Magnesium in PDB 9jfj: Crystal Structure of the Cytoplasmic Domain of Zras in Adp-Bound Form

All present enzymatic activity of Crystal Structure of the Cytoplasmic Domain of Zras in Adp-Bound Form:
2.7.13.3;

The structure of Crystal Structure of the Cytoplasmic Domain of Zras in Adp-Bound Form, PDB code: 9jfj was solved by N.Mahapatra, S.Pandey, P.Mahanta, R.Acharya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.36 / 2.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.87, 121.79, 88.43, 90, 126.04, 90
R / Rfree (%)	26.1 / 28.2

The binding sites of Magnesium atom in the Crystal Structure of the Cytoplasmic Domain of Zras in Adp-Bound Form (pdb code 9jfj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Cytoplasmic Domain of Zras in Adp-Bound Form, PDB code: 9jfj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Cytoplasmic Domain of Zras in Adp-Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Cytoplasmic Domain of Zras in Adp-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg800 b:68.8 occ:1.00 O1B A:ADP801 2.1 68.2 1.0 O2A A:ADP801 2.1 70.1 1.0 OD1 A:ASN367 2.2 66.0 1.0 CG A:ASN367 2.9 66.8 1.0 ND2 A:ASN367 3.1 71.8 1.0 PB A:ADP801 3.1 62.3 1.0 O3A A:ADP801 3.1 62.1 1.0 PA A:ADP801 3.2 74.3 1.0 O3B A:ADP801 3.8 66.9 1.0 O5' A:ADP801 3.9 71.2 1.0 OD1 A:ASN363 4.2 82.3 1.0 CA A:GLY423 4.2 60.9 1.0 O2B A:ADP801 4.3 75.3 1.0 CB A:ASN367 4.4 66.7 1.0 O1A A:ADP801 4.4 68.0 1.0 NZ A:LYS416 4.5 63.7 1.0 OE1 A:GLN370 4.6 62.9 1.0 N A:GLY423 4.7 60.7 1.0 O A:ASN363 4.7 71.1 1.0 O A:THR420 4.8 85.1 1.0 CA A:ASN367 4.8 64.5 1.0 C A:GLY423 4.8 66.7 1.0 N A:LEU424 4.9 62.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Cytoplasmic Domain of Zras in Adp-Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Cytoplasmic Domain of Zras in Adp-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg800 b:105.7 occ:1.00 OD1 B:ASN367 2.0 107.2 1.0 O2A B:ADP801 2.1 111.9 1.0 O1B B:ADP801 2.1 118.0 1.0 O3B B:ADP801 2.9 115.8 1.0 PB B:ADP801 2.9 123.6 1.0 CG B:ASN367 3.0 110.0 1.0 PA B:ADP801 3.3 106.0 1.0 ND2 B:ASN367 3.4 106.8 1.0 O3A B:ADP801 3.5 107.2 1.0 O5' B:ADP801 4.1 103.2 1.0 CA B:GLY423 4.1 87.7 1.0 O2B B:ADP801 4.3 117.1 1.0 OD1 B:ASN363 4.3 83.9 1.0 CB B:ASN367 4.4 102.8 1.0 N B:GLY423 4.5 89.8 1.0 OE1 B:GLN370 4.5 104.1 1.0 O1A B:ADP801 4.5 103.3 1.0 O B:ASN363 4.7 93.4 1.0 CA B:ASN367 4.7 102.8 1.0 N B:ASN367 4.8 99.3 1.0 CD1 B:LEU424 5.0 101.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Cytoplasmic Domain of Zras in Adp-Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Cytoplasmic Domain of Zras in Adp-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg800 b:99.2 occ:1.00 O2A C:ADP801 2.0 93.3 1.0 OD1 C:ASN367 2.0 105.5 1.0 O1B C:ADP801 2.1 108.4 1.0 O3A C:ADP801 2.8 102.8 1.0 PB C:ADP801 2.9 100.1 1.0 CG C:ASN367 2.9 98.6 1.0 PA C:ADP801 2.9 94.7 1.0 ND2 C:ASN367 3.1 96.8 1.0 O3B C:ADP801 3.4 109.7 1.0 O5' C:ADP801 3.8 97.1 1.0 O1A C:ADP801 4.1 104.0 1.0 CA C:GLY423 4.2 83.5 1.0 O2B C:ADP801 4.2 94.3 1.0 CB C:ASN367 4.3 93.3 1.0 N C:GLY423 4.4 97.6 1.0 OG1 C:THR420 4.5 101.2 1.0 OE1 C:GLN370 4.8 97.0 1.0 CA C:ASN367 5.0 89.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Cytoplasmic Domain of Zras in Adp-Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Cytoplasmic Domain of Zras in Adp-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg800 b:116.0 occ:1.00 O2A D:ADP801 2.0 113.9 1.0 O1B D:ADP801 2.1 127.2 1.0 OD1 D:ASN367 2.1 114.0 1.0 O3B D:ADP801 2.4 127.8 1.0 PB D:ADP801 2.5 118.5 1.0 CG D:ASN367 3.0 116.4 1.0 O3A D:ADP801 3.0 117.2 1.0 PA D:ADP801 3.0 113.8 1.0 ND2 D:ASN367 3.3 109.0 1.0 O5' D:ADP801 3.8 113.8 1.0 OE1 D:GLN370 3.9 132.1 1.0 O2B D:ADP801 4.0 123.4 1.0 O1A D:ADP801 4.3 112.7 1.0 CB D:ASN367 4.4 111.0 1.0 CA D:ASN367 4.8 121.3 1.0 C3' D:ADP801 4.9 117.8 1.0 CA D:GLY423 4.9 101.2 1.0

N.Mahapatra, P.Mahanta, S.Pandey, R.Acharya. Insights Into the Conformational Dynamics of the Cytoplasmic Domain of Metal-Sensing Sensor Histidine Kinase Zras. Proteins 2025.
ISSN: ESSN 1097-0134
PubMed: 40062583
DOI: 10.1002/PROT.26819