Sodium in PDB 7ndi: Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion

Protein crystallography data

The structure of Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion, PDB code: 7ndi was solved by A.Garg, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.77 / 2.88
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.701, 114.701, 257.309, 90, 90, 120
R / Rfree (%) 19.2 / 21.5

Other elements in 7ndi:

The structure of Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion (pdb code 7ndi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion, PDB code: 7ndi:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7ndi

Go back to Sodium Binding Sites List in 7ndi
Sodium binding site 1 out of 3 in the Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:99.0
occ:1.00
 O A:ASN151 2.4 92.1 1.0
O A:ALA146 2.4 59.6 1.0
O A:HIS149 2.4 65.0 1.0
O A:VAL154 2.5 69.4 1.0
O A:MET147 2.5 81.5 1.0
C A:MET147 2.7 78.4 1.0
CA A:MET147 2.9 60.8 1.0
C A:ALA146 3.3 62.0 1.0
C A:ASN151 3.5 93.6 1.0
C A:HIS149 3.5 72.0 1.0
N A:MET147 3.6 54.8 1.0
N A:SER148 3.6 77.2 1.0
C A:VAL154 3.7 77.1 1.0
N A:HIS149 3.8 55.3 1.0
C A:SER148 4.0 71.8 1.0
N A:SER156 4.1 62.8 1.0
CA A:LYS152 4.2 79.9 1.0
N A:VAL154 4.2 80.5 1.0
CA A:HIS149 4.2 49.9 1.0
CB A:SER156 4.2 68.5 1.0
CB A:MET147 4.2 50.0 1.0
N A:LYS152 4.3 86.3 1.0
N A:ASN151 4.3 80.3 1.0
CA A:SER148 4.3 62.5 1.0
C A:GLY150 4.4 88.7 1.0
CA A:VAL154 4.4 69.3 1.0
C A:LYS152 4.5 69.1 1.0
CA A:ASN151 4.5 89.7 1.0
O A:SER148 4.5 92.7 1.0
N A:GLY150 4.6 87.0 1.0
N A:PHE155 4.7 85.3 1.0
O A:GLY150 4.7 109.0 1.0
CA A:ALA146 4.7 67.7 1.0
SD A:MET147 4.8 83.2 1.0
N A:GLU153 4.8 70.3 1.0
CA A:GLY150 4.8 84.7 1.0
CA A:PHE155 4.8 67.3 1.0
CA A:SER156 4.8 63.4 1.0
CB A:VAL154 4.9 63.1 1.0
O A:LYS152 4.9 55.4 1.0
C A:PHE155 5.0 59.3 1.0
CB A:HIS149 5.0 61.5 1.0

Sodium binding site 2 out of 3 in 7ndi

Go back to Sodium Binding Sites List in 7ndi
Sodium binding site 2 out of 3 in the Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:97.7
occ:1.00
 O C:ASN151 2.4 74.2 1.0
O C:HIS149 2.4 52.6 1.0
O C:ALA146 2.4 70.5 1.0
O C:MET147 2.5 85.4 1.0
O C:VAL154 2.5 59.2 1.0
C C:MET147 2.7 82.6 1.0
CA C:MET147 2.9 69.4 1.0
C C:ALA146 3.3 69.0 1.0
C C:ASN151 3.5 86.3 1.0
C C:HIS149 3.5 68.5 1.0
N C:MET147 3.6 61.1 1.0
N C:SER148 3.6 77.9 1.0
C C:VAL154 3.7 69.2 1.0
N C:HIS149 3.8 58.9 1.0
C C:SER148 4.0 61.0 1.0
N C:SER156 4.1 67.5 1.0
CB C:SER156 4.2 62.1 1.0
CA C:HIS149 4.2 52.0 1.0
CA C:LYS152 4.2 66.7 1.0
CB C:MET147 4.3 54.5 1.0
N C:VAL154 4.3 69.3 1.0
N C:ASN151 4.3 75.6 1.0
N C:LYS152 4.3 87.2 1.0
CA C:SER148 4.3 52.4 1.0
C C:GLY150 4.4 89.4 1.0
CA C:VAL154 4.5 62.8 1.0
CA C:ASN151 4.5 80.7 1.0
O C:SER148 4.5 85.8 1.0
N C:GLY150 4.6 90.2 1.0
C C:LYS152 4.6 62.0 1.0
N C:PHE155 4.7 78.4 1.0
O C:GLY150 4.7 91.4 1.0
CA C:ALA146 4.7 66.6 1.0
CA C:SER156 4.8 71.6 1.0
CA C:PHE155 4.8 56.1 1.0
CA C:GLY150 4.8 95.5 1.0
SD C:MET147 4.8 67.6 1.0
N C:GLU153 4.9 74.9 1.0
CB C:VAL154 4.9 67.2 1.0
C C:PHE155 4.9 65.7 1.0
CB C:HIS149 4.9 54.7 1.0

Sodium binding site 3 out of 3 in 7ndi

Go back to Sodium Binding Sites List in 7ndi
Sodium binding site 3 out of 3 in the Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of ZC3H12C Pin Domain with MG2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:78.3
occ:1.00
 O D:ASN151 2.3 66.1 1.0
O D:HIS149 2.3 58.0 1.0
O D:VAL154 2.4 84.3 1.0
O D:MET147 2.4 69.2 1.0
O D:ALA146 2.5 73.0 1.0
C D:MET147 2.7 71.8 1.0
CA D:MET147 3.0 67.0 1.0
C D:ALA146 3.4 55.0 1.0
C D:HIS149 3.4 67.6 1.0
C D:ASN151 3.5 71.2 1.0
N D:SER148 3.6 74.8 1.0
C D:VAL154 3.6 73.8 1.0
N D:MET147 3.6 62.9 1.0
N D:HIS149 3.7 57.1 1.0
C D:SER148 3.9 60.6 1.0
N D:SER156 4.0 56.4 1.0
CB D:SER156 4.1 77.4 1.0
CA D:HIS149 4.1 58.2 1.0
N D:VAL154 4.2 67.3 1.0
N D:ASN151 4.2 70.2 1.0
CA D:SER148 4.3 67.6 1.0
CA D:LYS152 4.3 77.6 1.0
CB D:MET147 4.3 53.5 1.0
N D:LYS152 4.3 73.3 1.0
C D:GLY150 4.4 73.7 1.0
CA D:VAL154 4.4 56.4 1.0
O D:SER148 4.4 68.6 1.0
CA D:ASN151 4.5 73.3 1.0
N D:GLY150 4.5 71.2 1.0
C D:LYS152 4.6 61.4 1.0
N D:PHE155 4.6 62.3 1.0
CA D:SER156 4.7 73.5 1.0
O D:GLY150 4.7 89.6 1.0
CA D:PHE155 4.7 55.1 1.0
CA D:GLY150 4.7 66.4 1.0
CA D:ALA146 4.8 59.6 1.0
SD D:MET147 4.8 63.3 1.0
N D:GLU153 4.8 66.4 1.0
C D:PHE155 4.8 75.9 1.0
CB D:VAL154 4.9 57.6 1.0
CB D:HIS149 4.9 58.3 1.0

Reference:

A.Garg, Y.Roske, S.Yamada, T.Uehata, O.Takeuchi, U.Heinemann. Pin and Ccch Zn-Finger Domains Coordinate Rna Targeting in ZC3H12 Family Endoribonucleases. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33950203
DOI: 10.1093/NAR/GKAB316
Page generated: Mon Jul 12 16:03:13 2021

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