Calcium in PDB 6d5o: Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf

Enzymatic activity of Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf

All present enzymatic activity of Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf:
3.4.24.27;

Protein crystallography data

The structure of Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf, PDB code: 6d5o was solved by D.H.Juers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 13.97 / 2.00
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.931, 93.931, 131.656, 90.00, 90.00, 120.00
R / Rfree (%) 15.3 / 19.3

Other elements in 6d5o:

The structure of Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf (pdb code 6d5o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf, PDB code: 6d5o:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6d5o

Go back to Calcium Binding Sites List in 6d5o
Calcium binding site 1 out of 4 in the Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:15.5
occ:1.00
O A:GLU187 2.3 14.9 1.0
OE1 A:GLU177 2.4 17.1 1.0
O A:HOH549 2.5 12.4 1.0
OD1 A:ASP185 2.5 15.7 1.0
OD2 A:ASP138 2.5 14.4 1.0
OE1 A:GLU190 2.6 15.8 1.0
OE2 A:GLU190 2.6 15.6 1.0
OE2 A:GLU177 2.8 16.2 1.0
CD A:GLU190 2.9 15.9 1.0
CD A:GLU177 3.0 20.1 1.0
C A:GLU187 3.4 13.1 1.0
CG A:ASP138 3.5 25.3 1.0
CG A:ASP185 3.5 19.0 1.0
HB3 A:ASP138 3.6 14.6 1.0
HA A:ILE188 3.7 13.9 1.0
H A:GLU187 3.7 20.9 1.0
CA A:CA407 3.8 17.2 1.0
OD2 A:ASP185 3.8 14.4 1.0
H A:GLY189 3.8 13.7 1.0
HB2 A:GLU187 3.9 20.0 1.0
CB A:ASP138 4.1 14.6 1.0
H A:GLU190 4.1 15.0 1.0
N A:GLU187 4.2 20.9 1.0
N A:ILE188 4.2 13.0 1.0
H A:ASP185 4.2 15.8 1.0
O A:ASP185 4.2 18.3 1.0
CA A:GLU187 4.3 20.6 1.0
HD13 A:ILE188 4.3 19.1 1.0
O A:HOH599 4.3 34.2 1.0
HB2 A:ASP138 4.3 14.6 1.0
CA A:ILE188 4.3 13.9 1.0
CG A:GLU190 4.4 20.8 1.0
OD1 A:ASP138 4.4 18.9 1.0
CG A:GLU177 4.4 12.7 1.0
N A:GLY189 4.5 13.7 1.0
O A:HOH579 4.6 15.5 1.0
CB A:GLU187 4.6 20.0 1.0
HG3 A:GLU190 4.6 20.8 1.0
C A:ASP185 4.6 11.5 1.0
HB2 A:GLU177 4.7 15.3 1.0
CB A:ASP185 4.8 20.5 1.0
N A:ASP185 4.8 15.8 1.0
C A:ILE188 4.8 17.1 1.0
HB3 A:GLU177 4.8 15.3 1.0
O A:HOH510 4.8 19.8 1.0
HG2 A:GLU190 4.9 20.8 1.0
HA A:THR174 4.9 14.1 1.0
HG2 A:GLU177 4.9 12.7 1.0
HG3 A:GLU177 4.9 12.7 1.0
HB3 A:GLU190 4.9 13.7 1.0
CB A:GLU177 5.0 15.3 1.0
N A:GLU190 5.0 15.0 1.0
H A:ILE188 5.0 13.0 1.0

Calcium binding site 2 out of 4 in 6d5o

Go back to Calcium Binding Sites List in 6d5o
Calcium binding site 2 out of 4 in the Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:16.4
occ:1.00
O A:GLN61 2.2 15.2 1.0
O A:HOH627 2.3 20.6 1.0
OD1 A:ASP57 2.4 17.1 1.0
OD1 A:ASP59 2.4 19.4 1.0
O A:HOH513 2.5 15.0 1.0
O A:HOH519 2.5 19.5 1.0
OD2 A:ASP57 2.6 15.1 1.0
CG A:ASP57 2.8 18.3 1.0
H A:GLN61 3.3 15.1 1.0
CG A:ASP59 3.4 26.9 1.0
C A:GLN61 3.4 16.6 1.0
H A:ASP59 3.6 15.4 1.0
OD2 A:ASP59 3.7 21.9 1.0
HB2 A:GLN61 3.8 18.4 1.0
O A:HOH588 3.8 33.1 1.0
HA A:PHE62 4.0 19.3 1.0
N A:GLN61 4.0 15.1 1.0
H A:ALA58 4.1 14.3 1.0
CA A:GLN61 4.1 18.1 1.0
CB A:ASP57 4.3 14.0 1.0
N A:ASP59 4.4 15.4 1.0
CB A:GLN61 4.4 18.4 1.0
N A:PHE62 4.5 16.8 1.0
H A:ASN60 4.5 19.0 1.0
OD2 A:ASP67 4.6 18.4 1.0
CB A:ASP59 4.7 14.2 1.0
O A:HOH535 4.7 13.6 1.0
N A:ALA58 4.7 14.3 1.0
CA A:PHE62 4.7 19.3 1.0
HB2 A:ASP57 4.7 14.0 1.0
N A:ASN60 4.7 19.0 1.0
H A:PHE63 4.8 14.2 1.0
HB3 A:ASP57 4.8 14.0 1.0
HB3 A:GLN61 4.9 18.4 1.0
CA A:ASP59 4.9 18.9 1.0
HA A:ASP57 4.9 12.3 1.0
C A:ASP59 4.9 16.0 1.0
HB3 A:ALA58 5.0 17.8 1.0

Calcium binding site 3 out of 4 in 6d5o

Go back to Calcium Binding Sites List in 6d5o
Calcium binding site 3 out of 4 in the Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:18.5
occ:1.00
OG1 A:THR194 2.3 21.5 1.0
OD1 A:ASP200 2.3 19.9 1.0
O A:TYR193 2.3 14.0 1.0
O A:ILE197 2.4 26.5 1.0
O A:HOH514 2.4 20.1 1.0
O A:HOH607 2.4 23.8 1.0
O A:THR194 2.4 24.0 1.0
C A:THR194 3.3 25.6 1.0
CG A:ASP200 3.4 21.2 1.0
C A:TYR193 3.4 18.6 1.0
CB A:THR194 3.5 21.1 1.0
C A:ILE197 3.5 29.3 1.0
HB A:ILE197 3.6 28.8 1.0
H A:ILE197 3.6 27.8 1.0
OD2 A:ASP200 3.7 22.1 1.0
CA A:THR194 3.7 15.9 1.0
HB A:THR194 3.8 21.1 1.0
H A:ASP200 3.9 24.4 1.0
N A:THR194 3.9 18.0 1.0
HB3 A:TYR193 4.1 15.8 1.0
HD2 A:TYR193 4.2 24.1 1.0
HA A:SER198 4.2 35.1 1.0
CA A:ILE197 4.3 25.5 1.0
HA A:PRO195 4.3 21.8 1.0
N A:ILE197 4.3 27.8 1.0
N A:PRO195 4.3 19.1 1.0
CB A:ILE197 4.3 28.8 1.0
O A:ASP200 4.4 21.2 1.0
O A:GLU190 4.5 16.5 1.0
CA A:TYR193 4.5 16.5 1.0
HG22 A:ILE197 4.6 33.8 1.0
N A:SER198 4.6 33.6 1.0
HA A:THR194 4.7 15.9 1.0
N A:ASP200 4.7 24.4 1.0
CA A:PRO195 4.7 21.8 1.0
CG2 A:THR194 4.7 22.3 1.0
CB A:ASP200 4.7 17.4 1.0
CB A:TYR193 4.7 15.8 1.0
C A:ASP200 4.8 27.2 1.0
H A:THR194 4.8 18.0 1.0
CD2 A:TYR193 4.8 24.1 1.0
HG23 A:THR194 4.8 22.3 1.0
CA A:SER198 4.8 35.1 1.0
H A:GLY199 4.8 24.5 1.0
H A:TYR193 4.8 14.7 1.0
HG21 A:THR194 4.9 22.3 1.0
CA A:ASP200 5.0 21.0 1.0
C A:PRO195 5.0 31.8 1.0
N A:TYR193 5.0 14.7 1.0

Calcium binding site 4 out of 4 in 6d5o

Go back to Calcium Binding Sites List in 6d5o
Calcium binding site 4 out of 4 in the Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Hexagonal Thermolysin (295 K) in the Presence of 50% Dmf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:17.2
occ:1.00
OE2 A:GLU190 2.3 15.6 1.0
OD2 A:ASP185 2.3 14.4 1.0
O A:ASN183 2.3 19.2 1.0
OE2 A:GLU177 2.4 16.2 1.0
O A:HOH510 2.4 19.8 1.0
O A:HOH571 2.4 18.1 1.0
CG A:ASP185 3.2 19.0 1.0
CD A:GLU177 3.2 20.1 1.0
CD A:GLU190 3.3 15.9 1.0
C A:ASN183 3.5 17.4 1.0
HG3 A:GLU190 3.6 20.8 1.0
OD1 A:ASP185 3.6 15.7 1.0
HA A:PRO184 3.7 21.6 1.0
HB3 A:ASN183 3.7 25.9 1.0
CA A:CA404 3.8 15.5 1.0
OE1 A:GLU177 3.8 17.1 1.0
O A:LYS182 3.8 25.5 1.0
CG A:GLU190 3.8 20.8 1.0
HB2 A:ASN183 3.8 25.9 1.0
HG2 A:GLU190 3.8 20.8 1.0
H A:ASP185 4.0 15.8 1.0
CB A:ASN183 4.2 25.9 1.0
N A:ASP185 4.2 15.8 1.0
CA A:PRO184 4.2 21.6 1.0
HG2 A:GLU177 4.3 12.7 1.0
C A:PRO184 4.3 25.5 1.0
OD1 A:ASP191 4.3 17.1 1.0
CG A:GLU177 4.3 12.7 1.0
OE1 A:GLU190 4.3 15.8 1.0
HB3 A:ASP185 4.3 20.5 1.0
OD2 A:ASP191 4.3 21.0 1.0
N A:PRO184 4.3 21.4 1.0
CB A:ASP185 4.3 20.5 1.0
HG3 A:GLU177 4.4 12.7 1.0
CA A:ASN183 4.4 19.4 1.0
O A:HOH599 4.5 34.2 1.0
CG A:ASP191 4.6 25.3 1.0
C A:LYS182 4.9 24.1 1.0
CA A:ASP185 4.9 13.7 1.0
O A:PRO184 4.9 21.3 1.0

Reference:

D.H.Juers, C.A.Farley, C.P.Saxby, R.A.Cotter, J.K.B.Cahn, R.C.Holton-Burke, K.Harrison, Z.Wu. The Impact of Cryosolution Thermal Contraction on Proteins and Protein Crystals: Volumes, Conformation and Order. Acta Crystallogr D Struct V. 74 922 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30198901
DOI: 10.1107/S2059798318008793
Page generated: Sat Dec 12 06:02:24 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