Atomistry » Calcium » PDB 6ry5-6sau » 6s58
Atomistry »
  Calcium »
    PDB 6ry5-6sau »
      6s58 »

Calcium in PDB 6s58: Avaii Restriction Endonuclease in the Absence of Nucleic Acids

Protein crystallography data

The structure of Avaii Restriction Endonuclease in the Absence of Nucleic Acids, PDB code: 6s58 was solved by M.Kisiala, M.Kowalska, H.Korza, H.Czapinska, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.37 / 2.32
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 73.231, 102.733, 121.197, 90.00, 90.67, 90.00
R / Rfree (%) 21.6 / 25.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Avaii Restriction Endonuclease in the Absence of Nucleic Acids (pdb code 6s58). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Avaii Restriction Endonuclease in the Absence of Nucleic Acids, PDB code: 6s58:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6s58

Go back to Calcium Binding Sites List in 6s58
Calcium binding site 1 out of 5 in the Avaii Restriction Endonuclease in the Absence of Nucleic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Avaii Restriction Endonuclease in the Absence of Nucleic Acids within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:56.6
occ:1.00
O A:HOH408 2.3 59.3 1.0
O A:HOH411 2.3 53.9 1.0
O A:HOH429 2.3 46.1 1.0
O A:HOH406 2.3 50.6 1.0
OD1 A:ASP147 2.5 46.7 1.0
CG A:ASP147 3.8 44.8 1.0
OE2 A:GLU123 4.0 53.5 1.0
O A:VAL146 4.1 49.1 1.0
O A:VAL143 4.3 51.5 1.0
O A:CYS138 4.3 48.2 1.0
O A:HOH425 4.4 46.0 1.0
CA A:ASP147 4.4 45.9 1.0
CB A:ASP147 4.5 45.1 1.0
O A:GLY140 4.5 52.9 1.0
OD2 A:ASP147 4.7 49.1 1.0
OE1 A:GLU123 4.7 55.0 1.0
C A:VAL146 4.7 46.3 1.0
CD A:GLU123 4.8 50.1 1.0
O A:HOH431 4.8 48.1 1.0
N A:ASP147 4.9 45.2 1.0

Calcium binding site 2 out of 5 in 6s58

Go back to Calcium Binding Sites List in 6s58
Calcium binding site 2 out of 5 in the Avaii Restriction Endonuclease in the Absence of Nucleic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Avaii Restriction Endonuclease in the Absence of Nucleic Acids within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:85.5
occ:1.00
CG A:GLN161 3.7 51.6 1.0
CD A:GLN161 3.8 53.6 1.0
O A:ASN170 3.9 82.7 1.0
OD2 A:ASP147 3.9 49.1 1.0
O A:VAL162 4.0 52.9 1.0
NE2 A:GLN161 4.1 52.7 1.0
OD1 A:ASP147 4.2 46.7 1.0
OE1 A:GLN161 4.3 55.5 1.0
CG A:ASP147 4.5 44.8 1.0
O A:HOH431 4.5 48.1 1.0
O A:ALA145 4.6 55.7 1.0
ND2 A:ASN170 4.9 96.2 1.0
CG A:LYS163 4.9 61.6 1.0
OD1 A:ASN170 4.9 0.4 1.0
C A:VAL162 5.0 50.8 1.0
CG A:ASN170 5.0 99.1 1.0

Calcium binding site 3 out of 5 in 6s58

Go back to Calcium Binding Sites List in 6s58
Calcium binding site 3 out of 5 in the Avaii Restriction Endonuclease in the Absence of Nucleic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Avaii Restriction Endonuclease in the Absence of Nucleic Acids within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:80.3
occ:1.00
O C:HOH412 2.3 78.2 1.0
O C:HOH405 2.4 73.9 1.0
OD1 C:ASP147 2.4 53.8 1.0
O C:HOH406 2.7 60.4 1.0
CG C:ASP147 3.6 55.7 1.0
OE2 C:GLU123 3.8 71.5 1.0
OE1 C:GLU123 4.1 66.1 1.0
O C:GLY140 4.3 66.8 1.0
CD C:GLU123 4.3 66.3 1.0
O C:CYS138 4.4 57.3 1.0
O C:HOH409 4.4 72.9 1.0
O C:VAL146 4.4 68.6 1.0
OD2 C:ASP147 4.5 59.4 1.0
CB C:ASP147 4.5 57.2 1.0
CA C:ASP147 4.5 58.9 1.0
O C:VAL143 4.8 58.1 1.0
O C:HOH415 4.9 67.0 1.0
C C:VAL146 4.9 64.5 1.0

Calcium binding site 4 out of 5 in 6s58

Go back to Calcium Binding Sites List in 6s58
Calcium binding site 4 out of 5 in the Avaii Restriction Endonuclease in the Absence of Nucleic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Avaii Restriction Endonuclease in the Absence of Nucleic Acids within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:84.1
occ:1.00
OE1 D:GLU123 2.7 70.7 1.0
OD1 D:ASP147 2.9 80.4 1.0
CD D:GLU123 3.5 69.2 1.0
CG D:ASP147 3.6 79.1 1.0
OE2 D:GLU123 3.9 70.9 1.0
CA D:CA302 4.1 0.6 1.0
CB D:ASP147 4.1 76.5 1.0
O D:CYS138 4.3 59.5 1.0
OD2 D:ASP147 4.4 79.4 1.0
CA D:ASP147 4.5 75.4 1.0
O D:GLY140 4.5 73.4 1.0
CG D:GLU123 4.7 67.0 1.0
NE1 D:TRP137 4.9 51.6 1.0
O D:VAL146 5.0 78.4 1.0

Calcium binding site 5 out of 5 in 6s58

Go back to Calcium Binding Sites List in 6s58
Calcium binding site 5 out of 5 in the Avaii Restriction Endonuclease in the Absence of Nucleic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Avaii Restriction Endonuclease in the Absence of Nucleic Acids within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:0.6
occ:1.00
O D:VAL162 2.7 74.3 1.0
OD2 D:ASP147 2.7 79.4 1.0
OE2 D:GLU123 3.2 70.9 1.0
CG D:ASP147 3.4 79.1 1.0
OD1 D:ASP147 3.4 80.4 1.0
CD D:LYS163 3.8 0.4 1.0
CE D:LYS163 3.9 0.7 1.0
C D:VAL162 3.9 80.4 1.0
NZ D:LYS163 3.9 0.5 1.0
CD D:GLU123 3.9 69.2 1.0
CA D:CA301 4.1 84.1 1.0
OE1 D:GLU123 4.4 70.7 1.0
CG2 D:VAL162 4.6 74.8 1.0
CB D:ASP147 4.7 76.5 1.0
CA D:LYS163 4.7 86.9 1.0
N D:VAL162 4.7 82.5 1.0
N D:LYS163 4.8 82.9 1.0
CG D:GLU123 4.8 67.0 1.0
CG D:LYS163 4.8 97.1 1.0
CA D:VAL162 4.9 80.4 1.0

Reference:

M.Kisiala, M.Kowalska, M.Pastor, H.Korza, H.Czapinska, M.Bochtler. Restriction Endonucleases That Cleave Rna/Dna Heteroduplexes Bind Dsdna in A-Like Conformation Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
Page generated: Tue Jul 16 14:31:19 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy