pdb_00009ybi

Structure of the CBS pair domain from zebrafish magnesium transporter CNNM2

PDB DOI: https://doi.org/10.2210/pdb9YBI/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Danio rerio
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-09-17 Released: 2025-09-24
Deposition Author(s): Kozlov, G., Mahbub, L., Jin, M., Gehring, K.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.253 (Depositor), 0.253 (DCC)
R-Value Work:
0.235 (Depositor), 0.237 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of the CBS pair domain from zebrafish magnesium transporter CNNM2

Kozlov, G., Mahbub, L., Jin, M., Gehring, K.

To be published.

Macromolecule Content

Total Structure Weight: 35.93 kDa
Atom Count: 2,251
Modeled Residue Count: 296
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal transporter	A, B	158	Danio rerio	Mutation(s): 0 Gene Names: cnnm2a, im:7136247, si:ch211-67n3.4
UniProt
Find proteins for A2ATX7 (Danio rerio) Explore A2ATX7 Go to UniProtKB: A2ATX7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2ATX7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEN Query on BEN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.253 (Depositor), 0.253 (DCC)
R-Value Work: 0.235 (Depositor), 0.237 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.907	α = 90
b = 147.942	β = 90
c = 151.897	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2025-09-24
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.