4P1G | pdb_00004p1g

Crystal structure of the Bateman domain of murine magnesium transporter CNNM2 bound to AMP

PDB DOI: https://doi.org/10.2210/pdb4P1G/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-02-26 Released: 2015-03-04
Deposition Author(s): Corral-Rodriguez, M.A., Stuiver, M., Abascal-Palacios, G., Diercks, T., Oyenarte, I., Ereno-Orbea, J., Encinar, J.A., Spiwok, V., Terashima, H., Accardi, A., Muller, D., Martinez-Cruz, L.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.254 (Depositor), 0.242 (DCC)
R-Value Work:
0.212 (Depositor), 0.209 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural and ligand binding properties of the Bateman domain of human magnesium transporters CNNM2 and CNNM4

Corral-Rodriguez, M.A., Stuiver, M., Abascal-Palacios, G., Diercks, T., Oyenarte, I., Ereno-Orbea, J., Encinar, J.A., Spiwok, V., Terashima, H., Accardi, A., Muller, D., Martinez-Cruz, L.A.

To be published.

Macromolecule Content

Total Structure Weight: 17.74 kDa
Atom Count: 1,236
Modeled Residue Count: 152
Deposited Residue Count: 152
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal transporter CNNM2	A	152	Mus musculus	Mutation(s): 0 Gene Names: Cnnm2, Acdp2
UniProt & NIH Common Fund Data Resources
Find proteins for Q3TWN3 (Mus musculus) Explore Q3TWN3 Go to UniProtKB: Q3TWN3
IMPC: MGI:2151054
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3TWN3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.254 (Depositor), 0.242 (DCC)
R-Value Work: 0.212 (Depositor), 0.209 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.579	α = 90
b = 105.579	β = 90
c = 102.202	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PDB_EXTRACT	data extraction
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-03-04

Deposition Author(s):

Corral-Rodriguez, M.A.

Revision History (Full details and data files)

Version 1.0: 2015-03-04
Type: Initial release
Version 1.1: 2017-11-22
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Refinement description