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Calcium in PDB 5k7t: Microed Structure of Thermolysin at 2.5 A Resolution

Enzymatic activity of Microed Structure of Thermolysin at 2.5 A Resolution

All present enzymatic activity of Microed Structure of Thermolysin at 2.5 A Resolution:
3.4.24.27;

Other elements in 5k7t:

The structure of Microed Structure of Thermolysin at 2.5 A Resolution also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Microed Structure of Thermolysin at 2.5 A Resolution (pdb code 5k7t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Microed Structure of Thermolysin at 2.5 A Resolution, PDB code: 5k7t:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5k7t

Go back to Calcium Binding Sites List in 5k7t
Calcium binding site 1 out of 4 in the Microed Structure of Thermolysin at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Microed Structure of Thermolysin at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:2.6
occ:1.00
OE1 A:GLU409 2.6 5.2 1.0
OE1 A:GLU422 2.6 5.3 1.0
O A:GLU419 2.7 5.5 1.0
OD2 A:ASP370 2.8 4.3 1.0
OE2 A:GLU409 3.0 5.0 1.0
CD A:GLU409 3.1 5.2 1.0
CG A:ASP370 3.2 4.1 1.0
OD1 A:ASP417 3.2 5.0 1.0
CD A:GLU422 3.4 5.2 1.0
C A:GLU419 3.4 5.1 1.0
OE2 A:GLU422 3.5 5.0 1.0
OD1 A:ASP370 3.7 4.3 1.0
CB A:ASP370 3.8 3.6 1.0
N A:GLY421 3.9 4.7 1.0
N A:ILE420 4.1 5.3 1.0
CG A:ASP417 4.1 5.8 1.0
CA A:ILE420 4.1 5.4 1.0
O A:ASP417 4.2 5.3 1.0
CA A:GLU419 4.3 5.2 1.0
N A:GLU419 4.4 5.3 1.0
C A:ILE420 4.4 4.8 1.0
OD2 A:ASP417 4.4 6.6 1.0
CG A:GLU409 4.5 4.9 1.0
CB A:GLU419 4.6 5.2 1.0
N A:GLU422 4.6 5.3 1.0
C A:ASP417 4.8 5.8 1.0
CG A:GLU422 4.9 5.4 1.0
CA A:GLY421 4.9 4.8 1.0

Calcium binding site 2 out of 4 in 5k7t

Go back to Calcium Binding Sites List in 5k7t
Calcium binding site 2 out of 4 in the Microed Structure of Thermolysin at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Microed Structure of Thermolysin at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:16.6
occ:1.00
O A:ASN415 2.4 7.1 1.0
OE2 A:GLU422 2.5 5.0 1.0
OD2 A:ASP417 2.9 6.6 1.0
C A:ASN415 3.5 6.5 1.0
OD1 A:ASP423 3.5 5.2 1.0
CB A:ASN415 3.5 9.4 1.0
CD A:GLU422 3.6 5.2 1.0
O A:LYS414 3.9 8.8 1.0
CG A:GLU422 4.1 5.4 1.0
CG A:ASP417 4.1 5.8 1.0
CA A:ASN415 4.1 7.1 1.0
OE1 A:GLU409 4.3 5.2 1.0
CG A:ASP423 4.4 4.9 1.0
OD2 A:ASP423 4.5 4.7 1.0
N A:PRO416 4.6 6.8 1.0
OE1 A:GLU422 4.6 5.3 1.0
OD1 A:ASP417 4.7 5.0 1.0
CG A:ASN415 4.8 9.0 1.0
CA A:PRO416 4.8 6.2 1.0
C A:LYS414 4.8 8.8 1.0
CD A:GLU409 4.8 5.2 1.0
C A:PRO416 4.9 6.2 1.0
N A:ASN415 4.9 7.7 1.0

Calcium binding site 3 out of 4 in 5k7t

Go back to Calcium Binding Sites List in 5k7t
Calcium binding site 3 out of 4 in the Microed Structure of Thermolysin at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Microed Structure of Thermolysin at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:4.0
occ:1.00
O A:GLN293 2.3 3.5 1.0
OD1 A:ASP291 2.6 4.4 1.0
OD2 A:ASP289 2.7 3.4 1.0
OD1 A:ASP289 3.2 3.2 1.0
CG A:ASP289 3.3 3.5 1.0
CG A:ASP291 3.5 3.7 1.0
C A:GLN293 3.6 3.7 1.0
OD2 A:ASP291 3.6 3.6 1.0
OD2 A:ASP299 4.1 4.6 1.0
N A:GLN293 4.4 3.9 1.0
CA A:GLN293 4.5 4.2 1.0
N A:PHE294 4.5 3.8 1.0
CA A:PHE294 4.5 3.9 1.0
CB A:GLN293 4.7 4.6 1.0
CB A:ASP289 4.8 3.0 1.0
N A:ASP291 4.8 3.3 1.0
CB A:ASP291 4.9 4.8 1.0

Calcium binding site 4 out of 4 in 5k7t

Go back to Calcium Binding Sites List in 5k7t
Calcium binding site 4 out of 4 in the Microed Structure of Thermolysin at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Microed Structure of Thermolysin at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:8.1
occ:1.00
O A:TYR425 2.3 7.2 1.0
O A:HOH705 2.4 5.8 1.0
O A:ILE429 2.5 8.7 1.0
OD1 A:ASP432 2.6 8.1 1.0
O A:THR426 2.6 8.5 1.0
OG1 A:THR426 2.8 7.7 1.0
C A:TYR425 3.5 5.9 1.0
C A:ILE429 3.6 8.4 1.0
C A:THR426 3.6 9.7 1.0
CG A:ASP432 3.6 7.9 1.0
O A:ASP432 3.9 7.4 1.0
CB A:THR426 4.0 8.6 1.0
OD2 A:ASP432 4.1 7.7 1.0
CA A:THR426 4.1 7.8 1.0
CA A:SER430 4.1 9.1 1.0
O A:GLU422 4.2 5.3 1.0
N A:THR426 4.2 6.3 1.0
N A:SER430 4.3 10.1 1.0
N A:ASP432 4.5 8.4 1.0
C A:SER430 4.6 8.7 1.0
CA A:ILE429 4.6 9.3 1.0
N A:PRO427 4.6 9.4 1.0
C A:ASP432 4.6 6.9 1.0
CA A:TYR425 4.6 5.3 1.0
N A:GLY431 4.7 9.6 1.0
CB A:ILE429 4.7 9.5 1.0
N A:ILE429 4.8 9.3 1.0
CB A:TYR425 4.8 6.2 1.0
CA A:PRO427 4.8 8.8 1.0
CB A:ASP432 4.9 8.5 1.0
CA A:ASP432 4.9 8.1 1.0
CD2 A:TYR425 4.9 6.5 1.0
N A:TYR425 5.0 5.3 1.0

Reference:

M.J.De La Cruz, J.Hattne, D.Shi, P.Seidler, J.Rodriguez, F.E.Reyes, M.R.Sawaya, D.Cascio, S.C.Weiss, S.K.Kim, C.S.Hinck, A.P.Hinck, G.Calero, D.Eisenberg, T.Gonen. Atomic-Resolution Structures From Fragmented Protein Crystals with the Cryoem Method Microed. Nat. Methods V. 14 399 2017.
ISSN: ESSN 1548-7105
PubMed: 28192420
DOI: 10.1038/NMETH.4178
Page generated: Sat Dec 12 05:32:58 2020

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