Atomistry » Calcium » PDB 4lxz-4m71 » 4m65
Atomistry »
  Calcium »
    PDB 4lxz-4m71 »
      4m65 »

Calcium in PDB 4m65: In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand

Protein crystallography data

The structure of In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand, PDB code: 4m65 was solved by X.Yin, A.Scalia, L.Leroy, C.M.Cuttitta, G.M.Polizzo, D.L.Ericson, C.G.Roessler, O.Campos, R.Agarwal, M.Allaire, A.M.Orville, R.Jackimowicz, M.Y.Ma, R.M.Sweet, A.S.Soares, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.59 / 1.60
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.831, 92.831, 129.171, 90.00, 90.00, 120.00
R / Rfree (%) 13 / 15.9

Other elements in 4m65:

The structure of In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand (pdb code 4m65). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand, PDB code: 4m65:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4m65

Go back to Calcium Binding Sites List in 4m65
Calcium binding site 1 out of 5 in the In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:11.3
occ:1.00
OD2 A:ASP138 2.3 11.6 1.0
O A:GLU187 2.4 11.5 1.0
OE1 A:GLU177 2.4 11.4 1.0
O A:HOH505 2.4 12.3 1.0
OD1 A:ASP185 2.4 11.5 1.0
OE1 A:GLU190 2.5 11.4 1.0
OE2 A:GLU190 2.6 12.8 1.0
OE2 A:GLU177 2.8 12.5 1.0
CD A:GLU190 2.8 10.0 1.0
CD A:GLU177 2.9 12.0 1.0
C A:GLU187 3.4 12.0 1.0
CG A:ASP138 3.4 14.7 1.0
CG A:ASP185 3.4 12.4 1.0
CA A:CA402 3.8 13.6 1.0
OD2 A:ASP185 3.8 13.3 1.0
CB A:ASP138 4.0 11.8 1.0
O A:ASP185 4.2 12.8 1.0
N A:GLU187 4.2 13.4 1.0
O A:HOH716 4.2 29.4 1.0
N A:ILE188 4.3 12.7 1.0
CA A:GLU187 4.3 14.3 1.0
OD1 A:ASP138 4.3 13.2 1.0
CA A:ILE188 4.3 11.8 1.0
CG A:GLU190 4.3 12.9 1.0
CG A:GLU177 4.4 11.5 1.0
N A:GLY189 4.4 11.1 1.0
O A:HOH549 4.4 16.6 1.0
C A:ASP185 4.5 13.4 1.0
CB A:ASP185 4.7 14.4 1.0
CB A:GLU187 4.7 17.0 1.0
N A:ASP185 4.8 14.0 1.0
C A:ILE188 4.8 11.8 1.0
O A:HOH701 4.9 13.8 1.0
CB A:GLU177 4.9 10.6 1.0
CA A:ASP185 4.9 13.1 1.0
N A:GLU190 5.0 11.0 1.0

Calcium binding site 2 out of 5 in 4m65

Go back to Calcium Binding Sites List in 4m65
Calcium binding site 2 out of 5 in the In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:13.6
occ:1.00
OD2 A:ASP185 2.3 13.3 1.0
O A:ASN183 2.3 15.8 1.0
O A:HOH701 2.3 13.8 1.0
OE2 A:GLU190 2.3 12.8 1.0
OE2 A:GLU177 2.4 12.5 1.0
O A:HOH591 2.4 16.8 1.0
CG A:ASP185 3.1 12.4 1.0
CD A:GLU177 3.3 12.0 1.0
CD A:GLU190 3.3 10.0 1.0
C A:ASN183 3.4 13.6 1.0
OD1 A:ASP185 3.7 11.5 1.0
CG A:GLU190 3.8 12.9 1.0
OE1 A:GLU177 3.8 11.4 1.0
CA A:CA401 3.8 11.3 1.0
O A:LYS182 4.0 19.9 1.0
O A:HOH638 4.1 29.9 1.0
CA A:PRO184 4.2 12.9 1.0
CB A:ASN183 4.2 17.2 1.0
OD1 A:ASP191 4.2 17.8 1.0
N A:ASP185 4.2 14.0 1.0
OD2 A:ASP191 4.2 20.6 1.0
CG A:GLU177 4.2 11.5 1.0
C A:PRO184 4.2 14.7 1.0
N A:PRO184 4.3 14.6 1.0
CB A:ASP185 4.3 14.4 1.0
OE1 A:GLU190 4.3 11.4 1.0
O1 A:EDO415 4.4 57.5 1.0
CA A:ASN183 4.4 17.0 1.0
O A:HOH716 4.5 29.4 1.0
CG A:ASP191 4.5 18.9 1.0
CA A:ASP185 4.9 13.1 1.0
O A:PRO184 4.9 16.3 1.0
C A:LYS182 5.0 18.9 1.0

Calcium binding site 3 out of 5 in 4m65

Go back to Calcium Binding Sites List in 4m65
Calcium binding site 3 out of 5 in the In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:11.9
occ:1.00
O A:GLN61 2.3 11.8 1.0
O A:HOH636 2.3 16.6 1.0
OD1 A:ASP57 2.3 11.3 1.0
OD1 A:ASP59 2.4 13.0 1.0
O A:HOH513 2.4 15.9 1.0
O A:HOH521 2.5 14.6 1.0
OD2 A:ASP57 2.6 11.3 1.0
CG A:ASP57 2.8 11.6 1.0
CG A:ASP59 3.4 16.7 1.0
C A:GLN61 3.4 10.2 1.0
OD2 A:ASP59 3.8 17.1 1.0
O A:HOH517 3.9 18.2 1.0
N A:GLN61 4.0 10.8 1.0
CA A:GLN61 4.2 11.2 1.0
N A:ASP59 4.3 12.0 1.0
CB A:ASP57 4.4 10.8 1.0
CB A:GLN61 4.4 14.2 1.0
O A:HOH503 4.4 14.6 1.0
O A:HOH545 4.4 36.6 1.0
N A:PHE62 4.5 10.3 1.0
CB A:ASP59 4.6 13.4 1.0
O A:HOH650 4.6 39.4 1.0
O A:HOH511 4.6 12.6 1.0
OD2 A:ASP67 4.6 11.7 1.0
N A:ASN60 4.7 10.2 1.0
CA A:ASP59 4.7 12.5 1.0
N A:ALA58 4.8 11.4 1.0
CA A:PHE62 4.8 9.7 1.0
O A:HOH594 4.8 30.2 1.0
C A:ASP59 4.9 11.2 1.0

Calcium binding site 4 out of 5 in 4m65

Go back to Calcium Binding Sites List in 4m65
Calcium binding site 4 out of 5 in the In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:13.6
occ:1.00
O A:ILE197 2.3 15.7 1.0
O A:TYR193 2.3 12.1 1.0
O A:HOH552 2.4 13.1 1.0
OD1 A:ASP200 2.4 13.6 1.0
O1 A:EDO416 2.5 19.7 1.0
OG1 A:THR194 2.5 16.0 1.0
O A:THR194 2.5 15.1 1.0
C A:THR194 3.3 16.1 1.0
C A:TYR193 3.3 13.6 1.0
CG A:ASP200 3.4 12.4 1.0
C A:ILE197 3.5 21.1 1.0
C1 A:EDO416 3.5 22.2 1.0
CB A:THR194 3.5 14.2 1.0
CA A:THR194 3.7 14.1 1.0
N A:THR194 3.9 13.8 1.0
OD2 A:ASP200 3.9 15.0 1.0
CB A:ILE197 4.1 21.7 1.0
CA A:ILE197 4.1 20.4 1.0
N A:ILE197 4.2 21.4 1.0
N A:PRO195 4.3 15.5 1.0
C2 A:EDO416 4.4 21.2 1.0
O A:ASP200 4.5 18.2 1.0
N A:SER198 4.5 18.9 1.0
CA A:TYR193 4.5 14.6 1.0
O A:GLU190 4.6 13.0 1.0
N A:ASP200 4.7 15.8 1.0
CA A:SER198 4.7 21.0 1.0
CB A:TYR193 4.7 14.0 1.0
CG2 A:ILE197 4.7 20.9 1.0
CA A:PRO195 4.7 18.6 1.0
O A:HOH858 4.7 52.1 1.0
CD2 A:TYR193 4.7 15.8 1.0
CG2 A:THR194 4.7 14.2 1.0
CB A:ASP200 4.8 14.9 1.0
C A:ASP200 4.9 15.3 1.0
O A:HOH823 5.0 39.1 1.0
N A:GLY199 5.0 19.8 1.0
C A:SER198 5.0 18.9 1.0

Calcium binding site 5 out of 5 in 4m65

Go back to Calcium Binding Sites List in 4m65
Calcium binding site 5 out of 5 in the In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of In Situ Thermolysin Crystallized on A Mitegen Micromesh with Asparagine Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:17.2
occ:0.60
O A:HOH925 2.2 14.4 1.0
O A:HOH931 2.4 35.1 1.0
O A:HOH832 2.4 32.4 1.0
O A:HOH926 2.5 28.7 1.0
O A:HOH927 2.5 29.2 1.0
O A:HOH928 2.5 22.9 1.0
O A:TYR211 2.6 21.5 1.0
C A:TYR211 3.8 18.9 1.0
O A:HOH938 3.9 44.1 1.0
O A:HOH667 3.9 41.2 1.0
CB A:TYR211 4.0 15.4 1.0
O A:HOH851 4.1 56.9 1.0
OD1 A:ASP213 4.3 14.9 1.0
CA A:TYR211 4.4 15.5 1.0
O A:LEU202 4.4 12.9 1.0
OD2 A:ASP213 4.5 13.4 1.0
CG A:ASP213 4.7 13.8 1.0
N A:GLY212 4.9 17.8 1.0
O A:HOH542 4.9 26.8 1.0

Reference:

X.Yin, A.Scalia, L.Leroy, C.M.Cuttitta, G.M.Polizzo, D.L.Ericson, C.G.Roessler, O.Campos, R.Agarwal, M.Allaire, A.M.Orville, R.Jackimowicz, M.Y.Ma, R.M.Sweet, A.S.Soares. Hitting the Target: Fragment Screening with Acoustic in Situ Co-Crystallization of Proteins Plus Fragment Libraries on Pin-Mounted Data-Collection Micromeshes Acta Crystallogr.,Sect.D V. D70 1177.
ISSN: ISSN 0907-4449
Page generated: Sat Dec 12 04:58:06 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