Atomistry » Calcium » PDB 3aau-3ati » 3agv
Atomistry »
  Calcium »
    PDB 3aau-3ati »
      3agv »

Calcium in PDB 3agv: Crystal Structure of A Human Igg-Aptamer Complex

Protein crystallography data

The structure of Crystal Structure of A Human Igg-Aptamer Complex, PDB code: 3agv was solved by Y.Nomura, S.Sugiyama, T.Sakamoto, S.Miyakawa, H.Adachi, K.Takano, S.Murakami, T.Inoue, Y.Mori, Y.Nakamura, H.Matsumura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.37 / 2.15
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.587, 107.238, 79.458, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 27.7

Other elements in 3agv:

The structure of Crystal Structure of A Human Igg-Aptamer Complex also contains other interesting chemical elements:

Fluorine (F) 18 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Human Igg-Aptamer Complex (pdb code 3agv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A Human Igg-Aptamer Complex, PDB code: 3agv:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3agv

Go back to Calcium Binding Sites List in 3agv
Calcium binding site 1 out of 2 in the Crystal Structure of A Human Igg-Aptamer Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Human Igg-Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ca25

b:79.5
occ:1.00
O S:HOH249 2.0 0.5 1.0
O S:HOH236 2.3 41.8 1.0
O S:HOH248 2.4 65.4 1.0
O S:HOH235 2.5 66.1 1.0
O S:HOH247 2.5 78.2 1.0
OP2 S:G7 2.7 61.9 1.0
O6 S:G17 4.0 74.3 1.0
C2' S:UFT6 4.1 63.5 1.0
O6 S:G16 4.1 87.0 1.0
N7 S:G17 4.1 74.2 1.0
P S:G7 4.1 63.0 1.0
N7 S:G16 4.3 84.9 1.0
C3' S:UFT6 4.4 63.3 1.0
F2' S:UFT6 4.6 63.4 1.0
C6 S:G16 4.7 86.2 1.0
O3' S:UFT6 4.7 62.8 1.0
C5 S:G16 4.8 85.7 1.0
C6 S:G17 4.8 75.0 1.0
N4 S:CFZ11 4.8 81.6 1.0
C5' S:G7 4.8 56.4 1.0
C5 S:G17 4.8 75.3 1.0
O5' S:G7 5.0 59.9 1.0

Calcium binding site 2 out of 2 in 3agv

Go back to Calcium Binding Sites List in 3agv
Calcium binding site 2 out of 2 in the Crystal Structure of A Human Igg-Aptamer Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Human Igg-Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Ca25

b:56.6
occ:1.00
O U:HOH234 2.3 69.1 1.0
OP2 U:G7 2.4 46.8 1.0
O U:HOH233 2.5 56.2 1.0
O U:HOH244 2.6 66.4 1.0
O U:HOH246 3.3 0.2 1.0
O U:HOH245 3.5 0.3 1.0
P U:G7 3.9 46.2 1.0
O U:HOH134 4.0 39.2 1.0
O6 U:G16 4.0 72.5 1.0
O6 U:G17 4.3 49.2 1.0
C5' U:G7 4.5 43.1 1.0
O5' U:G7 4.6 45.0 1.0
OP1 U:G7 4.6 48.7 1.0
N7 U:G16 4.7 72.6 1.0
C2' U:UFT6 4.8 50.2 1.0
O3' U:UFT6 4.9 48.1 1.0
O U:HOH82 4.9 39.6 1.0
C6 U:G16 4.9 72.7 1.0
C3' U:UFT6 4.9 49.8 1.0
F2' U:UFT6 5.0 51.2 1.0

Reference:

Y.Nomura, S.Sugiyama, T.Sakamoto, S.Miyakawa, H.Adachi, K.Takano, S.Murakami, T.Inoue, Y.Mori, Y.Nakamura, H.Matsumura. Conformational Plasticity of Rna For Target Recognition As Revealed By the 2.15 A Crystal Structure of A Human Igg-Aptamer Complex Nucleic Acids Res. V. 38 7822 2010.
ISSN: ISSN 0305-1048
PubMed: 20675355
DOI: 10.1093/NAR/GKQ615
Page generated: Sat Dec 12 04:04:03 2020

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