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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy