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Calcium in PDB 7skx: Ab Initio Structure of Proteinase K From Electron-Counted Microed Data

Enzymatic activity of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data

All present enzymatic activity of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data:
3.4.21.64;

Other elements in 7skx:

The structure of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data also contains other interesting chemical elements:

Iodine (I) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data (pdb code 7skx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data, PDB code: 7skx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 7skx

Go back to Calcium Binding Sites List in 7skx
Calcium binding site 1 out of 5 in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:9.3
occ:1.00
 O C:PRO175 2.4 11.1 1.0
O C:VAL177 2.4 10.2 1.0
OD2 C:ASP200 2.5 12.9 1.0
O C:HOH458 2.5 15.2 1.0
O C:HOH432 2.5 17.0 1.0
O C:HOH419 2.5 17.9 1.0
O C:HOH533 2.5 15.5 1.0
OD1 C:ASP200 2.6 13.8 1.0
CG C:ASP200 2.8 11.2 1.0
C C:PRO175 3.5 10.5 1.0
C C:VAL177 3.6 8.8 1.0
HA C:CYS178 3.7 9.4 1.0
H C:THR179 3.8 8.5 1.0
HA C:PRO175 3.8 12.3 1.0
H C:VAL177 4.0 8.4 1.0
O C:HOH577 4.0 32.8 1.0
N C:VAL177 4.1 7.9 1.0
CA C:PRO175 4.2 12.2 1.0
O C:VAL198 4.2 13.2 1.0
O C:HOH597 4.3 23.8 1.0
CB C:ASP200 4.4 9.4 1.0
C C:SER176 4.4 9.6 1.0
N C:SER176 4.4 10.6 1.0
O C:GLU174 4.5 10.7 1.0
CA C:CYS178 4.5 9.7 1.0
HA C:SER176 4.5 10.6 1.0
N C:CYS178 4.5 8.8 1.0
HG21 C:VAL198 4.5 12.4 1.0
N C:THR179 4.5 7.9 1.0
CA C:VAL177 4.6 8.6 1.0
O C:HOH534 4.6 26.2 1.0
CA C:SER176 4.7 10.6 1.0
HB C:THR179 4.7 10.0 1.0
HB2 C:ASP200 4.7 9.8 1.0
O C:HOH594 4.7 39.7 1.0
HB3 C:ASP200 4.7 9.7 1.0
O C:HOH490 4.8 13.2 1.0
OG1 C:THR179 4.8 9.9 1.0
HG1 C:THR179 4.8 10.1 0.0
HG23 C:VAL198 4.9 11.9 1.0
O C:HOH585 4.9 25.3 1.0
HG23 C:VAL177 4.9 10.5 1.0
O C:SER176 4.9 12.8 1.0
SG C:CYS249 4.9 12.8 1.0
O C:HOH532 5.0 30.4 1.0

Calcium binding site 2 out of 5 in 7skx

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Calcium binding site 2 out of 5 in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca304

b:23.0
occ:1.00
 O C:THR16 2.4 17.1 1.0
O C:HOH506 2.4 27.5 1.0
O C:HOH559 2.4 26.6 1.0
OD2 C:ASP260 2.5 22.9 1.0
OD1 C:ASP260 2.5 20.2 1.0
CG C:ASP260 2.8 23.3 1.0
O C:HOH561 2.8 33.0 1.0
C C:THR16 3.5 13.6 1.0
HB C:THR16 3.5 16.2 1.0
HA C:SER17 3.7 18.6 1.0
HH22 C:ARG12 3.8 15.0 1.0
O C:HOH554 3.9 32.6 1.0
HD22 C:ASN257 4.0 17.3 1.0
HB3 C:ASN257 4.2 14.3 1.0
CB C:ASP260 4.3 20.3 1.0
CB C:THR16 4.3 16.6 1.0
CA C:THR16 4.3 14.7 1.0
HA C:THR16 4.4 14.8 1.0
N C:SER17 4.4 14.6 1.0
CA C:SER17 4.5 19.1 1.0
ND2 C:ASN257 4.5 18.5 1.0
HB3 C:ASP260 4.6 20.4 1.0
NH2 C:ARG12 4.6 15.5 1.0
O C:HOH625 4.7 34.5 1.0
HB3 C:SER17 4.7 23.6 1.0
HA C:ASP260 4.7 17.6 1.0
HH21 C:ARG12 4.7 15.1 1.0
HB2 C:ASP260 4.7 20.5 1.0
HD3 C:PRO18 4.8 19.9 1.0
OG1 C:THR16 4.9 17.3 1.0
CG C:ASN257 4.9 13.2 1.0
CB C:ASN257 5.0 14.7 1.0

Calcium binding site 3 out of 5 in 7skx

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Calcium binding site 3 out of 5 in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca305

b:41.9
occ:1.00
 HA2 C:GLY160 3.1 9.2 1.0
HB3 C:ALA158 3.3 9.3 1.0
HB1 C:ALA158 3.4 9.2 1.0
OG C:SER224 3.4 18.6 1.0
HA C:LEU133 3.7 13.8 1.0
O C:HOH491 3.7 17.7 1.0
HG C:SER224 3.7 18.1 0.0
CB C:ALA158 3.7 9.4 1.0
HD21 C:ASN161 3.7 22.1 1.0
OG1 C:THR223 3.8 10.1 1.0
HG1 C:THR223 3.8 9.8 0.0
C C:LEU133 4.0 14.7 1.0
HB2 C:ALA158 4.1 9.1 1.0
O C:LEU133 4.1 16.9 1.0
CA C:GLY160 4.1 9.5 1.0
ND2 C:ASN161 4.1 24.0 1.0
CA C:LEU133 4.2 13.5 1.0
H C:GLY160 4.2 8.4 1.0
N C:LEU133 4.2 12.6 1.0
H C:SER224 4.2 8.1 1.0
H C:LEU133 4.4 12.4 1.0
N C:GLY134 4.4 17.2 1.0
HD22 C:ASN161 4.4 21.3 1.0
HA3 C:GLY134 4.5 18.8 1.0
C C:SER132 4.5 12.4 1.0
H C:ASN161 4.5 11.4 1.0
N C:GLY160 4.5 8.0 1.0
N C:SER224 4.6 8.3 1.0
CG C:ASN161 4.6 15.8 1.0
CB C:SER224 4.6 12.2 1.0
OD1 C:ASN161 4.6 18.8 1.0
HA3 C:GLY160 4.7 9.3 1.0
HA C:SER224 4.7 9.9 1.0
O C:SER132 4.7 18.6 1.0
H C:GLY134 4.7 16.8 1.0
C C:GLY160 4.8 9.7 1.0
O C:HOH409 4.8 26.6 1.0
N C:ASN161 4.8 12.3 1.0
HA C:SER132 4.9 12.1 1.0
O C:HOH560 4.9 26.5 1.0
CA C:SER224 4.9 10.0 1.0
HB2 C:SER224 4.9 12.2 1.0
CA C:GLY134 5.0 19.5 1.0

Calcium binding site 4 out of 5 in 7skx

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Calcium binding site 4 out of 5 in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca306

b:57.4
occ:1.00
 H C:ASP98 2.7 12.7 1.0
HB2 C:ASP97 3.0 12.9 1.0
O C:HOH624 3.1 32.0 1.0
HA C:ASP97 3.2 12.2 1.0
O C:HOH545 3.2 17.6 1.0
HB3 C:TYR60 3.3 14.2 1.0
N C:ASP98 3.4 12.2 1.0
OD2 C:ASP98 3.6 21.3 1.0
HE3 C:LYS94 3.6 11.1 1.0
CG C:ASP98 3.6 15.3 1.0
HB2 C:ASP98 3.6 14.0 1.0
CB C:ASP97 3.8 12.3 1.0
CA C:ASP97 3.8 12.4 1.0
HZ2 C:LYS94 3.8 12.1 1.0
HB2 C:TYR60 3.9 14.6 1.0
CB C:TYR60 3.9 14.4 1.0
CB C:ASP98 4.0 14.3 1.0
C C:ASP97 4.0 11.3 1.0
OD1 C:ASP98 4.0 17.7 1.0
HD2 C:TYR61 4.0 17.8 1.0
CG C:TYR60 4.1 14.7 1.0
HE2 C:LYS94 4.2 11.7 1.0
HB3 C:ASP97 4.2 12.6 1.0
CE C:LYS94 4.2 11.5 1.0
HD1 C:TYR60 4.3 16.6 1.0
CA C:ASP98 4.3 13.2 1.0
CD1 C:TYR60 4.3 17.2 1.0
NZ C:LYS94 4.4 12.6 1.0
O C:HOH411 4.6 18.3 1.0
HZ1 C:LYS94 4.6 12.1 1.0
H C:TYR61 4.6 13.9 1.0
O C:HOH616 4.7 30.0 1.0
HA C:ASP98 4.8 13.3 1.0
HE2 C:TYR61 4.9 19.1 1.0
CD2 C:TYR60 4.9 13.3 1.0
CD2 C:TYR61 4.9 18.2 1.0
HB3 C:ASP98 5.0 14.6 1.0
CG C:ASP97 5.0 15.4 1.0

Calcium binding site 5 out of 5 in 7skx

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Calcium binding site 5 out of 5 in the Ab Initio Structure of Proteinase K From Electron-Counted Microed Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ab Initio Structure of Proteinase K From Electron-Counted Microed Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca307

b:58.0
occ:1.00
 HB3 C:SER63 3.0 16.2 1.0
HB3 C:MET55 3.3 12.8 1.0
HA C:LYS57 3.3 12.1 1.0
HG21 C:THR58 3.4 12.6 1.0
N C:LYS57 3.4 11.6 1.0
O C:HOH543 3.5 16.0 1.0
HB2 C:SER63 3.6 15.3 1.0
O C:HOH475 3.6 31.6 1.0
H C:LYS57 3.6 10.9 1.0
HG C:SER63 3.6 20.7 0.0
CB C:SER63 3.6 15.1 1.0
C C:VAL56 3.6 10.5 1.0
CA C:LYS57 3.7 12.2 1.0
C C:LYS57 3.7 10.3 1.0
H C:THR58 3.8 9.7 1.0
N C:THR58 3.9 9.7 1.0
O C:VAL56 4.0 14.4 1.0
HB2 C:MET55 4.0 12.8 1.0
CB C:MET55 4.1 13.2 1.0
OG C:SER63 4.1 21.1 1.0
HB C:THR58 4.1 11.6 1.0
C C:MET55 4.1 10.8 1.0
O C:MET55 4.1 12.4 1.0
HA C:VAL56 4.2 10.8 1.0
N C:VAL56 4.2 9.1 1.0
CG2 C:THR58 4.2 12.7 1.0
CA C:VAL56 4.3 11.0 1.0
HE3 C:MET55 4.3 13.1 1.0
O C:LYS57 4.3 9.9 1.0
HG22 C:THR58 4.5 12.4 1.0
O C:HOH423 4.5 38.4 1.0
CB C:THR58 4.6 11.3 1.0
H C:VAL56 4.6 9.8 1.0
CA C:MET55 4.7 10.9 1.0
CA C:THR58 4.8 9.4 1.0
HE2 C:MET55 4.9 13.5 1.0
CA C:SER63 4.9 14.8 1.0
HA C:SER63 5.0 14.3 1.0
HG23 C:THR58 5.0 12.5 1.0

Reference:

M.W.Martynowycz, M.T.B.Clabbers, J.Hattne, T.Gonen. Ab Initio Phasing Macromolecular Structures Using Electron-Counted Microed Data. Nat.Methods V. 19 724 2022.
ISSN: ESSN 1548-7105
PubMed: 35637302
DOI: 10.1038/S41592-022-01485-4
Page generated: Fri Jul 19 04:09:23 2024

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